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test_mapping.txt
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test_mapping.txt
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#SampleID BarcodeSequence LinkerPrimerSequence CARBOHYDRATE_PER LAST_TRAVEL NONFOODALLERGIES_BEESTINGS ASSIGNED_FROM_GEO RUN_DATE NONFOODALLERGIES_DRUG AGE TOT_MASS GENERAL_MEDS BODY_SITE MIGRAINE_FACTOR_2 MIGRAINE_FACTOR_3 TONSILS_REMOVED MIGRAINE_FACTOR_1 ELEVATION PET_LOCATIONS FLOSSING_FREQUENCY PROTEIN_PER CSECTION RACE COUNTRY_OF_BIRTH MACRONUTRIENT_PCT_TOTAL COSMETICS_FREQUENCY HOST_SUBJECT_ID GLUTEN ZIP LONGITUDE PET_CONTACT MIGRAINE_AGGRAVATION DIABETES_MEDICATION SAMPLE_PLATE PENICILLIN KEY_SEQ BODY_PRODUCT REGION MIGRAINE_FREQUENCY MIGRAINE_RELATIVES PLANT_PER SAMPLE MIGRAINE_PHOTOPHOBIA SITE_SAMPLED CURRENT_RESIDENCE_DURATION COUNTRY ANTIBIOTIC_SELECT MIGRAINE_NAUSEA COMMON_NAME FOODALLERGIES_TREENUTS MIGRAINE_AURA TARGET_GENE SEQUENCING_METH FLU_VACCINE_DATE PCR_PRIMERS MIGRAINE BMI ENV_BIOME WELL_ID TEETHBRUSHING_FREQUENCY NITROMIDAZOLE MIGRAINE_MEDICATIONS CONTRACEPTIVE SAMPLE_CENTER LIVINGWITH AGE_UNIT DIABETES_MEDICATIONS LIBRARY_CONSTRUCTION_PROTOCOL Description_duplicate TANNING_SPRAYS EXERCISE_FREQUENCY BIRTH_DATE SULFA_DRUG NONFOODALLERGIES_NO ENV_MATTER RACE_OTHER SKIN_CONDITION NONFOODALLERGIES_DANDER CONDITIONS_MEDICATION ACNE_MEDICATION TARGET_SUBFRAGMENT TITLE HEIGHT_IN ANTIBIOTIC_CONDITION DOG HOST_COMMON_NAME MIGRAINE_PAIN ROOMMATES PRIMER_PLATE SEX NONFOODALLERGIES_SUN EXERCISE_LOCATION COLLECTION_DATE ALTITUDE FOODALLERGIES_SHELLFISH QUINOLINE PERCENTAGE_FROM_CARBS FAT_PER SHARED_HOUSING PREGNANT_DUE_DATE ANONYMIZED_NAME SOFTENER RELATIONS MIGRAINE_PHONOPHOBIA SAMP_SIZE SUPPLEMENTS SMOKING_FREQUENCY NONFOODALLERGIES_POISONIVY TANNING_BEDS ALCOHOL_FREQUENCY DECEASED_PARENT STUDY_CENTER BODY_HABITAT DOMINANT_HAND DIABETES_DIAGNOSE_DATE SPECIAL_RESTRICTIONS CEPHALOSPORIN ENV_FEATURE SUPPLEMENTS_FIELDS SAMPLE_TIME APPENDIX_REMOVED DRINKING_WATER_SOURCE COMMUNAL_DINING SLEEP_DURATION DIET_TYPE RUN_CENTER DIET_RESTRICTIONS EXPERIMENT_CENTER LACTOSE HEIGHT_OR_LENGTH ANTIBIOTIC_MEDS IBD CAT DEPTH HOST_TAXID ILLUMINA_TECHNOLOGY TAXON_ID TYPES_OF_PLANTS MIGRAINEMEDS FIBER_GRAMS MAINFACTOR_OTHER_3 MAINFACTOR_OTHER_1 NAILS RUN_PREFIX PREGNANT PLATFORM DEODORANT_USE PETS MULTIVITAMIN PRIMARY_VEGETABLE WEIGHT_LBS MAINFACTOR_OTHER_2 ACNE_MEDICATION_OTC ANIMAL_PER MACHINE STUDY_ID FOODALLERGIES_OTHER_TEXT EXPERIMENT_DESIGN_DESCRIPTION FOODALLERGIES_OTHER WEIGHT_CHANGE PRIMARY_CARB DIABETES CITY ASTHMA POOL_FREQUENCY PKU STATE FRAT LATITUDE FOODALLERGIES_PEANUTS CHICKENPOX SEASONAL_ALLERGIES Description
000005749.1213126 CACACAAAGTCA GTGTGCCAGCMGCCGCGGTAA 40 More than one year ago None n 12/18/13 None 25.0 60.0 None UBERON:feces None None None None 21.9900589 Indoor, Outdoor Regularly (3-5 times/week) 40 None Caucasian Australia 100 Never 2191:1346155102 yes 2454 152.8966816 Moderate, Extensive None None None no None UBERON:feces None None None 55 5749 None Stool More than one year ago GAZ:Australia In the past year None human gut metagenome None None 16S rRNA sequencing by synthesis Not in the last year FWD:GTGCCAGCMGCCGCGGTAA; REV:GGACTACHVGGGTWTCTAAT None 20.67186456 ENVO:urban biome None Daily yes None None CCME no years None This analysis was done as in Caporaso et al 2011 Genome research. The PCR primers (F515/R806) were developed against the V4 region of the 16S rRNA (both bacteria and archaea), which we determined would yield optimal community clustering with reads of this length using a procedure similar to that of ref. 15. [For reference, this primer pair amplifies the region 533_786 in the Escherichia coli strain 83972 sequence (greengenes accession no. prokMSA_id:470367).] The reverse PCR primer is barcoded with a 12-base error-correcting Golay code to facilitate multiplexing of up to 1,500 samples per lane, and both PCR primers contain sequencer adapter regions. American Gut Project Stool sample None Daily 6/26/89 no None ENVO:feces None None None None None V4 American Gut Project 67 Blastocystis yes human None Two None male None Outdoors 9/18/13 0.0 None no Less than 25% 20 yes None 5749 no None None .1,g yes Daily None None Rarely (few times/month) None CCME UBERON:feces left None yes no ENVO:human-associated habitat vitamin c, zinc, cumin, turmeric, coriander, Fish oil, Glutamine, Betaine Hydrochloride 6:00 AM None City no 7-8 hours Omnivore CCME avoid nightshades, banana, onion, legumes, attempt mostly low fructose diet (improves GI discomfort) CCME yes 173.0 Metronidazole , Flagyl, Paromomycin None no 0 9606 MiSeq 408170 11 to 20 None 303 None None yes AGP6_rerun_L001 no Illumina I do not use deodorant or antiperspirant Freshwater Turtle (Emydura macquarii), Cockatiels, Moderate, Extensive, Indoor, Outdoor yes leafy greens, green beans 132 None None 45 MiSeq1 2191 None Fecal, oral and skin samples from round 3 MiSeq None None rice, fruit juice None bellingen None Rarely (few times/month) None NSW no -30.4520343 None None None American_Gut_round 6
000009670.1213024 CGGAGTAATCCT GTGTGCCAGCMGCCGCGGTAA 45 More than one year ago None n 12/18/13 yes 81.0 45.0 None UBERON:feces None None yes None 6.688742638 Housing... Daily 13 no Caucasian USA 100 Daily 2191:790612235 yes 95814-3220 -121.4941738 Contact... None None None no None UBERON:feces None None None None 9670 None Stool More than one year ago GAZ:United States of America Not in the last year None human gut metagenome None None 16S rRNA sequencing by synthesis Not in the last year FWD:GTGCCAGCMGCCGCGGTAA; REV:GGACTACHVGGGTWTCTAAT no 19.52777778 ENVO:urban biome None Daily no None No CCME no years None This analysis was done as in Caporaso et al 2011 Genome research. The PCR primers (F515/R806) were developed against the V4 region of the 16S rRNA (both bacteria and archaea), which we determined would yield optimal community clustering with reads of this length using a procedure similar to that of ref. 15. [For reference, this primer pair amplifies the region 533_786 in the Escherichia coli strain 83972 sequence (greengenes accession no. prokMSA_id:470367).] The reverse PCR primer is barcoded with a 12-base error-correcting Golay code to facilitate multiplexing of up to 1,500 samples per lane, and both PCR primers contain sequencer adapter regions. American Gut Project Stool sample None Daily 4/23/33 no None ENVO:feces None I do not have a skin condition None no no V4 American Gut Project 60 None no human None None None female None Indoors 10/4/13 0.0 None no 25 to 50% 42 yes None 9670 yes None None .1,g yes Never None None Never None CCME UBERON:feces right None no no ENVO:human-associated habitat probiotics, Ubiquinol, Vitamin D, Vitamin B12, Krill Oil, Peppermint Oil 12:40 PM no Filtered no 7-8 hours Omnivore CCME None CCME None 152.0 None I do not have IBD no 0 9606 MiSeq 408170 Less than 5 None 302 None None no AGP6_rerun_L001 no Illumina I use deodorant Contact..., Housing... yes Broccoli 100 None no None MiSeq1 2191 None Fecal, oral and skin samples from round 3 MiSeq None Decreased more than 10 pounds Fiber One Cereal I do not have diabetes sacramento no Never no CA no 38.5824933 None yes yes American_Gut_round 6
000003493.1213060 ATATCGCGATGA GTGTGCCAGCMGCCGCGGTAA 10 Within the past year None n 12/18/13 None 55.0 74.0 None UBERON:feces None None no None 4.185313702 Housing... Daily 55 no Caucasian USA 100 Never 2191:2557983668 yes 33073 -80.1819268 Contact... None None None no None UBERON:feces None None None 0 3493 None Stool More than one year ago GAZ:United States of America Not in the last year None human gut metagenome None None 16S rRNA sequencing by synthesis Not in the last year FWD:GTGCCAGCMGCCGCGGTAA; REV:GGACTACHVGGGTWTCTAAT no None ENVO:urban biome None Daily no None None CCME yes years None This analysis was done as in Caporaso et al 2011 Genome research. The PCR primers (F515/R806) were developed against the V4 region of the 16S rRNA (both bacteria and archaea), which we determined would yield optimal community clustering with reads of this length using a procedure similar to that of ref. 15. [For reference, this primer pair amplifies the region 533_786 in the Escherichia coli strain 83972 sequence (greengenes accession no. prokMSA_id:470367).] The reverse PCR primer is barcoded with a 12-base error-correcting Golay code to facilitate multiplexing of up to 1,500 samples per lane, and both PCR primers contain sequencer adapter regions. American Gut Project Stool sample None Occasionally (1-2 times/week) 8/6/59 no yes ENVO:feces None I do not have a skin condition None no no V4 American Gut Project 11 None no human None None None male None Indoors 11/9/13 0.0 None no 25 to 50% 35 no None 3493 None Spouse, Daughter, Son None .1,g yes Never None None Occasionally (1-2 times/week) None CCME UBERON:feces right None no no ENVO:human-associated habitat None 11:30 AM no Filtered None 6-7 hours Omnivore CCME None CCME no 28.0 None None yes 0 9606 MiSeq 408170 6 to 10 None 45 None None no AGP6_rerun_L001 no Illumina I use an antiperspirant Contact..., Housing... yes leafy greens 165 None no 100 MiSeq1 2191 None Fecal, oral and skin samples from round 3 MiSeq None Remained stable cereal I do not have diabetes coconut creek no Rarely (few times/month) no FL None 26.3003637 None yes no American_Gut_round 6
000010875.1213067 ACGCACATACAA GTGTGCCAGCMGCCGCGGTAA 55 Within the past 3 months None n 12/18/13 yes 53.0 73.0 None UBERON:feces None None no None 209.1370544 Housing... Never 26 no Caucasian USA 100 Never 2191:1379975708 no 94708 -122.259717 Contact... None None None no None UBERON:feces None None None 10 10875 None Stool More than one year ago GAZ:United States of America In the past 6 months None human gut metagenome None None 16S rRNA sequencing by synthesis In the past month FWD:GTGCCAGCMGCCGCGGTAA; REV:GGACTACHVGGGTWTCTAAT no 24.62932526 ENVO:urban biome None Daily no None None CCME yes years None This analysis was done as in Caporaso et al 2011 Genome research. The PCR primers (F515/R806) were developed against the V4 region of the 16S rRNA (both bacteria and archaea), which we determined would yield optimal community clustering with reads of this length using a procedure similar to that of ref. 15. [For reference, this primer pair amplifies the region 533_786 in the Escherichia coli strain 83972 sequence (greengenes accession no. prokMSA_id:470367).] The reverse PCR primer is barcoded with a 12-base error-correcting Golay code to facilitate multiplexing of up to 1,500 samples per lane, and both PCR primers contain sequencer adapter regions. American Gut Project Stool sample None Regularly (3-5 times/week) 1/1/61 no None ENVO:feces None I do not have a skin condition yes no no V4 American Gut Project 68 bronchitis no human None None None male None Indoors 11/13/13 0.0 None no 25 to 50% 19 no None 10875 yes partner None .1,g no Never None None Occasionally (1-2 times/week) None CCME UBERON:feces right None no no ENVO:human-associated habitat None 9:00 AM no City None 7-8 hours Omnivore CCME None CCME yes 173.0 doxycycline I do not have IBD no 0 9606 MiSeq 408170 21 to 30 None 125 None None no AGP6_rerun_L001 no Illumina I use an antiperspirant Contact..., Housing... no leafy greens 162 None no 90 MiSeq1 2191 soy, garlic, ginger, many fish, etc. Fecal, oral and skin samples from round 3 MiSeq yes Remained stable bread I do not have diabetes berkeley yes Rarely (few times/month) no CA None 37.9020612 None yes yes American_Gut_round 6
000004086.1213010 AGCGACGAAGAC GTGTGCCAGCMGCCGCGGTAA 65 Within the past 3 months None n 12/18/13 None 43.0 63.0 None UBERON:feces None None no None 298.0795593 Housing... Occasionally (1-2 times/week) 14 no Caucasian USA 100 Regularly (3-5 times/week) 2191:3794909020 no 91104 -118.1181199 Contact... None None None no None UBERON:feces None None None 95 4086 None Stool More than one year ago GAZ:United States of America Not in the last year None human gut metagenome None None 16S rRNA sequencing by synthesis Not in the last year FWD:GTGCCAGCMGCCGCGGTAA; REV:GGACTACHVGGGTWTCTAAT no 23.12828402 ENVO:urban biome None Daily no None No CCME yes years None This analysis was done as in Caporaso et al 2011 Genome research. The PCR primers (F515/R806) were developed against the V4 region of the 16S rRNA (both bacteria and archaea), which we determined would yield optimal community clustering with reads of this length using a procedure similar to that of ref. 15. [For reference, this primer pair amplifies the region 533_786 in the Escherichia coli strain 83972 sequence (greengenes accession no. prokMSA_id:470367).] The reverse PCR primer is barcoded with a 12-base error-correcting Golay code to facilitate multiplexing of up to 1,500 samples per lane, and both PCR primers contain sequencer adapter regions. American Gut Project Stool sample None Regularly (3-5 times/week) 1/29/71 no None ENVO:feces None I do not have a skin condition yes no no V4 American Gut Project 65 None yes human None None None female None Both 11/4/13 0.0 None no Less than 25% 21 no None 4086 yes partner None .1,g yes Never yes None Occasionally (1-2 times/week) None CCME UBERON:feces right None no no ENVO:human-associated habitat fish oil 8:30 AM no Filtered None 6-7 hours Vegetarian but eat seafood CCME None CCME no 165.0 None I do not have IBD no 0 9606 MiSeq 408170 11 to 20 None 163 None None yes AGP6_rerun_L001 no Illumina I use deodorant Contact..., Housing... yes greens 139 None no 5 MiSeq1 2191 None Fecal, oral and skin samples from round 3 MiSeq None Decreased more than 10 pounds apples I do not have diabetes pasadena no Never no CA None 34.1657707 None yes yes American_Gut_round 6
000010163.1213006 ATGGCCTGACTA GTGTGCCAGCMGCCGCGGTAA 55 More than one year ago None n 12/18/13 None 65.0 83.0 None UBERON:feces None None no None 38.65314865 Indoor Occasionally (1-2 times/week) 14 no Caucasian USA 99 Never 2191:2256743085 no 1985 -70.989778 Extensive None None None no None UBERON:feces None None None 70 10163 None Stool More than one year ago GAZ:United States of America Not in the last year None human gut metagenome None None 16S rRNA sequencing by synthesis In the past 6 months FWD:GTGCCAGCMGCCGCGGTAA; REV:GGACTACHVGGGTWTCTAAT no 27.31674018 ENVO:urban biome None Daily no None None CCME yes years None This analysis was done as in Caporaso et al 2011 Genome research. The PCR primers (F515/R806) were developed against the V4 region of the 16S rRNA (both bacteria and archaea), which we determined would yield optimal community clustering with reads of this length using a procedure similar to that of ref. 15. [For reference, this primer pair amplifies the region 533_786 in the Escherichia coli strain 83972 sequence (greengenes accession no. prokMSA_id:470367).] The reverse PCR primer is barcoded with a 12-base error-correcting Golay code to facilitate multiplexing of up to 1,500 samples per lane, and both PCR primers contain sequencer adapter regions. American Gut Project Stool sample None Daily 9/18/48 no None ENVO:feces None I do not have a skin condition None no no V4 American Gut Project 69 None yes human None None None male None Both 11/15/13 0.0 None no Less than 25% 30 no None 10163 no Wife None .1,g yes Never None None Daily None CCME UBERON:feces right None no no ENVO:human-associated habitat Fish Oil 1000mg, Ginko Biloba extract, Glucosamine 7:00 AM no Well None 5-6 hours Vegetarian CCME None CCME no 175.0 None I do not have IBD no 0 9606 MiSeq 408170 21 to 30 None 160 None None no AGP6_rerun_L001 no Illumina Not sure, but I use some form of deodorant/antiperspirant Dog, Extensive, Indoor yes onion 185 None no 30 MiSeq1 2191 None Fecal, oral and skin samples from round 3 MiSeq None Remained stable bread I do not have diabetes west newbury no Regularly (3-5 times/week) no MA None 42.8014795 None yes yes American_Gut_round 6
000010192.1212982 CGACATTTCTCT GTGTGCCAGCMGCCGCGGTAA 61 Within the past 3 months None n 12/18/13 None 55.0 71.0 None UBERON:feces None None no None 142.5300446 Outdoor, Outdoor Daily 21 no Caucasian USA 100 Never 2191:1231813748 no 23093 -78.0041649 Moderate, Moderate None None None no None UBERON:feces None None None 75 10192 None Stool More than one year ago GAZ:United States of America Not in the last year None human gut metagenome None None 16S rRNA sequencing by synthesis In the past year FWD:GTGCCAGCMGCCGCGGTAA; REV:GGACTACHVGGGTWTCTAAT no 22.52469388 ENVO:urban biome None Daily no None None CCME yes years None This analysis was done as in Caporaso et al 2011 Genome research. The PCR primers (F515/R806) were developed against the V4 region of the 16S rRNA (both bacteria and archaea), which we determined would yield optimal community clustering with reads of this length using a procedure similar to that of ref. 15. [For reference, this primer pair amplifies the region 533_786 in the Escherichia coli strain 83972 sequence (greengenes accession no. prokMSA_id:470367).] The reverse PCR primer is barcoded with a 12-base error-correcting Golay code to facilitate multiplexing of up to 1,500 samples per lane, and both PCR primers contain sequencer adapter regions. American Gut Project Stool sample None Daily 6/27/59 no None ENVO:feces None I do not have a skin condition None yes no V4 American Gut Project 70 None yes human None None None male None Outdoors 11/6/13 0.0 None no Less than 25% 18 no None 10192 yes Partner None .1,g no Never yes None Daily None CCME UBERON:feces right None no no ENVO:human-associated habitat None 7:40 AM no Well None 6-7 hours Omnivore CCME None CCME no 178.0 None I do not have IBD yes 0 9606 MiSeq 408170 6 to 10 None 216 None None yes AGP6_rerun_L001 no Illumina I use deodorant Horses, Chickens and Turkeys, Moderate, Moderate, Outdoor, Outdoor yes lettuce 157 None no 25 MiSeq1 2191 None Fecal, oral and skin samples from round 3 MiSeq None Remained stable bread I do not have diabetes louisa no Daily no VA None 38.0251394 None yes no American_Gut_round 6
000009043.1213080 GGCATGTTATCG GTGTGCCAGCMGCCGCGGTAA 28 Within the past year None n 12/18/13 None 44.0 70.0 None UBERON:feces Depression Medications; horomones no Stress 19.26420975 Housing... Regularly (3-5 times/week) 20 no Caucasian USA 92 Occasionally (1-2 times/week) 2191:3450161819 no 11201 -73.9859414 Contact... yes None None no None UBERON:feces None Weekly notsure 49 9043 None Stool More than one year ago GAZ:United States of America In the past year yes human gut metagenome None None 16S rRNA sequencing by synthesis In the past year FWD:GTGCCAGCMGCCGCGGTAA; REV:GGACTACHVGGGTWTCTAAT yes 26.6027832 ENVO:urban biome None Daily no imitrex I take the pill CCME no years None This analysis was done as in Caporaso et al 2011 Genome research. The PCR primers (F515/R806) were developed against the V4 region of the 16S rRNA (both bacteria and archaea), which we determined would yield optimal community clustering with reads of this length using a procedure similar to that of ref. 15. [For reference, this primer pair amplifies the region 533_786 in the Escherichia coli strain 83972 sequence (greengenes accession no. prokMSA_id:470367).] The reverse PCR primer is barcoded with a 12-base error-correcting Golay code to facilitate multiplexing of up to 1,500 samples per lane, and both PCR primers contain sequencer adapter regions. American Gut Project Stool sample None Regularly (3-5 times/week) 12/12/69 no None ENVO:feces None Psoriasis None yes yes V4 American Gut Project 64 chest infection no human None None None female yes Indoors 9/12/13 0.0 None no 51 to 75% 44 no None 9043 yes None None .1,g yes Never None None Regularly (3-5 times/week) None CCME UBERON:feces right None no no ENVO:human-associated habitat cod liver oil 8:30 AM no Filtered None 7-8 hours Omnivore CCME None CCME yes 163.0 zithromax I do not have IBD yes 0 9606 MiSeq 408170 11 to 20 yes 14.8 None None no AGP6_rerun_L001 no Illumina I use an antiperspirant Contact..., Housing... yes carrot 155 None yes 51 MiSeq1 2191 None Fecal, oral and skin samples from round 3 MiSeq None Remained stable Bread I do not have diabetes brooklyn no Never no NY None 40.6986772 None no None American_Gut_round 6
Blank33.E9.1213014 TAGCGCGAACTT GTGTGCCAGCMGCCGCGGTAA None None None n 12/18/13 None None None None None None None None None 1624.1 None None None None None None None None 2191:unknown None 80309 -105.79 None None None None None None None None None None None Blank33.E9 None Blank None GAZ:United States of America None None unclassified metagenome None None 16S rRNA sequencing by synthesis None FWD:GTGCCAGCMGCCGCGGTAA; REV:GGACTACHVGGGTWTCTAAT None None ENVO:aquatic biome None None None None None CCME None years None This analysis was done as in Caporaso et al 2011 Genome research. The PCR primers (F515/R806) were developed against the V4 region of the 16S rRNA (both bacteria and archaea), which we determined would yield optimal community clustering with reads of this length using a procedure similar to that of ref. 15. [For reference, this primer pair amplifies the region 533_786 in the Escherichia coli strain 83972 sequence (greengenes accession no. prokMSA_id:470367).] The reverse PCR primer is barcoded with a 12-base error-correcting Golay code to facilitate multiplexing of up to 1,500 samples per lane, and both PCR primers contain sequencer adapter regions. American Gut Project blank None None None None None ENVO:sterile water None None None None None V4 American Gut Project None None None None None None None unknown None None None 0.0 None None None None None None Blank33.E9 None None None .1,g None None None None None None CCME None unknown None None None ENVO:water None None None None None None None CCME None CCME None None None None None 0 None MiSeq 408169 None None None None None None AGP6_rerun_L001 None Illumina None None None None None None None None MiSeq1 2191 None Fecal, oral and skin samples from round 3 MiSeq None None None None boulder None None None CO None 40.02 None None None American_Gut_round 24
000010692.1213092 TGACTAATGGCC GTGTGCCAGCMGCCGCGGTAA 43 Within the past 3 months None n 12/18/13 None None None None UBERON:feces None None no None 27.20385742 Housing... Regularly (3-5 times/week) 16 no Caucasian None 92 Daily 2191:669155760 no 19130 -75.1749671 Contact... None None None yes None UBERON:feces None None None 37 10692 None Stool More than one year ago GAZ:United States of America In the past week None human gut metagenome None None 16S rRNA sequencing by synthesis In the past month FWD:GTGCCAGCMGCCGCGGTAA; REV:GGACTACHVGGGTWTCTAAT no None ENVO:urban biome None Daily no None None CCME yes years None This analysis was done as in Caporaso et al 2011 Genome research. The PCR primers (F515/R806) were developed against the V4 region of the 16S rRNA (both bacteria and archaea), which we determined would yield optimal community clustering with reads of this length using a procedure similar to that of ref. 15. [For reference, this primer pair amplifies the region 533_786 in the Escherichia coli strain 83972 sequence (greengenes accession no. prokMSA_id:470367).] The reverse PCR primer is barcoded with a 12-base error-correcting Golay code to facilitate multiplexing of up to 1,500 samples per lane, and both PCR primers contain sequencer adapter regions. American Gut Project Stool sample None Regularly (3-5 times/week) None no None ENVO:feces None Psoriasis None no no V4 American Gut Project None prophylactic, divitericulitis yes human None None None unknown None Indoors 10/28/13 0.0 None no Less than 25% 33 no None 10692 yes Husband None .1,g no Never None None Regularly (3-5 times/week) None CCME UBERON:feces right None no no ENVO:human-associated habitat None 8:00 AM no Bottled None 8 or more hours Omnivore CCME None CCME no None amoxicillin, doxycycline I do not have IBD no 0 9606 MiSeq 408170 Less than 5 None 147 None None no AGP6_rerun_L001 no Illumina I do not use deodorant or antiperspirant Contact..., Housing... yes potato None None no 62 MiSeq1 2191 None Fecal, oral and skin samples from round 3 MiSeq None Remained stable crackers, cereal, potatos I do not have diabetes philadelphia no Rarely (few times/month) no PA None 39.9682609 None yes no American_Gut_round 6
000001282.1212979 TTGGAACGGCTT GTGTGCCAGCMGCCGCGGTAA None More than one year ago yes n 5/20/13 yes 65.0 68.0 None UBERON:feces Lack of sleep Other yes Other 147.2527924 None Daily None no Caucasian USA 0 Occasionally (1-2 times/week) 2191:3636913616 yes 37075 -86.6199957 None None None None no None UBERON:feces None Monthly yes None 1282 yes Stool More than one year ago GAZ:United States of America In the past 6 months yes human gut metagenome yes None 16S rRNA sequencing by synthesis Not in the last year FWD:GTGCCAGCMGCCGCGGTAA; REV:GGACTACHVGGGTWTCTAAT yes 29.68222222 ENVO:urban biome None Daily no None No CCME no years None This analysis was done as in Caporaso et al 2011 Genome research. The PCR primers (F515/R806) were developed against the V4 region of the 16S rRNA (both bacteria and archaea), which we determined would yield optimal community clustering with reads of this length using a procedure similar to that of ref. 15. [For reference, this primer pair amplifies the region 533_786 in the Escherichia coli strain 83972 sequence (greengenes accession no. prokMSA_id:470367).] The reverse PCR primer is barcoded with a 12-base error-correcting Golay code to facilitate multiplexing of up to 1,500 samples per lane, and both PCR primers contain sequencer adapter regions. American Gut Project Stool sample None Occasionally (1-2 times/week) 1/1/49 no None ENVO:feces None None yes yes no V4 American Gut Project 60 None no human yes None None female yes Both 4/5/13 0.0 yes no None None no None 1282 no None yes .1,g yes Never yes None Never None CCME UBERON:feces right None yes no ENVO:human-associated habitat panothic acid,vit c,magnesium, probiotic,D3,B12 injec 12:00 PM no Bottled None 5-6 hours Omnivore CCME no latex foods, glutin, nut,ground vegetables, night shade veg, red meats, fish CCME no 152.0 None None no 0 9606 MiSeq 408170 None yes None structural,meiners allergies no Knight_AFG_16s_w_phiX_NoIndex_L001 no Illumina I use an antiperspirant None no None 152 None no None MiSeq1 2191 latex Foods,iodine,fish oil, strawberries,etc Fecal, oral and skin samples from round 3 MiSeq yes Decreased more than 10 pounds None I do not have diabetes hendersonville yes Never no TN None 36.3047735 yes no yes American_Gut_round 6
000009447.1212953 GCAACCGATTGT GTGTGCCAGCMGCCGCGGTAA 24 More than one year ago None n 12/18/13 None 42.0 59.0 None UBERON:feces None None yes None 113.8853073 Housing... Daily 18 no Caucasian USA 100 Never 2191:2328262118 yes 90039 -118.2585096 Contact... None None None no None UBERON:feces None None None 18 9447 None Stool More than one year ago GAZ:United States of America Not in the last year None human gut metagenome None None 16S rRNA sequencing by synthesis Not in the last year FWD:GTGCCAGCMGCCGCGGTAA; REV:GGACTACHVGGGTWTCTAAT no 20.35865449 ENVO:urban biome None Daily no None None CCME no years None This analysis was done as in Caporaso et al 2011 Genome research. The PCR primers (F515/R806) were developed against the V4 region of the 16S rRNA (both bacteria and archaea), which we determined would yield optimal community clustering with reads of this length using a procedure similar to that of ref. 15. [For reference, this primer pair amplifies the region 533_786 in the Escherichia coli strain 83972 sequence (greengenes accession no. prokMSA_id:470367).] The reverse PCR primer is barcoded with a 12-base error-correcting Golay code to facilitate multiplexing of up to 1,500 samples per lane, and both PCR primers contain sequencer adapter regions. American Gut Project Stool sample None Daily 9/13/71 no None ENVO:feces None Eczema None no no V4 American Gut Project 67 None no human None None None male None Outdoors 10/5/13 0.0 None no Less than 25% 58 no None 9447 no None None .1,g yes Never None None Rarely (few times/month) None CCME UBERON:feces right None yes no ENVO:human-associated habitat vitamin c, ubiquinol, Interfase Plus, menaquinone-7, curcumin, Yeastonil, magnesium, alpha lipoic acid, betaine hcl and pepsin, methyl-sulfonyl-methane, gymnema sylvestre, acetyl-glutathione, n-acetyl-l-cysteine, cat's claw, oregon grape root, scullcap, oregano oil, garlic, quercenase, activated charcoal, molybdenum, taurine, chromium, boron, vitamin K1, selenium, menatetrenone, acacia fiber, vanadium, soil-based probiotics, monolaurin, rutin, iodine, zinc 8:10 AM no Filtered None 7-8 hours Omnivore CCME no grain except white rice, no legumes, perfect health diet (paleo) CCME no 170.0 None I do not have IBD no 0 9606 MiSeq 408170 11 to 20 None 76 None None no AGP6_rerun_L001 no Illumina I use deodorant Contact..., Housing... no rice 130 None no 82 MiSeq1 2191 None Fecal, oral and skin samples from round 3 MiSeq None Remained stable rice I do not have diabetes los angeles no Never no CA None 34.1103407 None yes yes American_Gut_round 6
000007158.1212986 CCTCGATGCAGT GTGTGCCAGCMGCCGCGGTAA 35 Within the past month None n 12/18/13 None 69.0 71.0 None UBERON:feces None None no None None Housing... Daily 30 no Caucasian Switzerland 100 Daily 2191:3129029108 yes None None Contact... None None None no None UBERON:feces None None None 25 7158 None Stool More than one year ago GAZ:Switzerland In the past 6 months None human gut metagenome None None 16S rRNA sequencing by synthesis Not in the last year FWD:GTGCCAGCMGCCGCGGTAA; REV:GGACTACHVGGGTWTCTAAT None 23.41306228 ENVO:urban biome None Daily no None No CCME yes years None This analysis was done as in Caporaso et al 2011 Genome research. The PCR primers (F515/R806) were developed against the V4 region of the 16S rRNA (both bacteria and archaea), which we determined would yield optimal community clustering with reads of this length using a procedure similar to that of ref. 15. [For reference, this primer pair amplifies the region 533_786 in the Escherichia coli strain 83972 sequence (greengenes accession no. prokMSA_id:470367).] The reverse PCR primer is barcoded with a 12-base error-correcting Golay code to facilitate multiplexing of up to 1,500 samples per lane, and both PCR primers contain sequencer adapter regions. American Gut Project Stool sample None Occasionally (1-2 times/week) 1/28/45 no yes ENVO:feces None I do not have a skin condition None None no V4 American Gut Project 68 bronchitis no human None None None female None Indoors 11/13/13 0.0 None no Less than 25% 35 no None 7158 yes Husband None .1,g yes Never None None Occasionally (1-2 times/week) None CCME UBERON:feces right None no no ENVO:human-associated habitat pro biotics, zyflamend 10:40 AM None City None 7-8 hours None CCME None CCME no 175.0 None I do not have IBD no 0 9606 MiSeq 408170 6 to 10 None 200 None None no AGP6_rerun_L001 no Illumina I use an antiperspirant Contact..., Housing... yes avocado 154 None no 75 MiSeq1 2191 None Fecal, oral and skin samples from round 3 MiSeq None Remained stable vegetables I do not have diabetes 1884 villars sur ollon no Never no None None None None yes no American_Gut_round 6
000010236.1213021 CTCATCATGTTC GTGTGCCAGCMGCCGCGGTAA 42 More than one year ago None n 12/18/13 None 55.0 92.0 None UBERON:feces None None None None 180.3834534 Housing... Daily 15 None Caucasian United Kingdom 90 Never 2191:2347853377 None 28210 -80.8599193 Contact... None None None no None UBERON:feces None None None 50 10236 None Stool More than one year ago GAZ:United States of America Not in the last year None human gut metagenome None None 16S rRNA sequencing by synthesis Not in the last year FWD:GTGCCAGCMGCCGCGGTAA; REV:GGACTACHVGGGTWTCTAAT None 27.79996142 ENVO:urban biome None Daily no None None CCME None years None This analysis was done as in Caporaso et al 2011 Genome research. The PCR primers (F515/R806) were developed against the V4 region of the 16S rRNA (both bacteria and archaea), which we determined would yield optimal community clustering with reads of this length using a procedure similar to that of ref. 15. [For reference, this primer pair amplifies the region 533_786 in the Escherichia coli strain 83972 sequence (greengenes accession no. prokMSA_id:470367).] The reverse PCR primer is barcoded with a 12-base error-correcting Golay code to facilitate multiplexing of up to 1,500 samples per lane, and both PCR primers contain sequencer adapter regions. American Gut Project Stool sample None Occasionally (1-2 times/week) 5/10/59 no None ENVO:feces None I do not have a skin condition yes None None V4 American Gut Project 72 None None human None None None male None Outdoors 10/20/13 0.0 None no Less than 25% 33 None None 10236 None None None .1,g None Never yes None Daily None CCME UBERON:feces right None None no ENVO:human-associated habitat None 9:00 AM no City None 8 or more hours Omnivore CCME None CCME None 183.0 None I do not have IBD None 0 9606 MiSeq 408170 6 to 10 None 25 None None None AGP6_rerun_L001 no Illumina I use deodorant Contact..., Housing... None leafy greens 205 None None 50 MiSeq1 2191 None Fecal, oral and skin samples from round 3 MiSeq None Remained stable pasta I do not have diabetes charlotte None Rarely (few times/month) None NC None 35.1274285 None None yes American_Gut_round 6
Blank28.E4.1212992 GTTTCCGTGGTG GTGTGCCAGCMGCCGCGGTAA None None None n 12/18/13 None None None None None None None None None 1624.1 None None None None None None None None 2191:unknown None 80309 -105.79 None None None None None None None None None None None Blank28.E4 None Blank None GAZ:United States of America None None unclassified metagenome None None 16S rRNA sequencing by synthesis None FWD:GTGCCAGCMGCCGCGGTAA; REV:GGACTACHVGGGTWTCTAAT None None ENVO:aquatic biome None None None None None CCME None years None This analysis was done as in Caporaso et al 2011 Genome research. The PCR primers (F515/R806) were developed against the V4 region of the 16S rRNA (both bacteria and archaea), which we determined would yield optimal community clustering with reads of this length using a procedure similar to that of ref. 15. [For reference, this primer pair amplifies the region 533_786 in the Escherichia coli strain 83972 sequence (greengenes accession no. prokMSA_id:470367).] The reverse PCR primer is barcoded with a 12-base error-correcting Golay code to facilitate multiplexing of up to 1,500 samples per lane, and both PCR primers contain sequencer adapter regions. American Gut Project blank None None None None None ENVO:sterile water None None None None None V4 American Gut Project None None None None None None None unknown None None None 0.0 None None None None None None Blank28.E4 None None None .1,g None None None None None None CCME None unknown None None None ENVO:water None None None None None None None CCME None CCME None None None None None 0 None MiSeq 408169 None None None None None None AGP6_rerun_L001 None Illumina None None None None None None None None MiSeq1 2191 None Fecal, oral and skin samples from round 3 MiSeq None None None None boulder None None None CO None 40.02 None None None American_Gut_round 13
000003975.1213033 AGGTCATCTTGG GTGTGCCAGCMGCCGCGGTAA 44 More than one year ago None n 5/20/13 None 68.0 83.0 None UBERON:feces None None no None 65.6000824 None Daily 16 yes Caucasian USA 100 Never 2191:3713235602 no 97007 -122.8670454 None None None None no None UBERON:feces None None None 30 3975 None Stool More than one year ago GAZ:United States of America Not in the last year None human gut metagenome None None 16S rRNA sequencing by synthesis In the past year FWD:GTGCCAGCMGCCGCGGTAA; REV:GGACTACHVGGGTWTCTAAT None 28.12608131 ENVO:urban biome None Daily no None None CCME yes years None This analysis was done as in Caporaso et al 2011 Genome research. The PCR primers (F515/R806) were developed against the V4 region of the 16S rRNA (both bacteria and archaea), which we determined would yield optimal community clustering with reads of this length using a procedure similar to that of ref. 15. [For reference, this primer pair amplifies the region 533_786 in the Escherichia coli strain 83972 sequence (greengenes accession no. prokMSA_id:470367).] The reverse PCR primer is barcoded with a 12-base error-correcting Golay code to facilitate multiplexing of up to 1,500 samples per lane, and both PCR primers contain sequencer adapter regions. American Gut Project Stool sample None Occasionally (1-2 times/week) 10/30/45 no None ENVO:feces None I do not have a skin condition None no no V4 American Gut Project 68 None no human None None None male None Depends on the season 4/7/13 0.0 None no 25 to 50% 40 no None 3975 no Father, Wife, Grandfather None .1,g yes Never None None Regularly (3-5 times/week) None CCME UBERON:feces right None no no ENVO:human-associated habitat fish oil, b12, biotin, leutine 7:00 AM no Well None 6-7 hours Omnivore CCME None CCME no 173.0 None I do not have IBD no 0 9606 MiSeq 408170 11 to 20 None 203 None None no Knight_AFG_16s_w_phiX_NoIndex_L001 no Illumina I use deoderant None yes peas 185 None no 70 MiSeq1 2191 None Fecal, oral and skin samples from round 3 MiSeq None Remained stable quinoa I do not have diabetes aloha no Never no OR None 45.4942838 None yes no American_Gut_round 6
000010191.1213045 CTCTCTCACTTG GTGTGCCAGCMGCCGCGGTAA 25 Within the past month None n 12/18/13 None 56.0 77.0 None UBERON:feces None None no None 142.5300446 Indoor, Outdoor Daily 40 no Caucasian USA 100 Never 2191:155731051 no 23093 -78.0041649 Moderate, None None None None no None UBERON:feces None None None None 10191 None Stool More than one year ago GAZ:United States of America Not in the last year None human gut metagenome None None 16S rRNA sequencing by synthesis In the past year FWD:GTGCCAGCMGCCGCGGTAA; REV:GGACTACHVGGGTWTCTAAT no None ENVO:urban biome None Daily no None None CCME yes years None This analysis was done as in Caporaso et al 2011 Genome research. The PCR primers (F515/R806) were developed against the V4 region of the 16S rRNA (both bacteria and archaea), which we determined would yield optimal community clustering with reads of this length using a procedure similar to that of ref. 15. [For reference, this primer pair amplifies the region 533_786 in the Escherichia coli strain 83972 sequence (greengenes accession no. prokMSA_id:470367).] The reverse PCR primer is barcoded with a 12-base error-correcting Golay code to facilitate multiplexing of up to 1,500 samples per lane, and both PCR primers contain sequencer adapter regions. American Gut Project Stool sample None Regularly (3-5 times/week) 6/17/58 no None ENVO:feces None I do not have a skin condition yes yes no V4 American Gut Project None None yes human None None None male None Depends on the season 11/4/13 0.0 None no 25 to 50% 35 no None 10191 yes Partner None .1,g no Never None None Daily None CCME UBERON:feces right None no no ENVO:human-associated habitat None 9:25 AM no Filtered None 6-7 hours Omnivore CCME None CCME no None None I do not have IBD yes 0 9606 MiSeq 408170 11 to 20 None 200 None None no AGP6_rerun_L001 no Illumina I use deodorant dogs, cats, Moderate, None, Indoor, Outdoor yes leafy greens 170 None no None MiSeq1 2191 None Fecal, oral and skin samples from round 3 MiSeq None Remained stable pasta I do not have diabetes louisa yes Occasionally (1-2 times/week) no VA None 38.0251394 None yes yes American_Gut_round 6
000004215.1213063 CTGTGTCCATGG GTGTGCCAGCMGCCGCGGTAA 50 Within the past 3 months None n 12/18/13 yes 30.0 74.0 None UBERON:feces None None no None 1619.837158 Outdoor, Outdoor Regularly (3-5 times/week) 10 no Caucasian USA 100 Never 2191:4095514450 no 80303 -105.2077798 Moderate, Moderate None None None no None UBERON:feces None None None 90 4215 None Stool More than one year ago GAZ:United States of America Not in the last year None human gut metagenome yes None 16S rRNA sequencing by synthesis Not in the last year FWD:GTGCCAGCMGCCGCGGTAA; REV:GGACTACHVGGGTWTCTAAT no 23.01031541 ENVO:urban biome None Daily no None None CCME yes years None This analysis was done as in Caporaso et al 2011 Genome research. The PCR primers (F515/R806) were developed against the V4 region of the 16S rRNA (both bacteria and archaea), which we determined would yield optimal community clustering with reads of this length using a procedure similar to that of ref. 15. [For reference, this primer pair amplifies the region 533_786 in the Escherichia coli strain 83972 sequence (greengenes accession no. prokMSA_id:470367).] The reverse PCR primer is barcoded with a 12-base error-correcting Golay code to facilitate multiplexing of up to 1,500 samples per lane, and both PCR primers contain sequencer adapter regions. American Gut Project Stool sample None Regularly (3-5 times/week) 5/4/84 no None ENVO:feces None Eczema None no no V4 American Gut Project 71 None yes human None Three None unknown None Outdoors 10/13/13 0.0 None no Less than 25% 40 yes None 4215 no roommate None .1,g no Rarely (few times/month) None None Daily None CCME UBERON:feces right None no no ENVO:human-associated habitat None 12:00 PM no City no 6-7 hours Omnivore CCME None CCME no 180.0 None I do not have IBD no 0 9606 MiSeq 408170 11 to 20 None 267 None None yes AGP6_rerun_L001 no Illumina I use deodorant dog, dog, Moderate, Moderate, Outdoor, Outdoor no tomato 165 None no 10 MiSeq1 2191 None Fecal, oral and skin samples from round 3 MiSeq None Remained stable beer I do not have diabetes boulder no Rarely (few times/month) no CO no 40.0005378 None yes yes American_Gut_round 6
000006062.1212962 TATGAACGTCCG GTGTGCCAGCMGCCGCGGTAA 64 More than one year ago None n 12/18/13 None 65.0 60.0 None UBERON:feces None None yes None 701.0103149 Housing... Daily 15 no Caucasian USA 100 Never 2191:2693485258 no 96790 -156.3269338 Contact... None None None yes None UBERON:feces None None None 100 6062 None Stool More than one year ago GAZ:United States of America In the past 6 months None human gut metagenome None None 16S rRNA sequencing by synthesis Not in the last year FWD:GTGCCAGCMGCCGCGGTAA; REV:GGACTACHVGGGTWTCTAAT no 21.4644169 ENVO:urban biome None Daily no None No CCME no years None This analysis was done as in Caporaso et al 2011 Genome research. The PCR primers (F515/R806) were developed against the V4 region of the 16S rRNA (both bacteria and archaea), which we determined would yield optimal community clustering with reads of this length using a procedure similar to that of ref. 15. [For reference, this primer pair amplifies the region 533_786 in the Escherichia coli strain 83972 sequence (greengenes accession no. prokMSA_id:470367).] The reverse PCR primer is barcoded with a 12-base error-correcting Golay code to facilitate multiplexing of up to 1,500 samples per lane, and both PCR primers contain sequencer adapter regions. American Gut Project Stool sample None Daily 1/17/49 no None ENVO:feces None I do not have a skin condition None no no V4 American Gut Project 66 dental cleaning/prevention yes human None None None female None Outdoors 9/30/13 0.0 None no Less than 25% 21 no None 6062 on None None .1,g yes Never yes None Never None CCME UBERON:feces right None no no ENVO:human-associated habitat chinese herbal formula for joint pain 6:30 AM no Filtered None 5-6 hours Vegetarian CCME None CCME no 168.0 amoxicillin I do not have IBD yes 0 9606 MiSeq 408170 21 to 30 None 343 None None no AGP6_rerun_L001 None Illumina I do not use deodorant or antiperspirant Contact..., Housing... no kale 133 None no 0 MiSeq1 2191 None Fecal, oral and skin samples from round 3 MiSeq None Remained stable beans I do not have diabetes kula no Occasionally (1-2 times/week) no HI None 20.7909697 None no no American_Gut_round 6
000006807.1213039 GCTATCAAGACA GTGTGCCAGCMGCCGCGGTAA None Never None n 12/18/13 None 1.0 7.0 None UBERON:feces None None no None 70.80503082 Housing... Never None no Other USA 0 Never 2191:3668723225 no 6611 -73.2006639 Contact... None None None no None UBERON:feces None None None 60 6807 None Stool Within the past year GAZ:United States of America Not in the last year None human gut metagenome None None 16S rRNA sequencing by synthesis In the past month FWD:GTGCCAGCMGCCGCGGTAA; REV:GGACTACHVGGGTWTCTAAT no 13.4502551 ENVO:urban biome None Never no None No CCME yes years None This analysis was done as in Caporaso et al 2011 Genome research. The PCR primers (F515/R806) were developed against the V4 region of the 16S rRNA (both bacteria and archaea), which we determined would yield optimal community clustering with reads of this length using a procedure similar to that of ref. 15. [For reference, this primer pair amplifies the region 533_786 in the Escherichia coli strain 83972 sequence (greengenes accession no. prokMSA_id:470367).] The reverse PCR primer is barcoded with a 12-base error-correcting Golay code to facilitate multiplexing of up to 1,500 samples per lane, and both PCR primers contain sequencer adapter regions. American Gut Project Stool sample None Never 1/8/13 no yes ENVO:feces Half caucasian, half East Asian Eczema None no no V4 American Gut Project 28 None no human None None None female None None of the above 9/28/13 0.0 None no Less than 25% None no None 6807 yes Mom None .1,g no Never None None Never None CCME UBERON:feces ambidextrous None yes no ENVO:human-associated habitat None 6:40 AM no City None 8 or more hours Omnivore but no red meat CCME I am a primarily breastfed baby CCME no 71.0 None I do not have IBD no 0 9606 MiSeq 408170 11 to 20 None None None None no AGP6_rerun_L001 no Illumina I do not use deodorant or antiperspirant Contact..., Housing... yes peas 15 None no 40 MiSeq1 2191 None Fecal, oral and skin samples from round 3 MiSeq None Remained stable breastmilk I do not have diabetes trumbull no Never no CT None 41.2428563 None no no American_Gut_round 6
000001571.1212966 CGCCACGTGTAT GTGTGCCAGCMGCCGCGGTAA 25 More than one year ago None n 12/18/13 None 43.0 56.0 None UBERON:feces None None yes None 344.018158 Housing... Occasionally (1-2 times/week) 35 no Caucasian USA 100 Occasionally (1-2 times/week) 2191:4270936774 no 85013 -112.0863874 Contact... None None None no None UBERON:feces None None None 0 1571 None Stool More than one year ago GAZ:United States of America Not in the last year None human gut metagenome None None 16S rRNA sequencing by synthesis Not in the last year FWD:GTGCCAGCMGCCGCGGTAA; REV:GGACTACHVGGGTWTCTAAT no 21.45385742 ENVO:urban biome None Regularly (3-5 times/week) no None None CCME not_sure years None This analysis was done as in Caporaso et al 2011 Genome research. The PCR primers (F515/R806) were developed against the V4 region of the 16S rRNA (both bacteria and archaea), which we determined would yield optimal community clustering with reads of this length using a procedure similar to that of ref. 15. [For reference, this primer pair amplifies the region 533_786 in the Escherichia coli strain 83972 sequence (greengenes accession no. prokMSA_id:470367).] The reverse PCR primer is barcoded with a 12-base error-correcting Golay code to facilitate multiplexing of up to 1,500 samples per lane, and both PCR primers contain sequencer adapter regions. American Gut Project Stool sample None Regularly (3-5 times/week) 4/20/71 no None ENVO:feces None I do not have a skin condition None no no V4 American Gut Project 64 None yes human None None None unknown None Indoors 10/3/13 0.0 None no Less than 25% 40 no None 1571 no None None .1,g None Never None None Rarely (few times/month) None CCME UBERON:feces right None no no ENVO:human-associated habitat None 12:00 PM no Bottled None 8 or more hours Omnivore CCME None CCME no 163.0 None I do not have IBD no 0 9606 MiSeq 408170 11 to 20 None 10 None None no AGP6_rerun_L001 no Illumina I do not use deodorant or antiperspirant Contact..., Housing... yes Zucchini 125 None no 100 MiSeq1 2191 None Fecal, oral and skin samples from round 3 MiSeq None Remained stable Sweet potato I do not have diabetes phoenix no Occasionally (1-2 times/week) no AZ None 33.5080943 None yes None American_Gut_round 6
Blank28.H4.1213044 CCTACATGAGAC GTGTGCCAGCMGCCGCGGTAA None None None n 12/18/13 None None None None None None None None None 1624.1 None None None None None None None None 2191:unknown None 80309 -105.79 None None None None None None None None None None None Blank28.H4 None Blank None GAZ:United States of America None None unclassified metagenome None None 16S rRNA sequencing by synthesis None FWD:GTGCCAGCMGCCGCGGTAA; REV:GGACTACHVGGGTWTCTAAT None None ENVO:aquatic biome None None None None None CCME None years None This analysis was done as in Caporaso et al 2011 Genome research. The PCR primers (F515/R806) were developed against the V4 region of the 16S rRNA (both bacteria and archaea), which we determined would yield optimal community clustering with reads of this length using a procedure similar to that of ref. 15. [For reference, this primer pair amplifies the region 533_786 in the Escherichia coli strain 83972 sequence (greengenes accession no. prokMSA_id:470367).] The reverse PCR primer is barcoded with a 12-base error-correcting Golay code to facilitate multiplexing of up to 1,500 samples per lane, and both PCR primers contain sequencer adapter regions. American Gut Project blank None None None None None ENVO:sterile water None None None None None V4 American Gut Project None None None None None None None unknown None None None 0.0 None None None None None None Blank28.H4 None None None .1,g None None None None None None CCME None unknown None None None ENVO:water None None None None None None None CCME None CCME None None None None None 0 None MiSeq 408169 None None None None None None AGP6_rerun_L001 None Illumina None None None None None None None None MiSeq1 2191 None Fecal, oral and skin samples from round 3 MiSeq None None None None boulder None None None CO None 40.02 None None None American_Gut_round 17
000002250.1213140 CCGTGACAACTC GTGTGCCAGCMGCCGCGGTAA 45 More than one year ago None n 12/18/13 None None 47.0 None UBERON:feces None None no None 8.16073513 None Daily 35 no Caucasian USA 100 Daily 2191:3846476220 yes 33449 -80.2432839 None None None None no None UBERON:feces None None None 15 2250 None Stool More than one year ago GAZ:United States of America Not in the last year None human gut metagenome None None 16S rRNA sequencing by synthesis Not in the last year FWD:GTGCCAGCMGCCGCGGTAA; REV:GGACTACHVGGGTWTCTAAT no 17.47100592 ENVO:urban biome None Daily no None No CCME no years None This analysis was done as in Caporaso et al 2011 Genome research. The PCR primers (F515/R806) were developed against the V4 region of the 16S rRNA (both bacteria and archaea), which we determined would yield optimal community clustering with reads of this length using a procedure similar to that of ref. 15. [For reference, this primer pair amplifies the region 533_786 in the Escherichia coli strain 83972 sequence (greengenes accession no. prokMSA_id:470367).] The reverse PCR primer is barcoded with a 12-base error-correcting Golay code to facilitate multiplexing of up to 1,500 samples per lane, and both PCR primers contain sequencer adapter regions. American Gut Project Stool sample None Daily None no None ENVO:feces None I do not have a skin condition yes no no V4 American Gut Project 65 None no human None None None female None Outdoors 10/10/13 0.0 None no Less than 25% 20 no None 2250 on None None .1,g yes Never yes None Never None CCME UBERON:feces right None no no ENVO:human-associated habitat Biotics Livotrit Plus, Biotics Beta TCP, Biotics Thyrostim, Biotics BIO HPF, Biotics Nephra-zyme, Biotics Beta Plus, Biotics Super Phosphozyme, CALM Calcium/Magnesium, Dr. Schulze Intestinal Formula #1 8:00 AM no Filtered None 6-7 hours Omnivore CCME None CCME yes 165.0 None I do not have IBD no 0 9606 MiSeq 408170 11 to 20 None 50 None None no AGP6_rerun_L001 None Illumina I use an antiperspirant None no tomato 105 None yes 85 MiSeq1 2191 some cheeses Fecal, oral and skin samples from round 3 MiSeq yes Remained stable sweet potato I do not have diabetes wellington no Never no FL None 26.5907805 None yes no American_Gut_round 6
000010925.1212984 CTTCCCTAACTC GTGTGCCAGCMGCCGCGGTAA 61 Within the past 6 months yes n 12/18/13 yes 49.0 88.0 None UBERON:feces None None yes None 66.65675354 Housing... Regularly (3-5 times/week) 22 no Caucasian USA 100 Daily 2191:497124843 no 36117 -86.1914604 Contact... None None None no None UBERON:feces None None None 2 10925 None Stool Within the past 6 months GAZ:United States of America In the past year None human gut metagenome None None 16S rRNA sequencing by synthesis In the past month FWD:GTGCCAGCMGCCGCGGTAA; REV:GGACTACHVGGGTWTCTAAT no 31.47038567 ENVO:urban biome None Regularly (3-5 times/week) no None I take the pill CCME no years None This analysis was done as in Caporaso et al 2011 Genome research. The PCR primers (F515/R806) were developed against the V4 region of the 16S rRNA (both bacteria and archaea), which we determined would yield optimal community clustering with reads of this length using a procedure similar to that of ref. 15. [For reference, this primer pair amplifies the region 533_786 in the Escherichia coli strain 83972 sequence (greengenes accession no. prokMSA_id:470367).] The reverse PCR primer is barcoded with a 12-base error-correcting Golay code to facilitate multiplexing of up to 1,500 samples per lane, and both PCR primers contain sequencer adapter regions. American Gut Project Stool sample spray Regularly (3-5 times/week) 9/18/64 no None ENVO:feces None Rosacea yes yes no V4 American Gut Project 66 duodenum infection yes human None None None female None Indoors 11/6/13 0.0 None no 51 to 75% 17 no None 10925 yes None None .1,g yes Never yes None Daily None CCME UBERON:feces unknown None no no ENVO:human-associated habitat omega 3, b vitamins, calcium 7:00 AM no Filtered None 7-8 hours Omnivore CCME None CCME no 168.0 None I do not have IBD no 0 9606 MiSeq 408170 6 to 10 None 76 None None no AGP6_rerun_L001 no Illumina I use an antiperspirant Contact..., Housing... no lettuce 195 None no 98 MiSeq1 2191 None Fecal, oral and skin samples from round 3 MiSeq None None bread I do not have diabetes montgomery no Rarely (few times/month) no AL None 32.3822577 None yes yes American_Gut_round 6
000002060.1213065 GTTTCACGCGAA GTGTGCCAGCMGCCGCGGTAA 20 Never None n 12/18/13 None 16.0 68.0 None UBERON:feces None None no None 199.6077576 Housing... Never 30 yes Caucasian USA 100 Never 2191:790688530 yes 14472 -77.5902759 Contact... None None None no None UBERON:feces None None None None 2060 None Stool More than one year ago GAZ:United States of America Not in the last year None human gut metagenome None None 16S rRNA sequencing by synthesis Not in the last year FWD:GTGCCAGCMGCCGCGGTAA; REV:GGACTACHVGGGTWTCTAAT no 20.91846856 ENVO:urban biome None Daily no None None CCME yes years None This analysis was done as in Caporaso et al 2011 Genome research. The PCR primers (F515/R806) were developed against the V4 region of the 16S rRNA (both bacteria and archaea), which we determined would yield optimal community clustering with reads of this length using a procedure similar to that of ref. 15. [For reference, this primer pair amplifies the region 533_786 in the Escherichia coli strain 83972 sequence (greengenes accession no. prokMSA_id:470367).] The reverse PCR primer is barcoded with a 12-base error-correcting Golay code to facilitate multiplexing of up to 1,500 samples per lane, and both PCR primers contain sequencer adapter regions. American Gut Project Stool sample None Rarely (few times/month) 11/26/97 no yes ENVO:feces None Eczema None no no V4 American Gut Project 71 None no human None None None male None Indoors 11/15/13 0.0 None no Less than 25% 50 no None 2060 no sister None .1,g yes Never None None Never None CCME UBERON:feces right None yes no ENVO:human-associated habitat vitamin D, zinc, L-Glutamine, Chromium Picolinate, Ashwagandha 3:20 PM no Filtered None 7-8 hours Omnivore CCME gaps diet - no processed foods, minimal dairy, starches from vegetables, lots of animal fat and plant material CCME no 180.0 None I do not have IBD yes 0 9606 MiSeq 408170 6 to 10 None None None None no AGP6_rerun_L001 no Illumina I use deodorant Contact..., Housing... no spinich 150 None no None MiSeq1 2191 various food sensitivities Fecal, oral and skin samples from round 3 MiSeq None Remained stable unkmown I do not have diabetes honeoye falls no Rarely (few times/month) no NY None 42.9522855 None no no American_Gut_round 6
000001327.1213030 CCTCTGAGAGCT GTGTGCCAGCMGCCGCGGTAA 14 Within the past 3 months None n 12/18/13 None 66.0 115.0 None UBERON:feces None None yes None 250.0058899 Outdoor Daily 36 no Caucasian USA 100 Never 2191:457821962 no 48334 -83.3468784 Extensive None None None no None UBERON:feces None None None 5 1327 None Stool More than one year ago GAZ:United States of America In the past month None human gut metagenome None None 16S rRNA sequencing by synthesis Not in the last year FWD:GTGCCAGCMGCCGCGGTAA; REV:GGACTACHVGGGTWTCTAAT no 46.63501561 ENVO:urban biome None Daily no None No CCME no years None This analysis was done as in Caporaso et al 2011 Genome research. The PCR primers (F515/R806) were developed against the V4 region of the 16S rRNA (both bacteria and archaea), which we determined would yield optimal community clustering with reads of this length using a procedure similar to that of ref. 15. [For reference, this primer pair amplifies the region 533_786 in the Escherichia coli strain 83972 sequence (greengenes accession no. prokMSA_id:470367).] The reverse PCR primer is barcoded with a 12-base error-correcting Golay code to facilitate multiplexing of up to 1,500 samples per lane, and both PCR primers contain sequencer adapter regions. American Gut Project Stool sample None Regularly (3-5 times/week) 8/25/47 no yes ENVO:feces None Eczema None no no V4 American Gut Project 62 None no human None None None female None Both 11/11/13 0.0 None no Less than 25% 50 no None 1327 no None None .1,g yes Never None None Rarely (few times/month) None CCME UBERON:feces right None yes no ENVO:human-associated habitat Vitamin E - 1000 mg,Folic Acid Plus,Vitamin D3 - 2000 iu,Tart Cherry 1.2 grams,Melatonin Plus,MK-7 Gold 100 mcg, Hawaii BioAstin Natural Astaxanthin 4mg ,Vitamin C - 500 mg,Acidophilis Probiotic - 100 million organisms,Algal 900 - DHA,Co Q 10 - 200 mg,Resveratrol - 50 mg,Alpha Lipoic Acid 11:22 AM no Well None 7-8 hours Omnivore CCME <30 carbs CCME no 157.0 None I do not have IBD yes 0 9606 MiSeq 408170 6 to 10 None 83 None None no AGP6_rerun_L001 no Illumina I use deodorant cat, Extensive, Outdoor no spinach 255 None no 95 MiSeq1 2191 None Fecal, oral and skin samples from round 3 MiSeq None Increased more than 10 pounds fruit I do not have diabetes farmington hills no Regularly (3-5 times/week) no MI None 42.5049385 None yes no American_Gut_round 6
000001441.1213056 TTATGGTACGGA GTGTGCCAGCMGCCGCGGTAA 29 More than one year ago None n 12/18/13 yes 41.0 68.0 None UBERON:feces None None no None 301.3252869 Indoor Regularly (3-5 times/week) 20 no Caucasian USA 100 Occasionally (1-2 times/week) 2191:2024565639 yes 66208 -94.6295394 Moderate None None None no None UBERON:feces None None None 7 1441 None Stool More than one year ago GAZ:United States of America In the past year None human gut metagenome None None 16S rRNA sequencing by synthesis Not in the last year FWD:GTGCCAGCMGCCGCGGTAA; REV:GGACTACHVGGGTWTCTAAT no 24.95857988 ENVO:urban biome None Daily no None No CCME no years None This analysis was done as in Caporaso et al 2011 Genome research. The PCR primers (F515/R806) were developed against the V4 region of the 16S rRNA (both bacteria and archaea), which we determined would yield optimal community clustering with reads of this length using a procedure similar to that of ref. 15. [For reference, this primer pair amplifies the region 533_786 in the Escherichia coli strain 83972 sequence (greengenes accession no. prokMSA_id:470367).] The reverse PCR primer is barcoded with a 12-base error-correcting Golay code to facilitate multiplexing of up to 1,500 samples per lane, and both PCR primers contain sequencer adapter regions. American Gut Project Stool sample None Daily 4/19/73 no None ENVO:feces None I do not have a skin condition None no no V4 American Gut Project 65 strep no human None None None female None Both 10/3/13 0.0 None no Less than 25% 51 no None 1441 no None None .1,g yes Never None None Never None CCME UBERON:feces right None yes no ENVO:human-associated habitat fish oil, 5-HTP, DL-Phenylalanine, L-Tyrosine, L-Methionine, L-Glutamine, Alpha Lipoic Acid, HCL, Magnesium, B-complex, COQ10, Zinc, iodine, dhea, vitamin-d 2:00 PM no Filtered None 7-8 hours Omnivore CCME no dairy, no eggs CCME no 165.0 zithromax I do not have IBD yes 0 9606 MiSeq 408170 21 to 30 None 238 None None no AGP6_rerun_L001 no Illumina I use deodorant 1, Moderate, Indoor no leafy greens 150 None no 93 MiSeq1 2191 None Fecal, oral and skin samples from round 3 MiSeq None Remained stable carrots I do not have diabetes prairie village no Never no KS None 38.9950997 None yes no American_Gut_round 6
000003284.1213124 ATGCTGCAACAC GTGTGCCAGCMGCCGCGGTAA 40 Within the past 3 months None n 12/18/13 None 38.0 83.0 None UBERON:feces None None no None 1575.246948 Indoor Rarely (few times/month) 22 no Caucasian USA 100 Never 2191:4074251412 yes 80301 -105.2077798 Extensive None None None no None UBERON:feces None None None 20 3284 None Stool More than one year ago GAZ:United States of America Not in the last year None human gut metagenome None None 16S rRNA sequencing by synthesis Not in the last year FWD:GTGCCAGCMGCCGCGGTAA; REV:GGACTACHVGGGTWTCTAAT no 23.75 ENVO:urban biome None Daily no None None CCME yes years None This analysis was done as in Caporaso et al 2011 Genome research. The PCR primers (F515/R806) were developed against the V4 region of the 16S rRNA (both bacteria and archaea), which we determined would yield optimal community clustering with reads of this length using a procedure similar to that of ref. 15. [For reference, this primer pair amplifies the region 533_786 in the Escherichia coli strain 83972 sequence (greengenes accession no. prokMSA_id:470367).] The reverse PCR primer is barcoded with a 12-base error-correcting Golay code to facilitate multiplexing of up to 1,500 samples per lane, and both PCR primers contain sequencer adapter regions. American Gut Project Stool sample None Occasionally (1-2 times/week) 11/2/75 no None ENVO:feces None I do not have a skin condition yes yes no V4 American Gut Project 74 None yes human None None None male None Outdoors 8/31/13 0.0 None no 51 to 75% 38 no None 3284 no partner None .1,g yes Never yes None Occasionally (1-2 times/week) None CCME UBERON:feces right None no no ENVO:human-associated habitat melatonin 9:45 PM no Bottled None 6-7 hours Omnivore CCME None CCME yes 188.0 None I do not have IBD no 0 9606 MiSeq 408170 Less than 5 None 85 None None no AGP6_rerun_L001 no Illumina I use an antiperspirant 1, Extensive, Indoor no potatoes 185 None no 80 MiSeq1 2191 None Fecal, oral and skin samples from round 3 MiSeq None Decreased more than 10 pounds pizza I do not have diabetes boulder no Rarely (few times/month) no CO None 40.0406506 None yes yes American_Gut_round 6
000004192.1213137 AACCGATGTACC GTGTGCCAGCMGCCGCGGTAA 30 None None n 12/18/13 None 58.0 63.0 None UBERON:feces None None no None 157.6964264 Housing... Daily 20 no Caucasian USA 100 Regularly (3-5 times/week) 2191:2635379628 no 75214 -96.7440467 Contact... None None None no None UBERON:feces None None None 30 4192 None Stool More than one year ago GAZ:United States of America In the past month None human gut metagenome None None 16S rRNA sequencing by synthesis Not in the last year FWD:GTGCCAGCMGCCGCGGTAA; REV:GGACTACHVGGGTWTCTAAT no 21.28460208 ENVO:urban biome None Daily no None No CCME no years None This analysis was done as in Caporaso et al 2011 Genome research. The PCR primers (F515/R806) were developed against the V4 region of the 16S rRNA (both bacteria and archaea), which we determined would yield optimal community clustering with reads of this length using a procedure similar to that of ref. 15. [For reference, this primer pair amplifies the region 533_786 in the Escherichia coli strain 83972 sequence (greengenes accession no. prokMSA_id:470367).] The reverse PCR primer is barcoded with a 12-base error-correcting Golay code to facilitate multiplexing of up to 1,500 samples per lane, and both PCR primers contain sequencer adapter regions. American Gut Project Stool sample None Regularly (3-5 times/week) 10/18/55 no None ENVO:feces None I do not have a skin condition None no no V4 American Gut Project 68 Kidney infection yes human None None None female None None 9/18/13 0.0 None yes Less than 25% 50 no None 4192 no None None .1,g yes Never None None Never None CCME UBERON:feces right None yes no ENVO:human-associated habitat Magnesium 9:30 AM no City None 7-8 hours Omnivore CCME Avoid wheat CCME no 173.0 Cipro Ulcerative colitis yes 0 9606 MiSeq 408170 6 to 10 None 91 None None no AGP6_rerun_L001 no Illumina I do not use deodorant or antiperspirant Contact..., Housing... no Squash 140 None no 70 MiSeq1 2191 None Fecal, oral and skin samples from round 3 MiSeq None Increased more than 10 pounds Cabbage I do not have diabetes dallas no Rarely (few times/month) no TX None 32.824251 None yes no American_Gut_round 6
Blank28.D4.1213097 ACGGCGTTATGT GTGTGCCAGCMGCCGCGGTAA None None None n 12/18/13 None None None None None None None None None 1624.1 None None None None None None None None 2191:unknown None 80309 -105.79 None None None None None None None None None None None Blank28.D4 None Blank None GAZ:United States of America None None unclassified metagenome None None 16S rRNA sequencing by synthesis None FWD:GTGCCAGCMGCCGCGGTAA; REV:GGACTACHVGGGTWTCTAAT None None ENVO:aquatic biome None None None None None CCME None years None This analysis was done as in Caporaso et al 2011 Genome research. The PCR primers (F515/R806) were developed against the V4 region of the 16S rRNA (both bacteria and archaea), which we determined would yield optimal community clustering with reads of this length using a procedure similar to that of ref. 15. [For reference, this primer pair amplifies the region 533_786 in the Escherichia coli strain 83972 sequence (greengenes accession no. prokMSA_id:470367).] The reverse PCR primer is barcoded with a 12-base error-correcting Golay code to facilitate multiplexing of up to 1,500 samples per lane, and both PCR primers contain sequencer adapter regions. American Gut Project blank None None None None None ENVO:sterile water None None None None None V4 American Gut Project None None None None None None None unknown None None None 0.0 None None None None None None Blank28.D4 None None None .1,g None None None None None None CCME None unknown None None None ENVO:water None None None None None None None CCME None CCME None None None None None 0 None MiSeq 408169 None None None None None None AGP6_rerun_L001 None Illumina None None None None None None None None MiSeq1 2191 None Fecal, oral and skin samples from round 3 MiSeq None None None None boulder None None None CO None 40.02 None None None American_Gut_round 12
Blank33.F9.1213130 TCGAGCCGATCT GTGTGCCAGCMGCCGCGGTAA None None None n 12/18/13 None None None None None None None None None 1624.1 None None None None None None None None 2191:unknown None 80309 -105.79 None None None None None None None None None None None Blank33.F9 None Blank None GAZ:United States of America None None unclassified metagenome None None 16S rRNA sequencing by synthesis None FWD:GTGCCAGCMGCCGCGGTAA; REV:GGACTACHVGGGTWTCTAAT None None ENVO:aquatic biome None None None None None CCME None years None This analysis was done as in Caporaso et al 2011 Genome research. The PCR primers (F515/R806) were developed against the V4 region of the 16S rRNA (both bacteria and archaea), which we determined would yield optimal community clustering with reads of this length using a procedure similar to that of ref. 15. [For reference, this primer pair amplifies the region 533_786 in the Escherichia coli strain 83972 sequence (greengenes accession no. prokMSA_id:470367).] The reverse PCR primer is barcoded with a 12-base error-correcting Golay code to facilitate multiplexing of up to 1,500 samples per lane, and both PCR primers contain sequencer adapter regions. American Gut Project blank None None None None None ENVO:sterile water None None None None None V4 American Gut Project None None None None None None None unknown None None None 0.0 None None None None None None Blank33.F9 None None None .1,g None None None None None None CCME None unknown None None None ENVO:water None None None None None None None CCME None CCME None None None None None 0 None MiSeq 408169 None None None None None None AGP6_rerun_L001 None Illumina None None None None None None None None MiSeq1 2191 None Fecal, oral and skin samples from round 3 MiSeq None None None None boulder None None None CO None 40.02 None None None American_Gut_round 26
Blank33.G9.1213051 AACTGTTCGCGC GTGTGCCAGCMGCCGCGGTAA None None None n 12/18/13 None None None None None None None None None 1624.1 None None None None None None None None 2191:unknown None 80309 -105.79 None None None None None None None None None None None Blank33.G9 None Blank None GAZ:United States of America None None unclassified metagenome None None 16S rRNA sequencing by synthesis None FWD:GTGCCAGCMGCCGCGGTAA; REV:GGACTACHVGGGTWTCTAAT None None ENVO:aquatic biome None None None None None CCME None years None This analysis was done as in Caporaso et al 2011 Genome research. The PCR primers (F515/R806) were developed against the V4 region of the 16S rRNA (both bacteria and archaea), which we determined would yield optimal community clustering with reads of this length using a procedure similar to that of ref. 15. [For reference, this primer pair amplifies the region 533_786 in the Escherichia coli strain 83972 sequence (greengenes accession no. prokMSA_id:470367).] The reverse PCR primer is barcoded with a 12-base error-correcting Golay code to facilitate multiplexing of up to 1,500 samples per lane, and both PCR primers contain sequencer adapter regions. American Gut Project blank None None None None None ENVO:sterile water None None None None None V4 American Gut Project None None None None None None None unknown None None None 0.0 None None None None None None Blank33.G9 None None None .1,g None None None None None None CCME None unknown None None None ENVO:water None None None None None None None CCME None CCME None None None None None 0 None MiSeq 408169 None None None None None None AGP6_rerun_L001 None Illumina None None None None None None None None MiSeq1 2191 None Fecal, oral and skin samples from round 3 MiSeq None None None None boulder None None None CO None 40.02 None None None American_Gut_round 28
000009128.1213008 ACCTGGGAATAT GTGTGCCAGCMGCCGCGGTAA None Within the past 6 months None n 12/18/13 None 2.0 12.0 None UBERON:feces None None no None 25.51987648 Indoor Never None yes Caucasian USA 0 Never 2191:4130649718 no 11238 -73.9624327 None None None None no None UBERON:feces None None None 50 9128 None Stool More than one year ago GAZ:United States of America Not in the last year None human gut metagenome None None 16S rRNA sequencing by synthesis Not in the last year FWD:GTGCCAGCMGCCGCGGTAA; REV:GGACTACHVGGGTWTCTAAT no 20.30888889 ENVO:urban biome None Rarely (few times/month) no None None CCME yes years None This analysis was done as in Caporaso et al 2011 Genome research. The PCR primers (F515/R806) were developed against the V4 region of the 16S rRNA (both bacteria and archaea), which we determined would yield optimal community clustering with reads of this length using a procedure similar to that of ref. 15. [For reference, this primer pair amplifies the region 533_786 in the Escherichia coli strain 83972 sequence (greengenes accession no. prokMSA_id:470367).] The reverse PCR primer is barcoded with a 12-base error-correcting Golay code to facilitate multiplexing of up to 1,500 samples per lane, and both PCR primers contain sequencer adapter regions. American Gut Project Stool sample None Daily 6/4/12 no None ENVO:feces None I do not have a skin condition None no no V4 American Gut Project 30 None no human None None None male None Indoors 9/20/13 0.0 None no Less than 25% None no None 9128 no Mom, dad, Sister None .1,g None Never None None Never None CCME UBERON:feces right None no no ENVO:human-associated habitat None 8:30 AM no Filtered None 8 or more hours Omnivore CCME None CCME no 76.0 None I do not have IBD yes 0 9606 MiSeq 408170 6 to 10 None 77 None None no AGP6_rerun_L001 no Illumina I do not use deodorant or antiperspirant fish, None, Indoor no kale 26 None no 50 MiSeq1 2191 None Fecal, oral and skin samples from round 3 MiSeq None Increased more than 10 pounds bread I do not have diabetes brooklyn no Never no NY None 40.6805029 None no no American_Gut_round 6
000009443.1212988 AGACATACCGTA GTGTGCCAGCMGCCGCGGTAA None Within the past 3 months None n 12/18/13 yes 55.0 88.0 None UBERON:feces None None no None 106.1503067 Housing... Regularly (3-5 times/week) None no Caucasian USA 86 Daily 2191:2078026060 no 20910 -77.0391754 Contact... None None None no None UBERON:feces None None None 90 9443 None Stool Within the past 6 months GAZ:United States of America Not in the last year None human gut metagenome None None 16S rRNA sequencing by synthesis In the past year FWD:GTGCCAGCMGCCGCGGTAA; REV:GGACTACHVGGGTWTCTAAT no 30.53798173 ENVO:urban biome None Daily no None I take the pill CCME no years None This analysis was done as in Caporaso et al 2011 Genome research. The PCR primers (F515/R806) were developed against the V4 region of the 16S rRNA (both bacteria and archaea), which we determined would yield optimal community clustering with reads of this length using a procedure similar to that of ref. 15. [For reference, this primer pair amplifies the region 533_786 in the Escherichia coli strain 83972 sequence (greengenes accession no. prokMSA_id:470367).] The reverse PCR primer is barcoded with a 12-base error-correcting Golay code to facilitate multiplexing of up to 1,500 samples per lane, and both PCR primers contain sequencer adapter regions. American Gut Project Stool sample None Occasionally (1-2 times/week) 12/29/58 no None ENVO:feces None I do not have a skin condition None no no V4 American Gut Project 67 None no human None None None female None Indoors 9/20/13 0.0 None no Less than 25% None no None 9443 yes None None .1,g yes Never None None Daily None CCME UBERON:feces right None no no ENVO:human-associated habitat calcium 4:00 PM no City None 8 or more hours Omnivore CCME None CCME no 170.0 None I do not have IBD yes 0 9606 MiSeq 408170 6 to 10 None 84 None None no AGP6_rerun_L001 no Illumina I use an antiperspirant Contact..., Housing... yes lettuce 195 None no 10 MiSeq1 2191 None Fecal, oral and skin samples from round 3 MiSeq None Remained stable Dreamfields pasta I do not have diabetes silver spring no Never None MD None 39.0041504 None yes yes American_Gut_round 6
000010137.1212972 AACACTCGATCG GTGTGCCAGCMGCCGCGGTAA None Within the past year None n 12/18/13 None 57.0 56.0 None UBERON:feces None None yes None 198.0540009 Housing... Regularly (3-5 times/week) None no Caucasian USA 89 Regularly (3-5 times/week) 2191:2700103704 no 13078 -76.0623979 Contact... None None None no None UBERON:feces None None None 63 10137 None Stool More than one year ago GAZ:United States of America In the past year None human gut metagenome None None 16S rRNA sequencing by synthesis Not in the last year FWD:GTGCCAGCMGCCGCGGTAA; REV:GGACTACHVGGGTWTCTAAT no 20.01193756 ENVO:urban biome None Daily no None No CCME yes years None This analysis was done as in Caporaso et al 2011 Genome research. The PCR primers (F515/R806) were developed against the V4 region of the 16S rRNA (both bacteria and archaea), which we determined would yield optimal community clustering with reads of this length using a procedure similar to that of ref. 15. [For reference, this primer pair amplifies the region 533_786 in the Escherichia coli strain 83972 sequence (greengenes accession no. prokMSA_id:470367).] The reverse PCR primer is barcoded with a 12-base error-correcting Golay code to facilitate multiplexing of up to 1,500 samples per lane, and both PCR primers contain sequencer adapter regions. American Gut Project Stool sample None Daily 5/1/57 no None ENVO:feces None I do not have a skin condition yes yes no V4 American Gut Project 66 possible strep throat no human None None None female None Both 11/4/13 0.0 None no 25 to 50% None no None 10137 yes Husand None .1,g yes Never yes None Daily None CCME UBERON:feces right None no no ENVO:human-associated habitat Calcium Citrate w/ Vitamin D, Vitamin C, Fish Oil w. Omega 3 7:27 AM no Well None 8 or more hours Vegetarian but eat seafood CCME None CCME no 168.0 I don't remember I do not have IBD yes 0 9606 MiSeq 408170 21 to 30 None 206.4 None None no AGP6_rerun_L001 no Illumina Not sure, but I use some form of deodorant/antiperspirant Contact..., Housing... yes leafy greens 124 None no 37 MiSeq1 2191 None Fecal, oral and skin samples from round 3 MiSeq None Remained stable whole wheat bread I do not have diabetes jamesville no Rarely (few times/month) no NY None 42.955273 None yes yes American_Gut_round 6
000009241.1213050 GAGATCGCCTAT GTGTGCCAGCMGCCGCGGTAA None More than one year ago None n 12/18/13 yes None 63.0 None UBERON:feces None None None None 1647.610352 None Never None no Caucasian USA 0 Rarely (few times/month) 2191:3189425668 None 80219 -105.0382076 None None None None no None UBERON:feces None None None None 9241 None Stool None GAZ:United States of America Not in the last year None human gut metagenome None None 16S rRNA sequencing by synthesis None FWD:GTGCCAGCMGCCGCGGTAA; REV:GGACTACHVGGGTWTCTAAT no None ENVO:urban biome None Daily no None No CCME not_sure years None This analysis was done as in Caporaso et al 2011 Genome research. The PCR primers (F515/R806) were developed against the V4 region of the 16S rRNA (both bacteria and archaea), which we determined would yield optimal community clustering with reads of this length using a procedure similar to that of ref. 15. [For reference, this primer pair amplifies the region 533_786 in the Escherichia coli strain 83972 sequence (greengenes accession no. prokMSA_id:470367).] The reverse PCR primer is barcoded with a 12-base error-correcting Golay code to facilitate multiplexing of up to 1,500 samples per lane, and both PCR primers contain sequencer adapter regions. American Gut Project Stool sample None Occasionally (1-2 times/week) None no None ENVO:feces None I do not have a skin condition None None no V4 American Gut Project None None None human None None None female None None 9/9/13 0.0 None no None None no None 9241 no None None .1,g yes Never None None Never None CCME UBERON:feces unknown None no no ENVO:human-associated habitat multi-vits & mins, & chelated minerals 7:11 AM no City None 8 or more hours Omnivore CCME None CCME yes None None I do not have IBD None 0 9606 MiSeq 408170 Less than 5 None None None None no AGP6_rerun_L001 None Illumina I use deodorant None None None 141 None None None MiSeq1 2191 melon family Fecal, oral and skin samples from round 3 MiSeq yes Remained stable None I do not have diabetes denver no Never None CO None 39.6961606 None yes yes American_Gut_round 6
Blank33.D12.1213138 CGAGGTTCTGAT GTGTGCCAGCMGCCGCGGTAA None None None n 12/18/13 None None None None None None None None None 1624.1 None None None None None None None None 2191:unknown None 80309 -105.79 None None None None None None None None None None None Blank33.D12 None Blank None GAZ:United States of America None None unclassified metagenome None None 16S rRNA sequencing by synthesis None FWD:GTGCCAGCMGCCGCGGTAA; REV:GGACTACHVGGGTWTCTAAT None None ENVO:aquatic biome None None None None None CCME None years None This analysis was done as in Caporaso et al 2011 Genome research. The PCR primers (F515/R806) were developed against the V4 region of the 16S rRNA (both bacteria and archaea), which we determined would yield optimal community clustering with reads of this length using a procedure similar to that of ref. 15. [For reference, this primer pair amplifies the region 533_786 in the Escherichia coli strain 83972 sequence (greengenes accession no. prokMSA_id:470367).] The reverse PCR primer is barcoded with a 12-base error-correcting Golay code to facilitate multiplexing of up to 1,500 samples per lane, and both PCR primers contain sequencer adapter regions. American Gut Project blank None None None None None ENVO:sterile water None None None None None V4 American Gut Project None None None None None None None unknown None None None 0.0 None None None None None None Blank33.D12 None None None .1,g None None None None None None CCME None unknown None None None ENVO:water None None None None None None None CCME None CCME None None None None None 0 None MiSeq 408169 None None None None None None AGP6_rerun_L001 None Illumina None None None None None None None None MiSeq1 2191 None Fecal, oral and skin samples from round 3 MiSeq None None None None boulder None None None CO None 40.02 None None None American_Gut_round 21
Blank33.H12.1213121 GTCACTCCGAAC GTGTGCCAGCMGCCGCGGTAA None None None n 12/18/13 None None None None None None None None None 1624.1 None None None None None None None None 2191:unknown None 80309 -105.79 None None None None None None None None None None None Blank33.H12 None Blank None GAZ:United States of America None None unclassified metagenome None None 16S rRNA sequencing by synthesis None FWD:GTGCCAGCMGCCGCGGTAA; REV:GGACTACHVGGGTWTCTAAT None None ENVO:aquatic biome None None None None None CCME None years None This analysis was done as in Caporaso et al 2011 Genome research. The PCR primers (F515/R806) were developed against the V4 region of the 16S rRNA (both bacteria and archaea), which we determined would yield optimal community clustering with reads of this length using a procedure similar to that of ref. 15. [For reference, this primer pair amplifies the region 533_786 in the Escherichia coli strain 83972 sequence (greengenes accession no. prokMSA_id:470367).] The reverse PCR primer is barcoded with a 12-base error-correcting Golay code to facilitate multiplexing of up to 1,500 samples per lane, and both PCR primers contain sequencer adapter regions. American Gut Project blank None None None None None ENVO:sterile water None None None None None V4 American Gut Project None None None None None None None unknown None None None 0.0 None None None None None None Blank33.H12 None None None .1,g None None None None None None CCME None unknown None None None ENVO:water None None None None None None None CCME None CCME None None None None None 0 None MiSeq 408169 None None None None None None AGP6_rerun_L001 None Illumina None None None None None None None None MiSeq1 2191 None Fecal, oral and skin samples from round 3 MiSeq None None None None boulder None None None CO None 40.02 None None None American_Gut_round 29
000004214.1212943 CAGTCGTTAAGA GTGTGCCAGCMGCCGCGGTAA 50 Within the past 3 months None n 12/18/13 yes 30.0 74.0 None UBERON:feces None None no None 1619.837158 Outdoor, Outdoor Regularly (3-5 times/week) 10 no Caucasian USA 100 Never 2191:4095514450 no 80303 -105.2077798 Moderate, Moderate None None None no None UBERON:feces None None None 90 4214 None Stool More than one year ago GAZ:United States of America Not in the last year None human gut metagenome yes None 16S rRNA sequencing by synthesis Not in the last year FWD:GTGCCAGCMGCCGCGGTAA; REV:GGACTACHVGGGTWTCTAAT no 23.01031541 ENVO:urban biome None Daily no None None CCME yes years None This analysis was done as in Caporaso et al 2011 Genome research. The PCR primers (F515/R806) were developed against the V4 region of the 16S rRNA (both bacteria and archaea), which we determined would yield optimal community clustering with reads of this length using a procedure similar to that of ref. 15. [For reference, this primer pair amplifies the region 533_786 in the Escherichia coli strain 83972 sequence (greengenes accession no. prokMSA_id:470367).] The reverse PCR primer is barcoded with a 12-base error-correcting Golay code to facilitate multiplexing of up to 1,500 samples per lane, and both PCR primers contain sequencer adapter regions. American Gut Project Stool sample None Regularly (3-5 times/week) 5/4/84 no None ENVO:feces None Eczema None no no V4 American Gut Project 71 None yes human None Three None unknown None Outdoors 10/14/13 0.0 None no Less than 25% 40 yes None 4214 no roommate None .1,g no Rarely (few times/month) None None Daily None CCME UBERON:feces right None no no ENVO:human-associated habitat None 9:50 AM no City no 6-7 hours Omnivore CCME None CCME no 180.0 None I do not have IBD no 0 9606 MiSeq 408170 11 to 20 None 267 None None yes AGP6_rerun_L001 no Illumina I use deodorant dog, dog, Moderate, Moderate, Outdoor, Outdoor no tomato 165 None no 10 MiSeq1 2191 None Fecal, oral and skin samples from round 3 MiSeq None Remained stable beer I do not have diabetes boulder no Rarely (few times/month) no CO no 40.0005378 None yes yes American_Gut_round 6
000010866.1213132 GGAATTATCGGT GTGTGCCAGCMGCCGCGGTAA 25 More than one year ago None n 12/18/13 None 51.0 56.0 None UBERON:feces None None no None 667.2123413 Indoor Daily 40 no Caucasian USA 100 Regularly (3-5 times/week) 2191:2779785564 no 83814 -116.7804664 Extensive None None None no None UBERON:feces None None None 25 10866 None Stool More than one year ago GAZ:United States of America Not in the last year None human gut metagenome None None 16S rRNA sequencing by synthesis Not in the last year FWD:GTGCCAGCMGCCGCGGTAA; REV:GGACTACHVGGGTWTCTAAT no 20.79881657 ENVO:urban biome None Daily no None No CCME yes years None This analysis was done as in Caporaso et al 2011 Genome research. The PCR primers (F515/R806) were developed against the V4 region of the 16S rRNA (both bacteria and archaea), which we determined would yield optimal community clustering with reads of this length using a procedure similar to that of ref. 15. [For reference, this primer pair amplifies the region 533_786 in the Escherichia coli strain 83972 sequence (greengenes accession no. prokMSA_id:470367).] The reverse PCR primer is barcoded with a 12-base error-correcting Golay code to facilitate multiplexing of up to 1,500 samples per lane, and both PCR primers contain sequencer adapter regions. American Gut Project Stool sample spray Occasionally (1-2 times/week) 8/23/62 no yes ENVO:feces None I do not have a skin condition None yes no V4 American Gut Project 65 None yes human None None None female None Indoors 11/16/13 0.0 None no 25 to 50% 35 no None 10866 no Husband None .1,g yes Never None None Regularly (3-5 times/week) None CCME UBERON:feces left None no no ENVO:human-associated habitat B Complex CoQ10 Calcium Cinsulin Copper D DHEA EFA Evening Primrose Oil with GLA 5-HTP Gingko Biloba Ginseng Glucomannan Holy Basil Milk Thistle Resveratrol Turmeric 11:22 AM yes Filtered None 8 or more hours Omnivore CCME None CCME no 165.0 None I do not have IBD no 0 9606 MiSeq 408170 11 to 20 None 105 None None no AGP6_rerun_L001 no Illumina I use an antiperspirant Parrot, Extensive, Indoor yes spinach 125 None no 75 MiSeq1 2191 None Fecal, oral and skin samples from round 3 MiSeq None Remained stable wheat bread I do not have diabetes coeur d alene no Never no ID None 47.6776832 None yes no American_Gut_round 6
000010879.1213118 CTAGGATCACTG GTGTGCCAGCMGCCGCGGTAA 44 Within the past year None n 12/18/13 None 33.0 86.0 None UBERON:feces None None no None 89.4965744 Housing... Regularly (3-5 times/week) 19 not_sure Caucasian USA 100 Never 2191:1702328819 no 90038 -118.3315838 Contact... None None None no None UBERON:feces None None None 40 10879 None Stool More than one year ago GAZ:United States of America Not in the last year None human gut metagenome None None 16S rRNA sequencing by synthesis Not in the last year FWD:GTGCCAGCMGCCGCGGTAA; REV:GGACTACHVGGGTWTCTAAT no 27.25918367 ENVO:urban biome None Daily no None None CCME no years None This analysis was done as in Caporaso et al 2011 Genome research. The PCR primers (F515/R806) were developed against the V4 region of the 16S rRNA (both bacteria and archaea), which we determined would yield optimal community clustering with reads of this length using a procedure similar to that of ref. 15. [For reference, this primer pair amplifies the region 533_786 in the Escherichia coli strain 83972 sequence (greengenes accession no. prokMSA_id:470367).] The reverse PCR primer is barcoded with a 12-base error-correcting Golay code to facilitate multiplexing of up to 1,500 samples per lane, and both PCR primers contain sequencer adapter regions. American Gut Project Stool sample None Daily 11/17/80 no None ENVO:feces None I do not have a skin condition None yes no V4 American Gut Project 70 None yes human None None None male None Indoors 11/12/13 0.0 None no 25 to 50% 37 no None 10879 no None None .1,g yes Never None None Regularly (3-5 times/week) None CCME UBERON:feces right None no no ENVO:human-associated habitat Green Coffee Extract 6:00 AM no Filtered None 8 or more hours Omnivore CCME None CCME no 178.0 None I do not have IBD no 0 9606 MiSeq 408170 More than 30 None 140 None None no AGP6_rerun_L001 no Illumina I use deodorant Contact..., Housing... yes lettuce 190 None no 60 MiSeq1 2191 None Fecal, oral and skin samples from round 3 MiSeq None Remained stable oats I do not have diabetes los angeles no Rarely (few times/month) no CA None 34.0895186 None yes yes American_Gut_round 6
000001870.1212959 ACGAAGTCTACC GTGTGCCAGCMGCCGCGGTAA 47.1 More than one year ago None n 5/20/13 yes 56.0 74.0 None UBERON:feces None None no None 357.7580261 None Regularly (3-5 times/week) 22.3 no Caucasian None 95 Rarely (few times/month) 2191:2289956687 no 68521-1664 -96.7172907 None None None None no None UBERON:feces None None None 40 1870 None Stool More than one year ago GAZ:United States of America Not in the last year None human gut metagenome None None 16S rRNA sequencing by synthesis Not in the last year FWD:GTGCCAGCMGCCGCGGTAA; REV:GGACTACHVGGGTWTCTAAT no 27.45443787 ENVO:urban biome None Daily no None No CCME not_sure years None This analysis was done as in Caporaso et al 2011 Genome research. The PCR primers (F515/R806) were developed against the V4 region of the 16S rRNA (both bacteria and archaea), which we determined would yield optimal community clustering with reads of this length using a procedure similar to that of ref. 15. [For reference, this primer pair amplifies the region 533_786 in the Escherichia coli strain 83972 sequence (greengenes accession no. prokMSA_id:470367).] The reverse PCR primer is barcoded with a 12-base error-correcting Golay code to facilitate multiplexing of up to 1,500 samples per lane, and both PCR primers contain sequencer adapter regions. American Gut Project Stool sample None Occasionally (1-2 times/week) 10/21/57 no None ENVO:feces None I do not have a skin condition None yes None V4 American Gut Project 65 None yes human None None None female None Depends on the season 3/21/13 0.0 None no Less than 25% 25.5 no None 1870 no None None .1,g None Never yes None Occasionally (1-2 times/week) None CCME UBERON:feces left None yes no ENVO:human-associated habitat None 8:30 AM no City None 5-6 hours Omnivore but no red meat CCME low dairy, low wheat CCME no 165.0 None I do not have IBD no 0 9606 MiSeq 408170 11 to 20 None 147 None None no Knight_AFG_16s_w_phiX_NoIndex_L001 None Illumina I do not use deoderant or antiperspirant None yes leafy greens 165 None no 60 MiSeq1 2191 None Fecal, oral and skin samples from round 3 MiSeq None Remained stable rice I do not have diabetes lincoln no Never no NE None 40.8541169 None yes no American_Gut_round 6
000001352.1212998 CTTGACGAGGTT GTGTGCCAGCMGCCGCGGTAA None More than one year ago None n 12/18/13 None 27.0 83.0 None UBERON:feces None None yes None 267.7634277 Housing... Regularly (3-5 times/week) None yes Caucasian USA 70 Never 2191:450833475 no 53916 -88.837329 Contact... None None None no None UBERON:feces None None None 26 1352 None Stool Within the past month GAZ:United States of America Not in the last year None human gut metagenome None None 16S rRNA sequencing by synthesis In the past year FWD:GTGCCAGCMGCCGCGGTAA; REV:GGACTACHVGGGTWTCTAAT no 23.75 ENVO:urban biome None Daily no None None CCME no years None This analysis was done as in Caporaso et al 2011 Genome research. The PCR primers (F515/R806) were developed against the V4 region of the 16S rRNA (both bacteria and archaea), which we determined would yield optimal community clustering with reads of this length using a procedure similar to that of ref. 15. [For reference, this primer pair amplifies the region 533_786 in the Escherichia coli strain 83972 sequence (greengenes accession no. prokMSA_id:470367).] The reverse PCR primer is barcoded with a 12-base error-correcting Golay code to facilitate multiplexing of up to 1,500 samples per lane, and both PCR primers contain sequencer adapter regions. American Gut Project Stool sample None Regularly (3-5 times/week) 10/23/86 no yes ENVO:feces None I do not have a skin condition None yes no V4 American Gut Project 74 None no human None One None male None Indoors 9/17/13 0.0 None no Less than 25% None yes None 1352 no None None .1,g yes Never None None Occasionally (1-2 times/week) None CCME UBERON:feces left None yes no ENVO:human-associated habitat fish oil, amino acid complex 10:00 AM no City no 7-8 hours Omnivore CCME Voluntarily dairy and gluten free CCME no 188.0 None I do not have IBD no 0 9606 MiSeq 408170 11 to 20 None 245 None None no AGP6_rerun_L001 no Illumina Not sure, but I use some form of deodorant/antiperspirant Contact..., Housing... no onions 185 None no 74 MiSeq1 2191 None Fecal, oral and skin samples from round 3 MiSeq None Remained stable wild rice I do not have diabetes beaver dam no Rarely (few times/month) no WI no 43.4577692 None yes no American_Gut_round 6
000010833.1212945 CCACCCAGTAAC GTGTGCCAGCMGCCGCGGTAA 50 Within the past 6 months yes n 12/18/13 None 29.0 70.0 None UBERON:feces None None no None 668.5264282 Indoor Rarely (few times/month) 20 no Caucasian USA 100 Rarely (few times/month) 2191:3587348079 yes 89123 -115.1533426 Extensive None None None no None UBERON:feces None None None 70 10833 None Stool More than one year ago GAZ:United States of America Not in the last year None human gut metagenome None None 16S rRNA sequencing by synthesis Not in the last year FWD:GTGCCAGCMGCCGCGGTAA; REV:GGACTACHVGGGTWTCTAAT no 26.6027832 ENVO:urban biome None Daily no None No CCME no years None This analysis was done as in Caporaso et al 2011 Genome research. The PCR primers (F515/R806) were developed against the V4 region of the 16S rRNA (both bacteria and archaea), which we determined would yield optimal community clustering with reads of this length using a procedure similar to that of ref. 15. [For reference, this primer pair amplifies the region 533_786 in the Escherichia coli strain 83972 sequence (greengenes accession no. prokMSA_id:470367).] The reverse PCR primer is barcoded with a 12-base error-correcting Golay code to facilitate multiplexing of up to 1,500 samples per lane, and both PCR primers contain sequencer adapter regions. American Gut Project Stool sample None Regularly (3-5 times/week) 8/8/85 no None ENVO:feces None I do not have a skin condition None no no V4 American Gut Project 64 None yes human None One None female None Depends on the season 11/2/13 0.0 None no Less than 25% 30 yes None 10833 no None None .1,g yes Never None None Occasionally (1-2 times/week) None CCME UBERON:feces right None no no ENVO:human-associated habitat garcinia camboja, fiber, glucosamine 11:00 PM no Filtered no 5-6 hours Vegetarian CCME None CCME no 163.0 None I do not have IBD no 0 9606 MiSeq 408170 6 to 10 None 30 None None no AGP6_rerun_L001 no Illumina I use deodorant Dog, Extensive, Indoor no kale 155 None no 30 MiSeq1 2191 None Fecal, oral and skin samples from round 3 MiSeq None Remained stable potato I do not have diabetes las vegas no Rarely (few times/month) no NV no 36.0357492 None yes no American_Gut_round 6
000004820.1212987 ATTGCAAGCAAC GTGTGCCAGCMGCCGCGGTAA 23 Never yes n 12/18/13 None 39.0 72.0 None UBERON:feces None None no None 70.74841309 Housing... Daily 23 no Caucasian USA 99 Rarely (few times/month) 2191:4076977364 yes 93001 -119.2290053 Contact... None None None no None UBERON:feces None None None 0 4820 None Stool More than one year ago GAZ:United States of America In the past year None human gut metagenome None None 16S rRNA sequencing by synthesis Not in the last year FWD:GTGCCAGCMGCCGCGGTAA; REV:GGACTACHVGGGTWTCTAAT no 27.4609375 ENVO:urban biome None Daily no None No CCME yes years None This analysis was done as in Caporaso et al 2011 Genome research. The PCR primers (F515/R806) were developed against the V4 region of the 16S rRNA (both bacteria and archaea), which we determined would yield optimal community clustering with reads of this length using a procedure similar to that of ref. 15. [For reference, this primer pair amplifies the region 533_786 in the Escherichia coli strain 83972 sequence (greengenes accession no. prokMSA_id:470367).] The reverse PCR primer is barcoded with a 12-base error-correcting Golay code to facilitate multiplexing of up to 1,500 samples per lane, and both PCR primers contain sequencer adapter regions. American Gut Project Stool sample None Regularly (3-5 times/week) 4/12/75 no None ENVO:feces None I do not have a skin condition None no no V4 American Gut Project 64 Flu no human None None None female None Outdoors 11/6/13 0.0 None no Less than 25% 53 no None 4820 no Husband None .1,g yes Rarely (few times/month) None None Rarely (few times/month) None CCME UBERON:feces right None yes no ENVO:human-associated habitat Fish oil , zinc, magnesium 10:50 AM no Filtered None 8 or more hours Omnivore CCME try to be sugar and grain free CCME no 163.0 None I do not have IBD yes 0 9606 MiSeq 408170 11 to 20 None 38 None None no AGP6_rerun_L001 no Illumina I do not use deodorant or antiperspirant Contact..., Housing... yes leafy greens 160 None no 100 MiSeq1 2191 None Fecal, oral and skin samples from round 3 MiSeq None Increased more than 10 pounds vegatable and fruit I do not have diabetes ventura no Never no CA None 34.2746405 None yes yes American_Gut_round 6
000009671.1212949 AATAGCATGTCG GTGTGCCAGCMGCCGCGGTAA 40 More than one year ago None n 12/18/13 None 65.0 57.0 None UBERON:feces Stress None no Other 207.1616364 Housing... Regularly (3-5 times/week) 50 no Caucasian USA 100 Daily 2191:3957956701 no 29732 -81.0250784 Contact... None None None no None UBERON:feces None A few times a year yes 20 9671 yes Stool More than one year ago GAZ:United States of America In the past year None human gut metagenome None yes 16S rRNA sequencing by synthesis In the past year FWD:GTGCCAGCMGCCGCGGTAA; REV:GGACTACHVGGGTWTCTAAT yes 22.49458302 ENVO:urban biome None Daily no None No CCME no years None This analysis was done as in Caporaso et al 2011 Genome research. The PCR primers (F515/R806) were developed against the V4 region of the 16S rRNA (both bacteria and archaea), which we determined would yield optimal community clustering with reads of this length using a procedure similar to that of ref. 15. [For reference, this primer pair amplifies the region 533_786 in the Escherichia coli strain 83972 sequence (greengenes accession no. prokMSA_id:470367).] The reverse PCR primer is barcoded with a 12-base error-correcting Golay code to facilitate multiplexing of up to 1,500 samples per lane, and both PCR primers contain sequencer adapter regions. American Gut Project Stool sample None Regularly (3-5 times/week) 7/6/49 no None ENVO:feces None I do not have a skin condition None yes no V4 American Gut Project 63 bladder infection yes human None None None female None Outdoors 10/7/13 0.0 None yes Less than 25% 10 no None 9671 yes None None .1,g yes Never yes None Daily None CCME UBERON:feces right None no no ENVO:human-associated habitat omega 3, calcium, vit. D ,COQ10, probiotic, B12, SAM E 10:30 AM yes Well None 8 or more hours Omnivore CCME None CCME yes 160.0 cipro I do not have IBD no 0 9606 MiSeq 408170 6 to 10 no 104 None bright lights no AGP6_rerun_L001 no Illumina I use deodorant Contact..., Housing... no sweet potato 127 None no 80 MiSeq1 2191 None Fecal, oral and skin samples from round 3 MiSeq None Remained stable rice I do not have diabetes rock hill no Rarely (few times/month) no SC None 34.9248667 None yes no American_Gut_round 6
000009074.1213041 GCTAGTTATGGA GTGTGCCAGCMGCCGCGGTAA 34 Within the past 6 months None n 12/18/13 None 29.0 79.0 None UBERON:feces Stress None no Other 61.83166885 Housing... Never 18 no Caucasian USA 100 Never 2191:2907824909 yes 98103 -122.3425575 Contact... None None None no None UBERON:feces None Monthly yes 10 9074 None Stool More than one year ago GAZ:United States of America Not in the last year yes human gut metagenome None yes 16S rRNA sequencing by synthesis Not in the last year FWD:GTGCCAGCMGCCGCGGTAA; REV:GGACTACHVGGGTWTCTAAT yes 21.87111111 ENVO:urban biome None Daily no None None CCME no years None This analysis was done as in Caporaso et al 2011 Genome research. The PCR primers (F515/R806) were developed against the V4 region of the 16S rRNA (both bacteria and archaea), which we determined would yield optimal community clustering with reads of this length using a procedure similar to that of ref. 15. [For reference, this primer pair amplifies the region 533_786 in the Escherichia coli strain 83972 sequence (greengenes accession no. prokMSA_id:470367).] The reverse PCR primer is barcoded with a 12-base error-correcting Golay code to facilitate multiplexing of up to 1,500 samples per lane, and both PCR primers contain sequencer adapter regions. American Gut Project Stool sample None Daily 8/28/84 no None ENVO:feces None Eczema None no no V4 American Gut Project 75 None no human None None None male None Both 9/21/13 0.0 None no Less than 25% 48 no None 9074 no None None .1,g yes Never None None Rarely (few times/month) None CCME UBERON:feces right None yes no ENVO:human-associated habitat b6, zinc 12:20 PM no Filtered None 7-8 hours Omnivore CCME Ray Peat diet. no grains, beans, minimal vegetables CCME no 191.0 None I do not have IBD yes 0 9606 MiSeq 408170 11 to 20 no 25 None not sure, may be excess serotonin yes AGP6_rerun_L001 no Illumina I do not use deodorant or antiperspirant Contact..., Housing... no potato 175 None no 90 MiSeq1 2191 None Fecal, oral and skin samples from round 3 MiSeq None Remained stable orange juice, milk I do not have diabetes seattle no Rarely (few times/month) no WA None 47.6600087 None yes no American_Gut_round 6
000010876.1213040 TACGCAGCACTA GTGTGCCAGCMGCCGCGGTAA 46 More than one year ago None n 12/18/13 None 51.0 59.0 None UBERON:feces Foods; chocolate Foods; red wine yes Other 209.1370544 Housing... Regularly (3-5 times/week) 14 not_sure Caucasian USA 100 Occasionally (1-2 times/week) 2191:1370047246 no 94708 -122.259717 Contact... yes None None no None UBERON:feces None Monthly yes 40 10876 yes Stool More than one year ago GAZ:United States of America Not in the last year None human gut metagenome None None 16S rRNA sequencing by synthesis In the past month FWD:GTGCCAGCMGCCGCGGTAA; REV:GGACTACHVGGGTWTCTAAT yes 28.56140351 ENVO:urban biome None Daily no zomig No CCME yes years None This analysis was done as in Caporaso et al 2011 Genome research. The PCR primers (F515/R806) were developed against the V4 region of the 16S rRNA (both bacteria and archaea), which we determined would yield optimal community clustering with reads of this length using a procedure similar to that of ref. 15. [For reference, this primer pair amplifies the region 533_786 in the Escherichia coli strain 83972 sequence (greengenes accession no. prokMSA_id:470367).] The reverse PCR primer is barcoded with a 12-base error-correcting Golay code to facilitate multiplexing of up to 1,500 samples per lane, and both PCR primers contain sequencer adapter regions. American Gut Project Stool sample None Regularly (3-5 times/week) 1/1/63 no None ENVO:feces None I do not have a skin condition None no no V4 American Gut Project 57 None no human None None None female None Indoors 11/13/13 0.0 None no 25 to 50% 40 no None 10876 yes partner yes .1,g yes Never None None Occasionally (1-2 times/week) None CCME UBERON:feces right None no no ENVO:human-associated habitat magnesium, calcium, vitamin d, multi-vitamin, glucosamine 11:19 PM no City None 8 or more hours Omnivore CCME None CCME yes 145.0 None Ulcerative colitis no 0 9606 MiSeq 408170 More than 30 yes 125 None hormone swings no AGP6_rerun_L001 no Illumina I use an antiperspirant Contact..., Housing... yes leafy greens 132 None no 60 MiSeq1 2191 None Fecal, oral and skin samples from round 3 MiSeq None Decreased more than 10 pounds bread I do not have diabetes berkeley no Never no CA None 37.9020612 None yes no American_Gut_round 6
000009686.1213141 CGAAGCATCTAC GTGTGCCAGCMGCCGCGGTAA 50 More than one year ago None n 12/18/13 yes 57.0 77.0 None UBERON:feces None None no None 2.486505032 Housing... Daily 40 no Caucasian United Kingdom 100 Occasionally (1-2 times/week) 2191:2848013207 no 33031 -80.4882672 Contact... None None None no None UBERON:feces None None None 30 9686 None Stool More than one year ago GAZ:United States of America In the past 6 months None human gut metagenome None None 16S rRNA sequencing by synthesis In the past month FWD:GTGCCAGCMGCCGCGGTAA; REV:GGACTACHVGGGTWTCTAAT no 27.43572084 ENVO:urban biome None Daily no None No CCME no years None This analysis was done as in Caporaso et al 2011 Genome research. The PCR primers (F515/R806) were developed against the V4 region of the 16S rRNA (both bacteria and archaea), which we determined would yield optimal community clustering with reads of this length using a procedure similar to that of ref. 15. [For reference, this primer pair amplifies the region 533_786 in the Escherichia coli strain 83972 sequence (greengenes accession no. prokMSA_id:470367).] The reverse PCR primer is barcoded with a 12-base error-correcting Golay code to facilitate multiplexing of up to 1,500 samples per lane, and both PCR primers contain sequencer adapter regions. American Gut Project Stool sample None Never 5/27/57 no None ENVO:feces None I do not have a skin condition yes no no V4 American Gut Project 66 None no human None None None female None None 9/22/13 0.0 None no 25 to 50% 10 no None 9686 yes None None .1,g yes Never None None Never None CCME UBERON:feces right None no no ENVO:human-associated habitat probiotics 4:22 PM no Bottled None 8 or more hours Omnivore CCME None CCME no 168.0 None I do not have IBD None 0 9606 MiSeq 408170 6 to 10 None 270 None None no AGP6_rerun_L001 no Illumina I use deodorant Contact..., Housing... yes beans 170 None no 70 MiSeq1 2191 None Fecal, oral and skin samples from round 3 MiSeq None Remained stable chips I do not have diabetes homestead no Never no FL None 25.5305322 None yes no American_Gut_round 6
000003130.1212999 CTCTATTCCACC GTGTGCCAGCMGCCGCGGTAA 62 More than one year ago None n 12/18/13 None 49.0 90.0 None UBERON:feces None None no None 500.6595764 Housing... Daily 8 no Caucasian USA 100 Never 2191:4066443854 no 28753 -82.6840251 Contact... None None None no None UBERON:feces None None None 100 3130 None Stool More than one year ago GAZ:United States of America Not in the last year None human gut metagenome None None 16S rRNA sequencing by synthesis Not in the last year FWD:GTGCCAGCMGCCGCGGTAA; REV:GGACTACHVGGGTWTCTAAT no 25.67567568 ENVO:urban biome None Daily no None None CCME no years None This analysis was done as in Caporaso et al 2011 Genome research. The PCR primers (F515/R806) were developed against the V4 region of the 16S rRNA (both bacteria and archaea), which we determined would yield optimal community clustering with reads of this length using a procedure similar to that of ref. 15. [For reference, this primer pair amplifies the region 533_786 in the Escherichia coli strain 83972 sequence (greengenes accession no. prokMSA_id:470367).] The reverse PCR primer is barcoded with a 12-base error-correcting Golay code to facilitate multiplexing of up to 1,500 samples per lane, and both PCR primers contain sequencer adapter regions. American Gut Project Stool sample None Regularly (3-5 times/week) 10/10/64 no None ENVO:feces None I do not have a skin condition None no no V4 American Gut Project 74 None no human None One None male None Outdoors 9/20/13 0.0 None no Less than 25% 30 yes None 3130 no None None .1,g yes Never None None Never None CCME UBERON:feces right None no no ENVO:human-associated habitat Iodine, Vitamin D3, Molybdenum, Silicon, Vitamin K2, Vitamin C, Ginkgo Biloba 2:20 PM no Well no 8 or more hours Vegan CCME None CCME no 188.0 None I do not have IBD yes 0 9606 MiSeq 408170 11 to 20 None 140 None None no AGP6_rerun_L001 no Illumina I use deodorant Contact..., Housing... no Carrots 200 None no 0 MiSeq1 2191 None Fecal, oral and skin samples from round 3 MiSeq None Remained stable Potato I do not have diabetes marshall no Never no NC no 35.7973284 None yes no American_Gut_round 6
000003649.1213144 ACAACACTCCGA GTGTGCCAGCMGCCGCGGTAA 70 More than one year ago None n 5/20/13 None 61.0 113.0 None UBERON:feces None None no None 180.5917206 None Daily 20 no Caucasian USA 100 Never 2191:937184912 None 48226 -83.0495622 None None None None yes None UBERON:feces None None None 90 3649 None Stool Within the past year GAZ:United States of America In the past 6 months None human gut metagenome None None 16S rRNA sequencing by synthesis In the past 6 months FWD:GTGCCAGCMGCCGCGGTAA; REV:GGACTACHVGGGTWTCTAAT no 32.09459459 ENVO:urban biome None Daily no None None CCME no years None This analysis was done as in Caporaso et al 2011 Genome research. The PCR primers (F515/R806) were developed against the V4 region of the 16S rRNA (both bacteria and archaea), which we determined would yield optimal community clustering with reads of this length using a procedure similar to that of ref. 15. [For reference, this primer pair amplifies the region 533_786 in the Escherichia coli strain 83972 sequence (greengenes accession no. prokMSA_id:470367).] The reverse PCR primer is barcoded with a 12-base error-correcting Golay code to facilitate multiplexing of up to 1,500 samples per lane, and both PCR primers contain sequencer adapter regions. American Gut Project Stool sample None Occasionally (1-2 times/week) 1/25/53 no None ENVO:feces None I do not have a skin condition None no no V4 American Gut Project 74 respiratory infection no human None None None unknown None Depends on the season 4/22/13 0.0 None no Less than 25% 10 no None 3649 no None None .1,g yes Never None None Rarely (few times/month) None CCME UBERON:feces left None no no ENVO:human-associated habitat coenzyme Q, reservatrol, flax seed oil, fish oil, Vitamin B12, Vitamin D3 9:00 AM yes Filtered None 6-7 hours Vegetarian but eat seafood CCME None CCME no 187.0 amoxicillin I do not have IBD no 0 9606 MiSeq 408170 11 to 20 None 175 None None no Knight_AFG_16s_w_phiX_NoIndex_L001 no Illumina I use an antiperspirant None yes sweert potato 250 None no 10 MiSeq1 2191 None Fecal, oral and skin samples from round 3 MiSeq None Remained stable bread I do not have diabetes detroit yes Never no MI None 42.328245 None yes no American_Gut_round 6
000010900.1212969 GTCATAAGAACC GTGTGCCAGCMGCCGCGGTAA None Within the past 6 months None n 12/18/13 None 35.0 74.0 None UBERON:feces None None no None 51.82350922 Housing... Daily None no Caucasian USA 84 Never 2191:2409330809 no 98109 -122.3456919 Contact... None None None no None UBERON:feces None None None 40 10900 None Stool More than one year ago GAZ:United States of America Not in the last year None human gut metagenome None None 16S rRNA sequencing by synthesis Not in the last year FWD:GTGCCAGCMGCCGCGGTAA; REV:GGACTACHVGGGTWTCTAAT no 23.01031541 ENVO:urban biome None Daily no None None CCME no years None This analysis was done as in Caporaso et al 2011 Genome research. The PCR primers (F515/R806) were developed against the V4 region of the 16S rRNA (both bacteria and archaea), which we determined would yield optimal community clustering with reads of this length using a procedure similar to that of ref. 15. [For reference, this primer pair amplifies the region 533_786 in the Escherichia coli strain 83972 sequence (greengenes accession no. prokMSA_id:470367).] The reverse PCR primer is barcoded with a 12-base error-correcting Golay code to facilitate multiplexing of up to 1,500 samples per lane, and both PCR primers contain sequencer adapter regions. American Gut Project Stool sample None Regularly (3-5 times/week) 2/19/79 no None ENVO:feces None I do not have a skin condition yes no no V4 American Gut Project 71 None no human None None None male None Indoors 11/6/13 0.0 None no 25 to 50% None no None 10900 no None None .1,g yes Never None None Occasionally (1-2 times/week) None CCME UBERON:feces right None no no ENVO:human-associated habitat Vitamin C, Ubiquinol 9:30 AM no Filtered None 7-8 hours Omnivore CCME None CCME no 180.0 None I do not have IBD no 0 9606 MiSeq 408170 21 to 30 None 150 None None no AGP6_rerun_L001 no Illumina I use deodorant Contact..., Housing... no spinach 165 None no 60 MiSeq1 2191 None Fecal, oral and skin samples from round 3 MiSeq None Remained stable wheat I do not have diabetes seattle no Rarely (few times/month) no WA None 47.6288591 None yes yes American_Gut_round 6
Blank28.C4.1213011 CTACTTACATCC GTGTGCCAGCMGCCGCGGTAA None None None n 12/18/13 None None None None None None None None None 1624.1 None None None None None None None None 2191:unknown None 80309 -105.79 None None None None None None None None None None None Blank28.C4 None Blank None GAZ:United States of America None None unclassified metagenome None None 16S rRNA sequencing by synthesis None FWD:GTGCCAGCMGCCGCGGTAA; REV:GGACTACHVGGGTWTCTAAT None None ENVO:aquatic biome None None None None None CCME None years None This analysis was done as in Caporaso et al 2011 Genome research. The PCR primers (F515/R806) were developed against the V4 region of the 16S rRNA (both bacteria and archaea), which we determined would yield optimal community clustering with reads of this length using a procedure similar to that of ref. 15. [For reference, this primer pair amplifies the region 533_786 in the Escherichia coli strain 83972 sequence (greengenes accession no. prokMSA_id:470367).] The reverse PCR primer is barcoded with a 12-base error-correcting Golay code to facilitate multiplexing of up to 1,500 samples per lane, and both PCR primers contain sequencer adapter regions. American Gut Project blank None None None None None ENVO:sterile water None None None None None V4 American Gut Project None None None None None None None unknown None None None 0.0 None None None None None None Blank28.C4 None None None .1,g None None None None None None CCME None unknown None None None ENVO:water None None None None None None None CCME None CCME None None None None None 0 None MiSeq 408169 None None None None None None AGP6_rerun_L001 None Illumina None None None None None None None None MiSeq1 2191 None Fecal, oral and skin samples from round 3 MiSeq None None None None boulder None None None CO None 40.02 None None None American_Gut_round 11
Blank33.A9.1213123 GCTTAGATGTAG GTGTGCCAGCMGCCGCGGTAA None None None n 12/18/13 None None None None None None None None None 1624.1 None None None None None None None None 2191:unknown None 80309 -105.79 None None None None None None None None None None None Blank33.A9 None Blank None GAZ:United States of America None None unclassified metagenome None None 16S rRNA sequencing by synthesis None FWD:GTGCCAGCMGCCGCGGTAA; REV:GGACTACHVGGGTWTCTAAT None None ENVO:aquatic biome None None None None None CCME None years None This analysis was done as in Caporaso et al 2011 Genome research. The PCR primers (F515/R806) were developed against the V4 region of the 16S rRNA (both bacteria and archaea), which we determined would yield optimal community clustering with reads of this length using a procedure similar to that of ref. 15. [For reference, this primer pair amplifies the region 533_786 in the Escherichia coli strain 83972 sequence (greengenes accession no. prokMSA_id:470367).] The reverse PCR primer is barcoded with a 12-base error-correcting Golay code to facilitate multiplexing of up to 1,500 samples per lane, and both PCR primers contain sequencer adapter regions. American Gut Project blank None None None None None ENVO:sterile water None None None None None V4 American Gut Project None None None None None None None unknown None None None 0.0 None None None None None None Blank33.A9 None None None .1,g None None None None None None CCME None unknown None None None ENVO:water None None None None None None None CCME None CCME None None None None None 0 None MiSeq 408169 None None None None None None AGP6_rerun_L001 None Illumina None None None None None None None None MiSeq1 2191 None Fecal, oral and skin samples from round 3 MiSeq None None None None boulder None None None CO None 40.02 None None None American_Gut_round 18
000010913.1212973 TTGCACCGTCGA GTGTGCCAGCMGCCGCGGTAA 47 More than one year ago None n 12/18/13 None 41.0 52.0 None UBERON:feces None None no None 47.96184921 Confined Daily 14 None Caucasian USA 100 Regularly (3-5 times/week) 2191:1180285931 no 95136 -121.8505679 Little None None None no None UBERON:feces None None None 34 10913 None Stool More than one year ago GAZ:United States of America Not in the last year None human gut metagenome None None 16S rRNA sequencing by synthesis In the past year FWD:GTGCCAGCMGCCGCGGTAA; REV:GGACTACHVGGGTWTCTAAT no 19.73754883 ENVO:urban biome None Daily no None No CCME None years None This analysis was done as in Caporaso et al 2011 Genome research. The PCR primers (F515/R806) were developed against the V4 region of the 16S rRNA (both bacteria and archaea), which we determined would yield optimal community clustering with reads of this length using a procedure similar to that of ref. 15. [For reference, this primer pair amplifies the region 533_786 in the Escherichia coli strain 83972 sequence (greengenes accession no. prokMSA_id:470367).] The reverse PCR primer is barcoded with a 12-base error-correcting Golay code to facilitate multiplexing of up to 1,500 samples per lane, and both PCR primers contain sequencer adapter regions. American Gut Project Stool sample None Daily 12/11/72 no yes ENVO:feces None I do not have a skin condition None no no V4 American Gut Project 64 None no human None None None female None Outdoors 11/8/13 0.0 None no 51 to 75% 39 no None 10913 yes None None .1,g yes Never None None Never None CCME UBERON:feces right None None no ENVO:human-associated habitat Vitamin C 6:35 PM no Filtered None 7-8 hours Omnivore CCME None CCME no 163.0 None I do not have IBD no 0 9606 MiSeq 408170 11 to 20 None 97.5 None None no AGP6_rerun_L001 no Illumina Not sure, but I use some form of deodorant/antiperspirant Hamster, Little, Confined yes carrot 115 None yes 66 MiSeq1 2191 None Fecal, oral and skin samples from round 3 MiSeq None Remained stable bread/cereal I do not have diabetes san jose no Rarely (few times/month) no CA None 37.2692142 None yes yes American_Gut_round 6
000009605.1213003 CAGATTAACCAG GTGTGCCAGCMGCCGCGGTAA 54 More than one year ago None n 12/18/13 None 57.0 62.0 None UBERON:feces None None no None 29.45329857 Housing... Daily 15 no Caucasian USA 100 Daily 2191:4048858984 no 98501 -122.9006951 Contact... None None None no None UBERON:feces None None None 50 9605 None Stool More than one year ago GAZ:United States of America In the past year None human gut metagenome None None 16S rRNA sequencing by synthesis In the past year FWD:GTGCCAGCMGCCGCGGTAA; REV:GGACTACHVGGGTWTCTAAT no 23.51342773 ENVO:urban biome None Daily no None No CCME no years None This analysis was done as in Caporaso et al 2011 Genome research. The PCR primers (F515/R806) were developed against the V4 region of the 16S rRNA (both bacteria and archaea), which we determined would yield optimal community clustering with reads of this length using a procedure similar to that of ref. 15. [For reference, this primer pair amplifies the region 533_786 in the Escherichia coli strain 83972 sequence (greengenes accession no. prokMSA_id:470367).] The reverse PCR primer is barcoded with a 12-base error-correcting Golay code to facilitate multiplexing of up to 1,500 samples per lane, and both PCR primers contain sequencer adapter regions. American Gut Project Stool sample None Daily 9/19/56 no yes ENVO:feces None I do not have a skin condition None no no V4 American Gut Project 64 sinus infection no human None None None female None Both 9/28/13 0.0 None no Less than 25% 31 no None 9605 yes None None .1,g yes Never None None Never None CCME UBERON:feces right None no no ENVO:human-associated habitat livatone, magnesium, holy basil, probiotic, desiccated beef liver, biozyme, baby aspirin, glucosamine, cod liver oil 10:00 AM no City None 6-7 hours Omnivore CCME None CCME no 163.0 zythro? I do not have IBD yes 0 9606 MiSeq 408170 6 to 10 None 182 None None no AGP6_rerun_L001 no Illumina I use deodorant Contact..., Housing... yes leafy greans 137 None no 50 MiSeq1 2191 None Fecal, oral and skin samples from round 3 MiSeq None Remained stable grains I do not have diabetes olympia no Never no WA None 47.0378741 None yes yes American_Gut_round 6
000005737.1213059 TCGATTGGCCGT GTGTGCCAGCMGCCGCGGTAA None More than one year ago None n 12/18/13 None 62.0 80.0 None UBERON:feces None None no None 21.8799057 Indoor Regularly (3-5 times/week) None no Caucasian Australia 75 Never 2191:3784671373 no 6022 115.8058984 Extensive None None None no None UBERON:feces None None None 0 5737 None Stool More than one year ago GAZ:Australia Not in the last year None human gut metagenome None None 16S rRNA sequencing by synthesis Not in the last year FWD:GTGCCAGCMGCCGCGGTAA; REV:GGACTACHVGGGTWTCTAAT no 28.4040404 ENVO:urban biome None Daily no None None CCME yes years None This analysis was done as in Caporaso et al 2011 Genome research. The PCR primers (F515/R806) were developed against the V4 region of the 16S rRNA (both bacteria and archaea), which we determined would yield optimal community clustering with reads of this length using a procedure similar to that of ref. 15. [For reference, this primer pair amplifies the region 533_786 in the Escherichia coli strain 83972 sequence (greengenes accession no. prokMSA_id:470367).] The reverse PCR primer is barcoded with a 12-base error-correcting Golay code to facilitate multiplexing of up to 1,500 samples per lane, and both PCR primers contain sequencer adapter regions. American Gut Project Stool sample None Rarely (few times/month) 4/29/52 no None ENVO:feces None I do not have a skin condition None no None V4 American Gut Project 66 None yes human None None None unknown None None 9/18/13 0.0 None no 51 to 75% None no None 5737 no Partner None .1,g yes Regularly (3-5 times/week) None None Regularly (3-5 times/week) None CCME UBERON:feces unknown None no no ENVO:human-associated habitat probiotics 9:05 AM yes Filtered None 6-7 hours Omnivore CCME None CCME no 168.0 None I do not have IBD no 0 9606 MiSeq 408170 11 to 20 None None None None yes AGP6_rerun_L001 no Illumina I do not use deodorant or antiperspirant dogs, Extensive, Indoor yes broccoli 176 None no 100 MiSeq1 2191 None Fecal, oral and skin samples from round 3 MiSeq None Remained stable bread I do not have diabetes hamersley no Never no WA None -31.8509428 None yes no American_Gut_round 6
000009218.1213115 TCAGTCAGATGA GTGTGCCAGCMGCCGCGGTAA 34.2 Within the past 3 months None n 12/18/13 yes 51.0 68.0 None UBERON:feces None None no None 182.6841431 None Daily 21.7 no Caucasian USA 100 Occasionally (1-2 times/week) 2191:2051358067 yes 60612 -87.6926257 None None None None no None UBERON:feces None None None 0 9218 None Stool More than one year ago GAZ:United States of America Not in the last year None human gut metagenome None None 16S rRNA sequencing by synthesis Not in the last year FWD:GTGCCAGCMGCCGCGGTAA; REV:GGACTACHVGGGTWTCTAAT no 22.8049308 ENVO:urban biome None Daily no None No CCME yes years None This analysis was done as in Caporaso et al 2011 Genome research. The PCR primers (F515/R806) were developed against the V4 region of the 16S rRNA (both bacteria and archaea), which we determined would yield optimal community clustering with reads of this length using a procedure similar to that of ref. 15. [For reference, this primer pair amplifies the region 533_786 in the Escherichia coli strain 83972 sequence (greengenes accession no. prokMSA_id:470367).] The reverse PCR primer is barcoded with a 12-base error-correcting Golay code to facilitate multiplexing of up to 1,500 samples per lane, and both PCR primers contain sequencer adapter regions. American Gut Project Stool sample None Daily 12/1/62 no None ENVO:feces None Psoriasis None no no V4 American Gut Project 68 None no human None None None female None Outdoors 10/6/13 0.0 None no Less than 25% 44.1 no None 9218 no husband None .1,g yes Never yes None Regularly (3-5 times/week) None CCME UBERON:feces right None no no ENVO:human-associated habitat vitamin d, iodine, vitamin c, selenium, vitamin k 7:00 AM no Filtered None 7-8 hours Omnivore CCME None CCME no 173.0 None I do not have IBD yes 0 9606 MiSeq 408170 11 to 20 None 155 None None no AGP6_rerun_L001 None Illumina I do not use deodorant or antiperspirant 2 cats no carrots 150 None no 100 MiSeq1 2191 None Fecal, oral and skin samples from round 3 MiSeq None Remained stable rice I do not have diabetes chicago no Rarely (few times/month) no IL None 41.8816606 None yes no American_Gut_round 6
000009366.1213037 CCTAGTAAGCTG GTGTGCCAGCMGCCGCGGTAA 16 Within the past 3 months None n 12/18/13 None 70.0 79.0 None UBERON:feces None None no None 81.97623444 Housing... Daily 13 no Caucasian Canada 100 Rarely (few times/month) 2191:1235736504 no 94117 -122.4438929 Contact... None None None yes None UBERON:feces None None None 70 9366 None Stool More than one year ago GAZ:United States of America In the past month None human gut metagenome None None 16S rRNA sequencing by synthesis Not in the last year FWD:GTGCCAGCMGCCGCGGTAA; REV:GGACTACHVGGGTWTCTAAT no 30.03540039 ENVO:urban biome None Daily no None No CCME None years None This analysis was done as in Caporaso et al 2011 Genome research. The PCR primers (F515/R806) were developed against the V4 region of the 16S rRNA (both bacteria and archaea), which we determined would yield optimal community clustering with reads of this length using a procedure similar to that of ref. 15. [For reference, this primer pair amplifies the region 533_786 in the Escherichia coli strain 83972 sequence (greengenes accession no. prokMSA_id:470367).] The reverse PCR primer is barcoded with a 12-base error-correcting Golay code to facilitate multiplexing of up to 1,500 samples per lane, and both PCR primers contain sequencer adapter regions. American Gut Project Stool sample None Rarely (few times/month) 10/30/43 no None ENVO:feces None Rosacea yes yes no V4 American Gut Project 64 prophylaxis for dental work no human None None None female None Outdoors 11/15/13 0.0 None no Less than 25% 71 no None 9366 None None None .1,g yes Never None None Never None CCME UBERON:feces right None no no ENVO:human-associated habitat CoQ10, iFlora multi-probiotic, resveratrol, B-complex, Vitamin C, vitamin K1 & K2, berberine, Max DHA, vitamin D3 Complex, BioThyro, L-carnitine, fermented cod liver oil, Standard Process Thytrophin PMG, Standard Process Oculotrophin PMG, Standard Process Cataplex F 3:20 PM no Filtered None 6-7 hours Omnivore CCME None CCME no 163.0 amoxicillin 2 gm x 1 I do not have IBD no 0 9606 MiSeq 408170 6 to 10 None 131 None None None AGP6_rerun_L001 no Illumina I use deodorant Contact..., Housing... yes leafy greens 175 None no 30 MiSeq1 2191 None Fecal, oral and skin samples from round 3 MiSeq None Remained stable vegetables I do not have diabetes san francisco yes Never no CA None 37.7717185 None yes yes American_Gut_round 6
000004821.1213081 TAATGGTCGTAG GTGTGCCAGCMGCCGCGGTAA 38 Never None n 12/18/13 None 42.0 92.0 None UBERON:feces None None no None 70.74841309 Housing... Regularly (3-5 times/week) 16 no Caucasian USA 100 Never 2191:991211375 yes 93001 -119.2290053 Contact... None None None no None UBERON:feces None None None 5 4821 None Stool More than one year ago GAZ:United States of America Not in the last year None human gut metagenome None None 16S rRNA sequencing by synthesis Not in the last year FWD:GTGCCAGCMGCCGCGGTAA; REV:GGACTACHVGGGTWTCTAAT no 23.09165198 ENVO:urban biome None Daily no None None CCME yes years None This analysis was done as in Caporaso et al 2011 Genome research. The PCR primers (F515/R806) were developed against the V4 region of the 16S rRNA (both bacteria and archaea), which we determined would yield optimal community clustering with reads of this length using a procedure similar to that of ref. 15. [For reference, this primer pair amplifies the region 533_786 in the Escherichia coli strain 83972 sequence (greengenes accession no. prokMSA_id:470367).] The reverse PCR primer is barcoded with a 12-base error-correcting Golay code to facilitate multiplexing of up to 1,500 samples per lane, and both PCR primers contain sequencer adapter regions. American Gut Project Stool sample None Daily 8/7/72 no yes ENVO:feces None I do not have a skin condition None no no V4 American Gut Project 79 None no human None None None male None Outdoors 11/6/13 0.0 None no Less than 25% 46 no None 4821 no wifey None .1,g yes Never None None Rarely (few times/month) None CCME UBERON:feces right None no no ENVO:human-associated habitat Magnesium, Fish oil, zinc, BCAA 10:40 AM no Filtered None 8 or more hours Omnivore CCME None CCME no 201.0 None I do not have IBD yes 0 9606 MiSeq 408170 11 to 20 None 95 None None no AGP6_rerun_L001 no Illumina I do not use deodorant or antiperspirant Contact..., Housing... yes leafy greens 205 None no 95 MiSeq1 2191 None Fecal, oral and skin samples from round 3 MiSeq None Remained stable sports drink/gel I do not have diabetes ventura no Never no CA None 34.2746405 None no no American_Gut_round 6
000010937.1212954 CCAGTGGATATA GTGTGCCAGCMGCCGCGGTAA None More than one year ago None n 12/18/13 None 58.0 70.0 None UBERON:feces Stress Other yes Lack of sleep 157.7642365 Housing... Daily None no Caucasian USA 80 Daily 2191:1969000265 no 20777 -76.9577073 Contact... None None None no None UBERON:feces None A few times a year yes 15 10937 yes Stool More than one year ago GAZ:United States of America None yes human gut metagenome None None 16S rRNA sequencing by synthesis None FWD:GTGCCAGCMGCCGCGGTAA; REV:GGACTACHVGGGTWTCTAAT yes 22.2377551 ENVO:urban biome None Daily no None No CCME yes years None This analysis was done as in Caporaso et al 2011 Genome research. The PCR primers (F515/R806) were developed against the V4 region of the 16S rRNA (both bacteria and archaea), which we determined would yield optimal community clustering with reads of this length using a procedure similar to that of ref. 15. [For reference, this primer pair amplifies the region 533_786 in the Escherichia coli strain 83972 sequence (greengenes accession no. prokMSA_id:470367).] The reverse PCR primer is barcoded with a 12-base error-correcting Golay code to facilitate multiplexing of up to 1,500 samples per lane, and both PCR primers contain sequencer adapter regions. American Gut Project Stool sample None Regularly (3-5 times/week) 11/5/55 no None ENVO:feces None I do not have a skin condition None no no V4 American Gut Project 70 None yes human None None None female None Depends on the season 11/5/13 0.0 None no Less than 25% None no None 10937 no spouse None .1,g no Never None None Daily None CCME UBERON:feces right None yes no ENVO:human-associated habitat None 6:30 AM no Well None 7-8 hours Omnivore CCME Paleo CCME no 178.0 None I do not have IBD no 0 9606 MiSeq 408170 11 to 20 yes 142 Barometric pressure None no AGP6_rerun_L001 no Illumina I use an antiperspirant Contact..., Housing... yes Leafy greens 155 None no 85 MiSeq1 2191 None Fecal, oral and skin samples from round 3 MiSeq None Decreased more than 10 pounds Fruit I do not have diabetes highland no Rarely (few times/month) no MD None 39.1791249 None no no American_Gut_round 6
000010885.1213105 CCTGCTTCCTTC GTGTGCCAGCMGCCGCGGTAA 69 More than one year ago None n 12/18/13 yes 67.0 65.0 None UBERON:feces None None no None 182.7123718 Housing... Occasionally (1-2 times/week) 14 no Caucasian USA 100 Daily 2191:2770491477 no 45140 -84.263826 Contact... None None None no None UBERON:feces None None None 85 10885 None Stool More than one year ago GAZ:United States of America Not in the last year None human gut metagenome None None 16S rRNA sequencing by synthesis In the past month FWD:GTGCCAGCMGCCGCGGTAA; REV:GGACTACHVGGGTWTCTAAT no 24.12662722 ENVO:urban biome None Daily no None No CCME yes years None This analysis was done as in Caporaso et al 2011 Genome research. The PCR primers (F515/R806) were developed against the V4 region of the 16S rRNA (both bacteria and archaea), which we determined would yield optimal community clustering with reads of this length using a procedure similar to that of ref. 15. [For reference, this primer pair amplifies the region 533_786 in the Escherichia coli strain 83972 sequence (greengenes accession no. prokMSA_id:470367).] The reverse PCR primer is barcoded with a 12-base error-correcting Golay code to facilitate multiplexing of up to 1,500 samples per lane, and both PCR primers contain sequencer adapter regions. American Gut Project Stool sample None Occasionally (1-2 times/week) 12/2/46 no None ENVO:feces None I do not have a skin condition None None no V4 American Gut Project 65 None no human None None None female None Outdoors 11/6/13 0.0 None no 25 to 50% 17 no None 10885 no husband None .1,g yes Never yes None Rarely (few times/month) None CCME UBERON:feces right None yes no ENVO:human-associated habitat Seniors multi vitamin 6:40 AM no Filtered None 6-7 hours Omnivore CCME simple sugars create vaginal infections CCME no 165.0 None I do not have IBD no 0 9606 MiSeq 408170 6 to 10 None 104 None None no AGP6_rerun_L001 no Illumina I use an antiperspirant Contact..., Housing... yes lettuce 145 None no 15 MiSeq1 2191 None Fecal, oral and skin samples from round 3 MiSeq None Remained stable breads I do not have diabetes loveland no Rarely (few times/month) no OH None 39.2689476 None yes no American_Gut_round 6
Blank28.G4.1213062 TTGGGCCACATA GTGTGCCAGCMGCCGCGGTAA None None None n 12/18/13 None None None None None None None None None 1624.1 None None None None None None None None 2191:unknown None 80309 -105.79 None None None None None None None None None None None Blank28.G4 None Blank None GAZ:United States of America None None unclassified metagenome None None 16S rRNA sequencing by synthesis None FWD:GTGCCAGCMGCCGCGGTAA; REV:GGACTACHVGGGTWTCTAAT None None ENVO:aquatic biome None None None None None CCME None years None This analysis was done as in Caporaso et al 2011 Genome research. The PCR primers (F515/R806) were developed against the V4 region of the 16S rRNA (both bacteria and archaea), which we determined would yield optimal community clustering with reads of this length using a procedure similar to that of ref. 15. [For reference, this primer pair amplifies the region 533_786 in the Escherichia coli strain 83972 sequence (greengenes accession no. prokMSA_id:470367).] The reverse PCR primer is barcoded with a 12-base error-correcting Golay code to facilitate multiplexing of up to 1,500 samples per lane, and both PCR primers contain sequencer adapter regions. American Gut Project blank None None None None None ENVO:sterile water None None None None None V4 American Gut Project None None None None None None None unknown None None None 0.0 None None None None None None Blank28.G4 None None None .1,g None None None None None None CCME None unknown None None None ENVO:water None None None None None None None CCME None CCME None None None None None 0 None MiSeq 408169 None None None None None None AGP6_rerun_L001 None Illumina None None None None None None None None MiSeq1 2191 None Fecal, oral and skin samples from round 3 MiSeq None None None None boulder None None None CO None 40.02 None None None American_Gut_round 15
000003495.1212958 TGCTACAGACGT GTGTGCCAGCMGCCGCGGTAA 50 More than one year ago None n 12/18/13 None 5.0 16.0 None UBERON:feces None None no None 4.185313702 Housing... Rarely (few times/month) 20 yes Caucasian USA 100 Never 2191:3320468452 no 33073 -80.1819268 Contact... None None None no None UBERON:feces None None None 60 3495 None Stool More than one year ago GAZ:United States of America In the past 6 months None human gut metagenome None None 16S rRNA sequencing by synthesis In the past year FWD:GTGCCAGCMGCCGCGGTAA; REV:GGACTACHVGGGTWTCTAAT no None ENVO:urban biome None Daily no None No CCME yes years None This analysis was done as in Caporaso et al 2011 Genome research. The PCR primers (F515/R806) were developed against the V4 region of the 16S rRNA (both bacteria and archaea), which we determined would yield optimal community clustering with reads of this length using a procedure similar to that of ref. 15. [For reference, this primer pair amplifies the region 533_786 in the Escherichia coli strain 83972 sequence (greengenes accession no. prokMSA_id:470367).] The reverse PCR primer is barcoded with a 12-base error-correcting Golay code to facilitate multiplexing of up to 1,500 samples per lane, and both PCR primers contain sequencer adapter regions. American Gut Project Stool sample None Daily 3/13/09 no None ENVO:feces None Eczema None no no V4 American Gut Project None suspected UTI no human None None None female None None 11/10/13 0.0 None no 25 to 50% 30 no None 3495 yes Mother, Father, Brother None .1,g no Never None None Never None CCME UBERON:feces right None yes no ENVO:human-associated habitat None 8:20 AM no Filtered None 8 or more hours Omnivore CCME mostly gluten free CCME no None None I do not have IBD yes 0 9606 MiSeq 408170 6 to 10 None 25 None None no AGP6_rerun_L001 no Illumina I do not use deodorant or antiperspirant Contact..., Housing... yes tomato 36 None no 40 MiSeq1 2191 None Fecal, oral and skin samples from round 3 MiSeq None Remained stable milk I do not have diabetes coconut creek no Rarely (few times/month) no FL None 26.3003637 None no no American_Gut_round 6
000001183.1212980 TCTGAGGTTGCC GTGTGCCAGCMGCCGCGGTAA None More than one year ago None n 12/18/13 None 59.0 99.0 None UBERON:feces None None no None 115.5155487 Housing... Regularly (3-5 times/week) None no Caucasian USA 0 Never 2191:1099553940 None 21239 -76.5892774 Contact... None no None no None UBERON:feces None None None None 1183 None Stool More than one year ago GAZ:United States of America Not in the last year None human gut metagenome None None 16S rRNA sequencing by synthesis In the past year FWD:GTGCCAGCMGCCGCGGTAA; REV:GGACTACHVGGGTWTCTAAT no 37.75878906 ENVO:urban biome None Daily no None No CCME no years None This analysis was done as in Caporaso et al 2011 Genome research. The PCR primers (F515/R806) were developed against the V4 region of the 16S rRNA (both bacteria and archaea), which we determined would yield optimal community clustering with reads of this length using a procedure similar to that of ref. 15. [For reference, this primer pair amplifies the region 533_786 in the Escherichia coli strain 83972 sequence (greengenes accession no. prokMSA_id:470367).] The reverse PCR primer is barcoded with a 12-base error-correcting Golay code to facilitate multiplexing of up to 1,500 samples per lane, and both PCR primers contain sequencer adapter regions. American Gut Project Stool sample None Rarely (few times/month) 6/21/55 no None ENVO:feces None None None yes no V4 American Gut Project 64 None yes human None None None female None Indoors 9/23/13 0.0 None no None None no None 1183 yes None None .1,g no Never yes None Rarely (few times/month) None CCME UBERON:feces right 1/1/08 no no ENVO:human-associated habitat None 2:35 PM no City None 5-6 hours Omnivore CCME None CCME no 163.0 None I do not have IBD no 0 9606 MiSeq 408170 None None None None None None AGP6_rerun_L001 no Illumina I use an antiperspirant Contact..., Housing... no None 220 None no None MiSeq1 2191 None Fecal, oral and skin samples from round 3 MiSeq None Remained stable None Type II baltimore no Never no MD None 39.3614334 None yes no American_Gut_round 6
000004286.1213078 GCGAAGTTGGGA GTGTGCCAGCMGCCGCGGTAA 53 Within the past month None n 12/18/13 None 31.0 56.0 None UBERON:feces None None no None 298.0795593 Housing... Occasionally (1-2 times/week) 15 no Caucasian USA 94 Never 2191:69144438 no 91104 -118.1181199 Contact... None None None no None UBERON:feces None None None 30 4286 None Stool More than one year ago GAZ:United States of America Not in the last year None human gut metagenome None None 16S rRNA sequencing by synthesis Not in the last year FWD:GTGCCAGCMGCCGCGGTAA; REV:GGACTACHVGGGTWTCTAAT no 25.24418271 ENVO:urban biome None Daily no None No CCME not_sure years None This analysis was done as in Caporaso et al 2011 Genome research. The PCR primers (F515/R806) were developed against the V4 region of the 16S rRNA (both bacteria and archaea), which we determined would yield optimal community clustering with reads of this length using a procedure similar to that of ref. 15. [For reference, this primer pair amplifies the region 533_786 in the Escherichia coli strain 83972 sequence (greengenes accession no. prokMSA_id:470367).] The reverse PCR primer is barcoded with a 12-base error-correcting Golay code to facilitate multiplexing of up to 1,500 samples per lane, and both PCR primers contain sequencer adapter regions. American Gut Project Stool sample None Regularly (3-5 times/week) 3/9/83 no yes ENVO:feces None I do not have a skin condition None no no V4 American Gut Project 59 None no human None Three None female None Outdoors 10/3/13 0.0 None no Less than 25% 26 yes None 4286 no None None .1,g yes Never None None Regularly (3-5 times/week) None CCME UBERON:feces right None no no ENVO:human-associated habitat vitamin D, vitamin B, Fish oil, melatonin 9:45 AM no Filtered no 6-7 hours Vegetarian but eat seafood CCME None CCME yes 151.0 None I do not have IBD no 0 9606 MiSeq 408170 6 to 10 None 130 None None yes AGP6_rerun_L001 no Illumina I use deodorant Contact..., Housing... no Spinach 125 None no 70 MiSeq1 2191 None Fecal, oral and skin samples from round 3 MiSeq None Remained stable Bread I do not have diabetes pasadena no Rarely (few times/month) no CA no 34.1657707 None yes no American_Gut_round 6
000009216.1213001 GTACTGAAGATC GTGTGCCAGCMGCCGCGGTAA 30 More than one year ago None n 12/18/13 None 60.0 74.0 None UBERON:feces None None no None 182.6841431 Housing... Daily 40 no Caucasian USA 100 Occasionally (1-2 times/week) 2191:3544394186 no 60612 -87.6926257 Contact... None None None no None UBERON:feces None None None 20 9216 None Stool More than one year ago GAZ:United States of America Not in the last year None human gut metagenome None None 16S rRNA sequencing by synthesis Not in the last year FWD:GTGCCAGCMGCCGCGGTAA; REV:GGACTACHVGGGTWTCTAAT no 28.3190918 ENVO:urban biome None Daily no None No CCME no years None This analysis was done as in Caporaso et al 2011 Genome research. The PCR primers (F515/R806) were developed against the V4 region of the 16S rRNA (both bacteria and archaea), which we determined would yield optimal community clustering with reads of this length using a procedure similar to that of ref. 15. [For reference, this primer pair amplifies the region 533_786 in the Escherichia coli strain 83972 sequence (greengenes accession no. prokMSA_id:470367).] The reverse PCR primer is barcoded with a 12-base error-correcting Golay code to facilitate multiplexing of up to 1,500 samples per lane, and both PCR primers contain sequencer adapter regions. American Gut Project Stool sample None Occasionally (1-2 times/week) 8/17/54 no yes ENVO:feces None I do not have a skin condition None yes no V4 American Gut Project 64 None no human None None None female None Outdoors 10/7/13 0.0 None no Less than 25% 30 no None 9216 no None None .1,g yes Never None None Rarely (few times/month) None CCME UBERON:feces right None no no ENVO:human-associated habitat CQ10 7:15 AM no City None 8 or more hours Omnivore CCME None CCME no 163.0 None I do not have IBD yes 0 9606 MiSeq 408170 6 to 10 None 70 None None no AGP6_rerun_L001 no Illumina I do not use deodorant or antiperspirant Contact..., Housing... no romaine lettuce 165 None None 80 MiSeq1 2191 None Fecal, oral and skin samples from round 3 MiSeq None Remained stable rice crackers I do not have diabetes chicago no Rarely (few times/month) no IL None 41.8816606 None no no American_Gut_round 6
Blank33.D9.1212964 CGGCCTAAGTTC GTGTGCCAGCMGCCGCGGTAA None None None n 12/18/13 None None None None None None None None None 1624.1 None None None None None None None None 2191:unknown None 80309 -105.79 None None None None None None None None None None None Blank33.D9 None Blank None GAZ:United States of America None None unclassified metagenome None None 16S rRNA sequencing by synthesis None FWD:GTGCCAGCMGCCGCGGTAA; REV:GGACTACHVGGGTWTCTAAT None None ENVO:aquatic biome None None None None None CCME None years None This analysis was done as in Caporaso et al 2011 Genome research. The PCR primers (F515/R806) were developed against the V4 region of the 16S rRNA (both bacteria and archaea), which we determined would yield optimal community clustering with reads of this length using a procedure similar to that of ref. 15. [For reference, this primer pair amplifies the region 533_786 in the Escherichia coli strain 83972 sequence (greengenes accession no. prokMSA_id:470367).] The reverse PCR primer is barcoded with a 12-base error-correcting Golay code to facilitate multiplexing of up to 1,500 samples per lane, and both PCR primers contain sequencer adapter regions. American Gut Project blank None None None None None ENVO:sterile water None None None None None V4 American Gut Project None None None None None None None unknown None None None 0.0 None None None None None None Blank33.D9 None None None .1,g None None None None None None CCME None unknown None None None ENVO:water None None None None None None None CCME None CCME None None None None None 0 None MiSeq 408169 None None None None None None AGP6_rerun_L001 None Illumina None None None None None None None None MiSeq1 2191 None Fecal, oral and skin samples from round 3 MiSeq None None None None boulder None None None CO None 40.02 None None None American_Gut_round 22
000006826.1213098 TCCGTGGTATAG GTGTGCCAGCMGCCGCGGTAA 57 More than one year ago None n 12/18/13 None 79.0 66.0 None UBERON:feces None None no None 33.25356674 Housing... Daily 12 no Caucasian Germany 100 Daily 2191:1005005301 no 7921 -74.6751731 Contact... None None None no None UBERON:feces None None None 85 6826 None Stool More than one year ago GAZ:United States of America In the past week None human gut metagenome None None 16S rRNA sequencing by synthesis Not in the last year FWD:GTGCCAGCMGCCGCGGTAA; REV:GGACTACHVGGGTWTCTAAT no 26.70083247 ENVO:urban biome None Daily no None No CCME yes years None This analysis was done as in Caporaso et al 2011 Genome research. The PCR primers (F515/R806) were developed against the V4 region of the 16S rRNA (both bacteria and archaea), which we determined would yield optimal community clustering with reads of this length using a procedure similar to that of ref. 15. [For reference, this primer pair amplifies the region 533_786 in the Escherichia coli strain 83972 sequence (greengenes accession no. prokMSA_id:470367).] The reverse PCR primer is barcoded with a 12-base error-correcting Golay code to facilitate multiplexing of up to 1,500 samples per lane, and both PCR primers contain sequencer adapter regions. American Gut Project Stool sample None Occasionally (1-2 times/week) 8/1/35 no None ENVO:feces None I do not have a skin condition None yes no V4 American Gut Project 62 Bladder infection no human None None None female None Outdoors 9/29/13 0.0 None yes Less than 25% 31 no None 6826 no daughter None .1,g yes Never None None Occasionally (1-2 times/week) None CCME UBERON:feces right None None no ENVO:human-associated habitat L-Glutamine, Spirulina, Wheatgrass, Procera, Calcium/Magnesium 11:45 AM yes Bottled None 5-6 hours Omnivore CCME None CCME no 157.0 Cipro I do not have IBD no 0 9606 MiSeq 408170 11 to 20 None 25 None None no AGP6_rerun_L001 no Illumina I use deodorant Contact..., Housing... yes Kale 146 None no 15 MiSeq1 2191 None Fecal, oral and skin samples from round 3 MiSeq None Remained stable Quinoa I do not have diabetes bedminster no Never no NJ None 40.6431955 None yes no American_Gut_round 6
Blank33.B9.1213109 CAATCGGCTTGC GTGTGCCAGCMGCCGCGGTAA None None None n 12/18/13 None None None None None None None None None 1624.1 None None None None None None None None 2191:unknown None 80309 -105.79 None None None None None None None None None None None Blank33.B9 None Blank None GAZ:United States of America None None unclassified metagenome None None 16S rRNA sequencing by synthesis None FWD:GTGCCAGCMGCCGCGGTAA; REV:GGACTACHVGGGTWTCTAAT None None ENVO:aquatic biome None None None None None CCME None years None This analysis was done as in Caporaso et al 2011 Genome research. The PCR primers (F515/R806) were developed against the V4 region of the 16S rRNA (both bacteria and archaea), which we determined would yield optimal community clustering with reads of this length using a procedure similar to that of ref. 15. [For reference, this primer pair amplifies the region 533_786 in the Escherichia coli strain 83972 sequence (greengenes accession no. prokMSA_id:470367).] The reverse PCR primer is barcoded with a 12-base error-correcting Golay code to facilitate multiplexing of up to 1,500 samples per lane, and both PCR primers contain sequencer adapter regions. American Gut Project blank None None None None None ENVO:sterile water None None None None None V4 American Gut Project None None None None None None None unknown None None None 0.0 None None None None None None Blank33.B9 None None None .1,g None None None None None None CCME None unknown None None None ENVO:water None None None None None None None CCME None CCME None None None None None 0 None MiSeq 408169 None None None None None None AGP6_rerun_L001 None Illumina None None None None None None None None MiSeq1 2191 None Fecal, oral and skin samples from round 3 MiSeq None None None None boulder None None None CO None 40.02 None None None American_Gut_round 19
000009193.1213038 CAAAGCGGTATT GTGTGCCAGCMGCCGCGGTAA 10 More than one year ago None n 12/18/13 None 49.0 59.0 None UBERON:feces None None no None 19.69497681 Outdoor Daily 20 no Caucasian USA 100 Daily 2191:2192960349 yes 98290 -122.0981848 Moderate None None None no None UBERON:feces None None None 20 9193 None Stool More than one year ago GAZ:United States of America Not in the last year None human gut metagenome None None 16S rRNA sequencing by synthesis Not in the last year FWD:GTGCCAGCMGCCGCGGTAA; REV:GGACTACHVGGGTWTCTAAT no 20.35865449 ENVO:urban biome None Daily no None No CCME no years None This analysis was done as in Caporaso et al 2011 Genome research. The PCR primers (F515/R806) were developed against the V4 region of the 16S rRNA (both bacteria and archaea), which we determined would yield optimal community clustering with reads of this length using a procedure similar to that of ref. 15. [For reference, this primer pair amplifies the region 533_786 in the Escherichia coli strain 83972 sequence (greengenes accession no. prokMSA_id:470367).] The reverse PCR primer is barcoded with a 12-base error-correcting Golay code to facilitate multiplexing of up to 1,500 samples per lane, and both PCR primers contain sequencer adapter regions. American Gut Project Stool sample None Regularly (3-5 times/week) 10/11/64 no None ENVO:feces None Rosacea None no no V4 American Gut Project 67 None yes human None None None female None Outdoors 9/30/13 0.0 None no Less than 25% 70 no None 9193 no None None .1,g yes Never None bed Rarely (few times/month) None CCME UBERON:feces right None yes no ENVO:human-associated habitat Iodine, Vit K, CLO 10:30 AM no Well None 7-8 hours Omnivore CCME Ketogenic Diet CCME no 170.0 None I do not have IBD no 0 9606 MiSeq 408170 6 to 10 None 157 None None no AGP6_rerun_L001 no Illumina I do not use deodorant or antiperspirant Chickens, Moderate, Outdoor no cabbage 130 None no 80 MiSeq1 2191 None Fecal, oral and skin samples from round 3 MiSeq None Remained stable avocado I do not have diabetes snohomish no Never no WA None 47.9128756 None yes yes American_Gut_round 6
000010231.1213111 TCGGCGATCATC GTGTGCCAGCMGCCGCGGTAA 41 More than one year ago None n 12/18/13 yes 58.0 50.0 None UBERON:feces None None None None 732.1132202 Outdoor Regularly (3-5 times/week) 22 no Caucasian USA 100 Daily 2191:1900038397 None 85719 -110.9447027 Little None None None no None UBERON:feces None None None 50 10231 None Stool More than one year ago GAZ:United States of America Not in the last year None human gut metagenome None None 16S rRNA sequencing by synthesis None FWD:GTGCCAGCMGCCGCGGTAA; REV:GGACTACHVGGGTWTCTAAT no 17.91391185 ENVO:urban biome None Daily no None No CCME no years None This analysis was done as in Caporaso et al 2011 Genome research. The PCR primers (F515/R806) were developed against the V4 region of the 16S rRNA (both bacteria and archaea), which we determined would yield optimal community clustering with reads of this length using a procedure similar to that of ref. 15. [For reference, this primer pair amplifies the region 533_786 in the Escherichia coli strain 83972 sequence (greengenes accession no. prokMSA_id:470367).] The reverse PCR primer is barcoded with a 12-base error-correcting Golay code to facilitate multiplexing of up to 1,500 samples per lane, and both PCR primers contain sequencer adapter regions. American Gut Project Stool sample None Regularly (3-5 times/week) 3/13/56 no None ENVO:feces None I do not have a skin condition None no no V4 American Gut Project 66 None no human None None None female None Outdoors 11/14/13 0.0 None no Less than 25% 37 no None 10231 yes None None .1,g yes Never None None Rarely (few times/month) None CCME UBERON:feces right None no no ENVO:human-associated habitat cod lover oil, colostrum, pro-biotic, pancreatic enzyme complex, Chinese Herbal Gall Bladder formula 6:00 AM no Filtered None 8 or more hours Omnivore CCME None CCME no 168.0 None I do not have IBD no 0 9606 MiSeq 408170 More than 30 None 151 None None no AGP6_rerun_L001 no Illumina None desert tortoise, Little, Outdoor yes tomato 111 None no 50 MiSeq1 2191 None Fecal, oral and skin samples from round 3 MiSeq None Remained stable potato I do not have diabetes tucson no Never no AZ None 32.2546522 None None no American_Gut_round 6
000007157.1213017 GATATACCAGTG GTGTGCCAGCMGCCGCGGTAA 35 Within the past month None n 12/18/13 None 66.0 67.0 None UBERON:feces None None no None None Housing... Daily 20 no Caucasian Switzerland 100 Occasionally (1-2 times/week) 2191:91038763 no None None Contact... None None None no None UBERON:feces None None None 40 7157 None Stool More than one year ago GAZ:Switzerland In the past 6 months None human gut metagenome yes None 16S rRNA sequencing by synthesis Not in the last year FWD:GTGCCAGCMGCCGCGGTAA; REV:GGACTACHVGGGTWTCTAAT no 22.34883218 ENVO:urban biome None Daily no None None CCME yes years None This analysis was done as in Caporaso et al 2011 Genome research. The PCR primers (F515/R806) were developed against the V4 region of the 16S rRNA (both bacteria and archaea), which we determined would yield optimal community clustering with reads of this length using a procedure similar to that of ref. 15. [For reference, this primer pair amplifies the region 533_786 in the Escherichia coli strain 83972 sequence (greengenes accession no. prokMSA_id:470367).] The reverse PCR primer is barcoded with a 12-base error-correcting Golay code to facilitate multiplexing of up to 1,500 samples per lane, and both PCR primers contain sequencer adapter regions. American Gut Project Stool sample None Regularly (3-5 times/week) 8/15/48 no None ENVO:feces None I do not have a skin condition yes no no V4 American Gut Project 68 sore throat no human None None None unknown None Both 11/14/13 0.0 yes no Less than 25% 45 no None 7157 yes Wife None .1,g yes Never None None Occasionally (1-2 times/week) None CCME UBERON:feces right None no no ENVO:human-associated habitat Zyflamend, Multivitamins 4:00 PM no City None 8 or more hours Omnivore CCME None CCME no 175.0 None I do not have IBD no 0 9606 MiSeq 408170 11 to 20 None 60 None None yes AGP6_rerun_L001 no Illumina Not sure, but I use some form of deodorant/antiperspirant Contact..., Housing... yes avocado 147 None no 60 MiSeq1 2191 None Fecal, oral and skin samples from round 3 MiSeq yes None None I do not have diabetes 1884 villars sur ollon no Never no None None None yes yes yes American_Gut_round 6
000009716.1213025 TAAAGACCCGTA GTGTGCCAGCMGCCGCGGTAA None More than one year ago None n 12/18/13 yes 52.0 85.0 None UBERON:tongue None None yes None 49.28567123 Outdoor, Indoor Regularly (3-5 times/week) None no Caucasian USA 0 Rarely (few times/month) 2191:1621317286 no 20770 -76.8755282 Extensive, Extensive None None None no None UBERON:saliva None None None 75 9716 None Mouth More than one year ago GAZ:United States of America Not in the last year None human oral metagenome None None 16S rRNA sequencing by synthesis Not in the last year FWD:GTGCCAGCMGCCGCGGTAA; REV:GGACTACHVGGGTWTCTAAT no 25.49459877 ENVO:urban biome None Daily no None No CCME no years None This analysis was done as in Caporaso et al 2011 Genome research. The PCR primers (F515/R806) were developed against the V4 region of the 16S rRNA (both bacteria and archaea), which we determined would yield optimal community clustering with reads of this length using a procedure similar to that of ref. 15. [For reference, this primer pair amplifies the region 533_786 in the Escherichia coli strain 83972 sequence (greengenes accession no. prokMSA_id:470367).] The reverse PCR primer is barcoded with a 12-base error-correcting Golay code to facilitate multiplexing of up to 1,500 samples per lane, and both PCR primers contain sequencer adapter regions. American Gut Project Mouth sample None Regularly (3-5 times/week) 9/9/61 no None ENVO:saliva None I do not have a skin condition None no no V4 American Gut Project 72 None no human None None None female None Outdoors 9/20/13 0.0 None no Less than 25% None no None 9716 no None None .1,g yes Rarely (few times/month) yes None Regularly (3-5 times/week) None CCME UBERON:oral cavity right None no no ENVO:human-associated habitat 1 cold eze daily 8:35 AM no City None 7-8 hours Omnivore CCME None CCME no 183.0 None I do not have IBD yes 0 9606 MiSeq 447426 21 to 30 None 180 None None no AGP6_rerun_L001 no Illumina I use deodorant cat, cat, Extensive, Extensive, Outdoor, Indoor no spinich/lettuce 188 None no 25 MiSeq1 2191 None Fecal, oral and skin samples from round 3 MiSeq None Remained stable rice I do not have diabetes greenbelt no Rarely (few times/month) no MD None 39.0045544 None yes yes American_Gut_round 6
000001549.1212975 AATGTCACCAGA GTGTGCCAGCMGCCGCGGTAA 55 More than one year ago None n 5/20/13 None 64.0 70.0 None UBERON:feces None None no None 1518.597778 None Daily 20 yes Caucasian USA 100 Never 2191:3062770315 no 80503 -105.1019275 None None None None no None UBERON:feces None None None 90 1549 None Stool More than one year ago GAZ:United States of America Not in the last year None human gut metagenome None None 16S rRNA sequencing by synthesis In the past 6 months FWD:GTGCCAGCMGCCGCGGTAA; REV:GGACTACHVGGGTWTCTAAT no 22.2377551 ENVO:urban biome None Daily no None None CCME None years None This analysis was done as in Caporaso et al 2011 Genome research. The PCR primers (F515/R806) were developed against the V4 region of the 16S rRNA (both bacteria and archaea), which we determined would yield optimal community clustering with reads of this length using a procedure similar to that of ref. 15. [For reference, this primer pair amplifies the region 533_786 in the Escherichia coli strain 83972 sequence (greengenes accession no. prokMSA_id:470367).] The reverse PCR primer is barcoded with a 12-base error-correcting Golay code to facilitate multiplexing of up to 1,500 samples per lane, and both PCR primers contain sequencer adapter regions. American Gut Project Stool sample None Regularly (3-5 times/week) 1/18/50 no yes ENVO:feces None I do not have a skin condition None yes no V4 American Gut Project 70 None no human None None None male None Both 4/3/13 0.0 None no 25 to 50% 25 no None 1549 no None None .1,g no Never None None Regularly (3-5 times/week) None CCME UBERON:feces right None no no ENVO:human-associated habitat None 9:00 AM no City None 7-8 hours Vegetarian but eat seafood CCME None CCME no 178.0 None I do not have IBD yes 0 9606 MiSeq 408170 11 to 20 None 280 None None no Knight_AFG_16s_w_phiX_NoIndex_L001 no Illumina I use an antiperspirant Cat yes None 155 None no 10 MiSeq1 2191 None Fecal, oral and skin samples from round 3 MiSeq None Decreased more than 10 pounds None I do not have diabetes longmont no Rarely (few times/month) no CO None 40.1672068 None yes yes American_Gut_round 6
000009556.1212974 CCAGGGACTTCT GTGTGCCAGCMGCCGCGGTAA 33 More than one year ago None n 12/18/13 yes 44.0 52.0 None UBERON:feces None None no None 288.4195862 Indoor, Indoor, Indoor Occasionally (1-2 times/week) 17 no Caucasian USA 100 Rarely (few times/month) 2191:3556451710 yes 30307 -84.3279093 Extensive, Little, Little None None None no None UBERON:feces None None None 15 9556 None Stool More than one year ago GAZ:United States of America Not in the last year None human gut metagenome None None 16S rRNA sequencing by synthesis Not in the last year FWD:GTGCCAGCMGCCGCGGTAA; REV:GGACTACHVGGGTWTCTAAT no 17.63581315 ENVO:urban biome None Daily no None No CCME no years None This analysis was done as in Caporaso et al 2011 Genome research. The PCR primers (F515/R806) were developed against the V4 region of the 16S rRNA (both bacteria and archaea), which we determined would yield optimal community clustering with reads of this length using a procedure similar to that of ref. 15. [For reference, this primer pair amplifies the region 533_786 in the Escherichia coli strain 83972 sequence (greengenes accession no. prokMSA_id:470367).] The reverse PCR primer is barcoded with a 12-base error-correcting Golay code to facilitate multiplexing of up to 1,500 samples per lane, and both PCR primers contain sequencer adapter regions. American Gut Project Stool sample None Occasionally (1-2 times/week) 9/28/69 no yes ENVO:feces None Eczema yes no no V4 American Gut Project 68 None yes human None None None female None Depends on the season 11/4/13 0.0 yes no Less than 25% 50 no None 9556 yes None None .1,g yes Never None None Never None CCME UBERON:feces right None yes no ENVO:human-associated habitat cod liver oil, ubiquinol, quercetin, rutin, vsl#3 probiotic, lysine, astragalus, magnesium, selenium, calcium, chromium, biotin, zinc, aloe vera, caprylic acid, borage oil, vit a, vit d, vit e, vit c 8:30 AM no Filtered None 6-7 hours Omnivore but no red meat CCME no gluten, grains, soy, low oxalate, low histamine CCME no 173.0 None I do not have IBD yes 0 9606 MiSeq 408170 6 to 10 None 130 None None no AGP6_rerun_L001 no Illumina I do not use deodorant or antiperspirant dog, dog, cat, Extensive, Little, Little, Indoor, Indoor, Indoor no broccoli 116 None no 85 MiSeq1 2191 None Fecal, oral and skin samples from round 3 MiSeq None Remained stable rice I do not have diabetes atlanta no Never no GA None 33.7724417 None yes yes American_Gut_round 6
000001897.1213046 CATGTGCTTAGG GTGTGCCAGCMGCCGCGGTAA None More than one year ago None n 12/18/13 None 66.0 74.0 None UBERON:feces None None no None 337.5294189 Housing... Regularly (3-5 times/week) None None Caucasian Canada 79 Never 2191:3196009376 no N2H5K8 -80.4894834 Contact... None None None no None UBERON:feces None None None 70 1897 None Stool More than one year ago GAZ:Canada Not in the last year None human gut metagenome None None 16S rRNA sequencing by synthesis Not in the last year FWD:GTGCCAGCMGCCGCGGTAA; REV:GGACTACHVGGGTWTCTAAT no 22.3755787 ENVO:urban biome None Daily no None None CCME no years None This analysis was done as in Caporaso et al 2011 Genome research. The PCR primers (F515/R806) were developed against the V4 region of the 16S rRNA (both bacteria and archaea), which we determined would yield optimal community clustering with reads of this length using a procedure similar to that of ref. 15. [For reference, this primer pair amplifies the region 533_786 in the Escherichia coli strain 83972 sequence (greengenes accession no. prokMSA_id:470367).] The reverse PCR primer is barcoded with a 12-base error-correcting Golay code to facilitate multiplexing of up to 1,500 samples per lane, and both PCR primers contain sequencer adapter regions. American Gut Project Stool sample None Daily 7/29/48 no yes ENVO:feces None I do not have a skin condition None no no V4 American Gut Project 72 None no human None None None male None Both 9/2/13 0.0 None no 25 to 50% None no None 1897 no None None .1,g no Never None None Daily None CCME UBERON:feces unknown None no no ENVO:human-associated habitat None 2:20 PM no Bottled None 6-7 hours Vegetarian CCME None CCME no 183.0 None I do not have IBD no 0 9606 MiSeq 408170 11 to 20 None 245 None None no AGP6_rerun_L001 no Illumina I do not use deodorant or antiperspirant Contact..., Housing... no leafy green 165 None no 30 MiSeq1 2191 None Fecal, oral and skin samples from round 3 MiSeq None Remained stable bread I do not have diabetes kitchener no Rarely (few times/month) no ON None 43.4585851 None yes no American_Gut_round 6
000009613.1213018 ATAATTGCCGAG GTGTGCCAGCMGCCGCGGTAA 45 More than one year ago None n 12/18/13 None None 54.0 None UBERON:feces None None yes None 120.4650574 Indoor Daily 25 yes Caucasian USA 100 Daily 2191:838124377 no 94517 -121.9357925 Extensive None None None no None UBERON:feces None None None 70 9613 None Stool More than one year ago GAZ:United States of America In the past month None human gut metagenome None None 16S rRNA sequencing by synthesis Not in the last year FWD:GTGCCAGCMGCCGCGGTAA; REV:GGACTACHVGGGTWTCTAAT no 19.96686391 ENVO:urban biome None Daily no None No CCME yes years None This analysis was done as in Caporaso et al 2011 Genome research. The PCR primers (F515/R806) were developed against the V4 region of the 16S rRNA (both bacteria and archaea), which we determined would yield optimal community clustering with reads of this length using a procedure similar to that of ref. 15. [For reference, this primer pair amplifies the region 533_786 in the Escherichia coli strain 83972 sequence (greengenes accession no. prokMSA_id:470367).] The reverse PCR primer is barcoded with a 12-base error-correcting Golay code to facilitate multiplexing of up to 1,500 samples per lane, and both PCR primers contain sequencer adapter regions. American Gut Project Stool sample None Regularly (3-5 times/week) None no None ENVO:feces None I do not have a skin condition None no no V4 American Gut Project 65 None no human None None None female None Outdoors 9/22/13 0.0 None no More than 76% 30 no None 9613 yes Spouse None .1,g no Never yes None Daily None CCME UBERON:feces left None no no ENVO:human-associated habitat None 8:20 AM no Bottled None 7-8 hours Omnivore CCME None CCME no 165.0 Cyclamine, Amoxocillin I do not have IBD yes 0 9606 MiSeq 408170 6 to 10 None 20 None None no AGP6_rerun_L001 no Illumina I use deodorant Cats, Extensive, Indoor yes Tomato 120 None no 30 MiSeq1 2191 None Fecal, oral and skin samples from round 3 MiSeq None Remained stable None I do not have diabetes clayton no Never no CA None 37.9410341 None no no American_Gut_round 6
000003974.1212948 CAGAGCTAATTG GTGTGCCAGCMGCCGCGGTAA 42 More than one year ago None n 5/20/13 None 68.0 None None UBERON:feces None None no None 65.6000824 None Daily 31 no Caucasian USA 100 Daily 2191:325431373 no 97007 -122.8670454 None None None None no None UBERON:feces None None None 30 3974 None Stool More than one year ago GAZ:United States of America Not in the last year None human gut metagenome None None 16S rRNA sequencing by synthesis Not in the last year FWD:GTGCCAGCMGCCGCGGTAA; REV:GGACTACHVGGGTWTCTAAT no None ENVO:urban biome None Daily no None No CCME yes years None This analysis was done as in Caporaso et al 2011 Genome research. The PCR primers (F515/R806) were developed against the V4 region of the 16S rRNA (both bacteria and archaea), which we determined would yield optimal community clustering with reads of this length using a procedure similar to that of ref. 15. [For reference, this primer pair amplifies the region 533_786 in the Escherichia coli strain 83972 sequence (greengenes accession no. prokMSA_id:470367).] The reverse PCR primer is barcoded with a 12-base error-correcting Golay code to facilitate multiplexing of up to 1,500 samples per lane, and both PCR primers contain sequencer adapter regions. American Gut Project Stool sample None Regularly (3-5 times/week) 11/23/45 no None ENVO:feces None I do not have a skin condition None no no V4 American Gut Project 63 None yes human None None None female None Both 4/7/13 0.0 None no 25 to 50% 27 no None 3974 no Husband, Daughter, Grandson None .1,g yes Never None None Rarely (few times/month) None CCME UBERON:feces right None no no ENVO:human-associated habitat fishj oil, biotin 7:00 AM no Well None 7-8 hours Omnivore CCME None CCME None 160.0 None I do not have IBD no 0 9606 MiSeq 408170 11 to 20 None 161 None None no Knight_AFG_16s_w_phiX_NoIndex_L001 None Illumina Not sure, but I use some form of deoderant/antiperspirant None yes peas None None no 70 MiSeq1 2191 None Fecal, oral and skin samples from round 3 MiSeq None Remained stable quinoa I do not have diabetes aloha no Rarely (few times/month) no OR None 45.4942838 None yes no American_Gut_round 6
000004090.1213020 CTTCGACTTTCC GTGTGCCAGCMGCCGCGGTAA 66 Within the past 3 months None n 12/18/13 None 42.0 76.0 None UBERON:feces None None no None 298.0795593 Indoor Daily 14 no Caucasian None 100 Daily 2191:3043024761 no 91104 -118.1181199 Extensive None None None no None UBERON:feces None None None 90 4090 None Stool More than one year ago GAZ:United States of America None None human gut metagenome None None 16S rRNA sequencing by synthesis In the past year FWD:GTGCCAGCMGCCGCGGTAA; REV:GGACTACHVGGGTWTCTAAT no None ENVO:urban biome None Daily no None No CCME yes years None This analysis was done as in Caporaso et al 2011 Genome research. The PCR primers (F515/R806) were developed against the V4 region of the 16S rRNA (both bacteria and archaea), which we determined would yield optimal community clustering with reads of this length using a procedure similar to that of ref. 15. [For reference, this primer pair amplifies the region 533_786 in the Escherichia coli strain 83972 sequence (greengenes accession no. prokMSA_id:470367).] The reverse PCR primer is barcoded with a 12-base error-correcting Golay code to facilitate multiplexing of up to 1,500 samples per lane, and both PCR primers contain sequencer adapter regions. American Gut Project Stool sample None Daily 3/10/72 no None ENVO:feces None I do not have a skin condition None no no V4 American Gut Project None None yes human None None None female None Indoors 11/4/13 0.0 None no Less than 25% 20 no None 4090 yes partner None .1,g no Never None None Occasionally (1-2 times/week) None CCME UBERON:feces left None no no ENVO:human-associated habitat None 7:30 PM no Filtered None 6-7 hours Omnivore CCME None CCME no None None I do not have IBD no 0 9606 MiSeq 408170 11 to 20 None 166 None None no AGP6_rerun_L001 no Illumina I use an antiperspirant Dog, Extensive, Indoor no carrot 168 None no 10 MiSeq1 2191 None Fecal, oral and skin samples from round 3 MiSeq None Remained stable sweet potato I do not have diabetes pasadena no Rarely (few times/month) no CA None 34.1657707 None yes no American_Gut_round 6
000010303.1213054 TGGTTATGGCAC GTGTGCCAGCMGCCGCGGTAA 45 Within the past month None n 12/18/13 yes 72.0 92.0 None UBERON:feces None None yes None 27.20385742 Housing... Daily 17 no Caucasian USA 100 Never 2191:385125276 no 19130 -75.1749671 Contact... None None None no None UBERON:feces None None None 46 10303 None Stool More than one year ago GAZ:United States of America In the past month None human gut metagenome None None 16S rRNA sequencing by synthesis In the past month FWD:GTGCCAGCMGCCGCGGTAA; REV:GGACTACHVGGGTWTCTAAT no 27.79996142 ENVO:urban biome None Daily no None None CCME yes years None This analysis was done as in Caporaso et al 2011 Genome research. The PCR primers (F515/R806) were developed against the V4 region of the 16S rRNA (both bacteria and archaea), which we determined would yield optimal community clustering with reads of this length using a procedure similar to that of ref. 15. [For reference, this primer pair amplifies the region 533_786 in the Escherichia coli strain 83972 sequence (greengenes accession no. prokMSA_id:470367).] The reverse PCR primer is barcoded with a 12-base error-correcting Golay code to facilitate multiplexing of up to 1,500 samples per lane, and both PCR primers contain sequencer adapter regions. American Gut Project Stool sample None Regularly (3-5 times/week) 12/24/41 no None ENVO:feces None Psoriasis yes yes no V4 American Gut Project 72 virulent chest infection yes human None None None male None Indoors 10/28/13 0.0 None no More than 76% 38 no None 10303 yes daughter, wife None .1,g yes Never yes None Daily None CCME UBERON:feces right None no no ENVO:human-associated habitat chondroitin, glucosamine, vitamin D (3000 IU) 8:05 AM None Bottled None 8 or more hours Omnivore CCME None CCME no None erythromicin I do not have IBD no 0 9606 MiSeq 408170 6 to 10 None 252 None None no AGP6_rerun_L001 no Illumina I use an antiperspirant Contact..., Housing... yes potatoes 205 None no 54 MiSeq1 2191 penicillin (severe) and pretty allergic to all statins Fecal, oral and skin samples from round 3 MiSeq yes Remained stable cereal, bread, cookies I do not have diabetes philadelphia yes Rarely (few times/month) no PA None 39.9682609 None yes yes American_Gut_round 6
000001408.1213048 TAATGCCCAGGT GTGTGCCAGCMGCCGCGGTAA 35 Within the past 6 months None n 12/18/13 None 33.0 73.0 None UBERON:feces None None no None 180.5838623 Housing... Rarely (few times/month) 40 no Caucasian USA 100 Occasionally (1-2 times/week) 2191:2862468475 no 60607 -87.650714 Contact... None None None no None UBERON:feces None None None 65 1408 None Stool More than one year ago GAZ:United States of America Not in the last year None human gut metagenome None None 16S rRNA sequencing by synthesis Not in the last year FWD:GTGCCAGCMGCCGCGGTAA; REV:GGACTACHVGGGTWTCTAAT no None ENVO:urban biome None Daily no None No CCME yes years None This analysis was done as in Caporaso et al 2011 Genome research. The PCR primers (F515/R806) were developed against the V4 region of the 16S rRNA (both bacteria and archaea), which we determined would yield optimal community clustering with reads of this length using a procedure similar to that of ref. 15. [For reference, this primer pair amplifies the region 533_786 in the Escherichia coli strain 83972 sequence (greengenes accession no. prokMSA_id:470367).] The reverse PCR primer is barcoded with a 12-base error-correcting Golay code to facilitate multiplexing of up to 1,500 samples per lane, and both PCR primers contain sequencer adapter regions. American Gut Project Stool sample None Occasionally (1-2 times/week) 8/5/81 no yes ENVO:feces None I do not have a skin condition None no no V4 American Gut Project None None no human None None None female None Depends on the season 9/28/13 0.0 None no Less than 25% 25 no None 1408 no Mother None .1,g no Never None None Rarely (few times/month) None CCME UBERON:feces right None no no ENVO:human-associated habitat None 11:30 AM no Bottled None 7-8 hours Omnivore CCME None CCME no None None I do not have IBD no 0 9606 MiSeq 408170 None None None None None yes AGP6_rerun_L001 no Illumina I do not use deodorant or antiperspirant Contact..., Housing... no carrots 162 None no 35 MiSeq1 2191 None Fecal, oral and skin samples from round 3 MiSeq None Decreased more than 10 pounds fruit I do not have diabetes chicago no Never no IL None 41.8733696 None yes yes American_Gut_round 6
Blank28.H2.1213090 CATGCCAACATG GTGTGCCAGCMGCCGCGGTAA None None None n 12/18/13 None None None None None None None None None 1624.1 None None None None None None None None 2191:unknown None 80309 -105.79 None None None None None None None None None None None Blank28.H2 None Blank None GAZ:United States of America None None unclassified metagenome None None 16S rRNA sequencing by synthesis None FWD:GTGCCAGCMGCCGCGGTAA; REV:GGACTACHVGGGTWTCTAAT None None ENVO:aquatic biome None None None None None CCME None years None This analysis was done as in Caporaso et al 2011 Genome research. The PCR primers (F515/R806) were developed against the V4 region of the 16S rRNA (both bacteria and archaea), which we determined would yield optimal community clustering with reads of this length using a procedure similar to that of ref. 15. [For reference, this primer pair amplifies the region 533_786 in the Escherichia coli strain 83972 sequence (greengenes accession no. prokMSA_id:470367).] The reverse PCR primer is barcoded with a 12-base error-correcting Golay code to facilitate multiplexing of up to 1,500 samples per lane, and both PCR primers contain sequencer adapter regions. American Gut Project blank None None None None None ENVO:sterile water None None None None None V4 American Gut Project None None None None None None None unknown None None None 0.0 None None None None None None Blank28.H2 None None None .1,g None None None None None None CCME None unknown None None None ENVO:water None None None None None None None CCME None CCME None None None None None 0 None MiSeq 408169 None None None None None None AGP6_rerun_L001 None Illumina None None None None None None None None MiSeq1 2191 None Fecal, oral and skin samples from round 3 MiSeq None None None None boulder None None None CO None 40.02 None None None American_Gut_round 16
Blank33.F12.1213084 GCAATCCTTGCG GTGTGCCAGCMGCCGCGGTAA None None None n 12/18/13 None None None None None None None None None 1624.1 None None None None None None None None 2191:unknown None 80309 -105.79 None None None None None None None None None None None Blank33.F12 None Blank None GAZ:United States of America None None unclassified metagenome None None 16S rRNA sequencing by synthesis None FWD:GTGCCAGCMGCCGCGGTAA; REV:GGACTACHVGGGTWTCTAAT None None ENVO:aquatic biome None None None None None CCME None years None This analysis was done as in Caporaso et al 2011 Genome research. The PCR primers (F515/R806) were developed against the V4 region of the 16S rRNA (both bacteria and archaea), which we determined would yield optimal community clustering with reads of this length using a procedure similar to that of ref. 15. [For reference, this primer pair amplifies the region 533_786 in the Escherichia coli strain 83972 sequence (greengenes accession no. prokMSA_id:470367).] The reverse PCR primer is barcoded with a 12-base error-correcting Golay code to facilitate multiplexing of up to 1,500 samples per lane, and both PCR primers contain sequencer adapter regions. American Gut Project blank None None None None None ENVO:sterile water None None None None None V4 American Gut Project None None None None None None None unknown None None None 0.0 None None None None None None Blank33.F12 None None None .1,g None None None None None None CCME None unknown None None None ENVO:water None None None None None None None CCME None CCME None None None None None 0 None MiSeq 408169 None None None None None None AGP6_rerun_L001 None Illumina None None None None None None None None MiSeq1 2191 None Fecal, oral and skin samples from round 3 MiSeq None None None None boulder None None None CO None 40.02 None None None American_Gut_round 25
000010893.1213052 GGACGTTAACTA GTGTGCCAGCMGCCGCGGTAA 38 More than one year ago None n 12/18/13 None 71.0 86.0 None UBERON:feces None None yes None 338.5785522 Housing... Rarely (few times/month) 26 no Caucasian USA 100 Never 2191:2650818365 no 30183 -84.5521524 Contact... None None None no None UBERON:feces None None None 35 10893 None Stool More than one year ago GAZ:United States of America Not in the last year None human gut metagenome None None 16S rRNA sequencing by synthesis Not in the last year FWD:GTGCCAGCMGCCGCGGTAA; REV:GGACTACHVGGGTWTCTAAT no None ENVO:urban biome None Daily no None None CCME no years None This analysis was done as in Caporaso et al 2011 Genome research. The PCR primers (F515/R806) were developed against the V4 region of the 16S rRNA (both bacteria and archaea), which we determined would yield optimal community clustering with reads of this length using a procedure similar to that of ref. 15. [For reference, this primer pair amplifies the region 533_786 in the Escherichia coli strain 83972 sequence (greengenes accession no. prokMSA_id:470367).] The reverse PCR primer is barcoded with a 12-base error-correcting Golay code to facilitate multiplexing of up to 1,500 samples per lane, and both PCR primers contain sequencer adapter regions. American Gut Project Stool sample None Regularly (3-5 times/week) 11/14/42 no None ENVO:feces None I do not have a skin condition None no no V4 American Gut Project None None no human None None None male None Outdoors 11/12/13 0.0 None no Less than 25% 36 no None 10893 no None None .1,g no Never None None Never None CCME UBERON:feces right None no no ENVO:human-associated habitat None 8:20 AM no Filtered None 6-7 hours Omnivore CCME None CCME no None None I do not have IBD no 0 9606 MiSeq 408170 6 to 10 None 59 None None no AGP6_rerun_L001 no Illumina I do not use deodorant or antiperspirant Contact..., Housing... no Tomatos 190 None no 65 MiSeq1 2191 None Fecal, oral and skin samples from round 3 MiSeq None Remained stable bread I do not have diabetes waleska no Never no GA None 34.3164826 None yes no American_Gut_round 6
000009542.1213009 CCAGACCGCTAT GTGTGCCAGCMGCCGCGGTAA None More than one year ago None n 12/18/13 None 32.0 68.0 None UBERON:feces None None no None 185.0700836 Housing... Daily None no Caucasian Canada 83 Never 2191:2388151232 no L0S 1E3 -79.2831681 Contact... None None None no None UBERON:feces None None None 62 9542 None Stool More than one year ago GAZ:Canada Not in the last year None human gut metagenome None None 16S rRNA sequencing by synthesis Not in the last year FWD:GTGCCAGCMGCCGCGGTAA; REV:GGACTACHVGGGTWTCTAAT no 22.14870825 ENVO:urban biome None Daily no None None CCME yes years None This analysis was done as in Caporaso et al 2011 Genome research. The PCR primers (F515/R806) were developed against the V4 region of the 16S rRNA (both bacteria and archaea), which we determined would yield optimal community clustering with reads of this length using a procedure similar to that of ref. 15. [For reference, this primer pair amplifies the region 533_786 in the Escherichia coli strain 83972 sequence (greengenes accession no. prokMSA_id:470367).] The reverse PCR primer is barcoded with a 12-base error-correcting Golay code to facilitate multiplexing of up to 1,500 samples per lane, and both PCR primers contain sequencer adapter regions. American Gut Project Stool sample None Regularly (3-5 times/week) 6/24/82 no None ENVO:feces None I do not have a skin condition None no no V4 American Gut Project 69 None no human None None None male None Outdoors 9/25/13 0.0 None no Less than 25% None no None 9542 no Mother None .1,g yes Never None None Regularly (3-5 times/week) None CCME UBERON:feces right None no no ENVO:human-associated habitat Probiotic supplement, Bonesure 10:00 AM no City None 7-8 hours Omnivore CCME None CCME no 175.0 None I do not have IBD no 0 9606 MiSeq 408170 11 to 20 None 240 None None no AGP6_rerun_L001 no Illumina I use deodorant Contact..., Housing... no varied 150 None no 38 MiSeq1 2191 None Fecal, oral and skin samples from round 3 MiSeq None Remained stable bread I do not have diabetes fonthill no Never no ONTARIO None 43.0514979 None yes no American_Gut_round 6
000010138.1213061 GCACATAGTCGT GTGTGCCAGCMGCCGCGGTAA 40 Within the past 3 months None n 12/18/13 None 54.0 74.0 None UBERON:feces None None no None 31.0247345 Housing... Daily 50 no Asian or Pacific Islander USA 100 Never 2191:3971242609 no 11050 -73.6981858 Contact... None None None no None UBERON:feces None None None 80 10138 None Stool More than one year ago GAZ:United States of America Not in the last year None human gut metagenome None None 16S rRNA sequencing by synthesis In the past month FWD:GTGCCAGCMGCCGCGGTAA; REV:GGACTACHVGGGTWTCTAAT no 25.08542388 ENVO:urban biome None Daily no None None CCME no years None This analysis was done as in Caporaso et al 2011 Genome research. The PCR primers (F515/R806) were developed against the V4 region of the 16S rRNA (both bacteria and archaea), which we determined would yield optimal community clustering with reads of this length using a procedure similar to that of ref. 15. [For reference, this primer pair amplifies the region 533_786 in the Escherichia coli strain 83972 sequence (greengenes accession no. prokMSA_id:470367).] The reverse PCR primer is barcoded with a 12-base error-correcting Golay code to facilitate multiplexing of up to 1,500 samples per lane, and both PCR primers contain sequencer adapter regions. American Gut Project Stool sample None Regularly (3-5 times/week) 10/22/59 no None ENVO:feces None I do not have a skin condition None no no V4 American Gut Project 68 None no human None None None male None Depends on the season 11/11/13 0.0 None no Less than 25% 10 no None 10138 no None None .1,g yes Never None None Occasionally (1-2 times/week) None CCME UBERON:feces ambidextrous None no no ENVO:human-associated habitat saw palmetto, resveratrol, fish oil, lutein and zeaxanthin, vitamin e, vitamin c, vitamin d, melatonin 8:20 AM no City None 6-7 hours Omnivore CCME None CCME no 173.0 None I do not have IBD no 0 9606 MiSeq 408170 6 to 10 None 100 None None no AGP6_rerun_L001 no Illumina I use deodorant Contact..., Housing... yes leafy greens, carrots,onions 165 None None 20 MiSeq1 2191 None Fecal, oral and skin samples from round 3 MiSeq None Remained stable bread I do not have diabetes port washington no Never no NY None 40.8256561 None yes no American_Gut_round 6
000010232.1212970 GGAGGAGCAATA GTGTGCCAGCMGCCGCGGTAA 29 Within the past 6 months None n 12/18/13 None 60.0 95.0 None UBERON:feces None None no None 75.96387482 Housing... Occasionally (1-2 times/week) 27 no Caucasian USA 100 Never 2191:3755660176 no 22205 -77.142764 Contact... None None None no None UBERON:feces None None None 40 10232 None Stool More than one year ago GAZ:United States of America Not in the last year None human gut metagenome None None 16S rRNA sequencing by synthesis In the past 6 months FWD:GTGCCAGCMGCCGCGGTAA; REV:GGACTACHVGGGTWTCTAAT no 26.24533333 ENVO:urban biome None Regularly (3-5 times/week) no None None CCME no years None This analysis was done as in Caporaso et al 2011 Genome research. The PCR primers (F515/R806) were developed against the V4 region of the 16S rRNA (both bacteria and archaea), which we determined would yield optimal community clustering with reads of this length using a procedure similar to that of ref. 15. [For reference, this primer pair amplifies the region 533_786 in the Escherichia coli strain 83972 sequence (greengenes accession no. prokMSA_id:470367).] The reverse PCR primer is barcoded with a 12-base error-correcting Golay code to facilitate multiplexing of up to 1,500 samples per lane, and both PCR primers contain sequencer adapter regions. American Gut Project Stool sample None Occasionally (1-2 times/week) 5/6/54 no yes ENVO:feces None I do not have a skin condition None no no V4 American Gut Project 75 None no human None None None male None Indoors 11/16/13 0.0 None no 25 to 50% 44 no None 10232 yes None None .1,g yes Never None None Regularly (3-5 times/week) None CCME UBERON:feces right None no no ENVO:human-associated habitat fish oil, ginger, testerone, plant steroils 12:00 PM no City None 7-8 hours Omnivore CCME None CCME no 191.0 None I do not have IBD no 0 9606 MiSeq 408170 Less than 5 None 181 None None no AGP6_rerun_L001 no Illumina I do not use deodorant or antiperspirant Contact..., Housing... yes kale 210 None no 60 MiSeq1 2191 None Fecal, oral and skin samples from round 3 MiSeq None Remained stable rice I do not have diabetes arlington no Rarely (few times/month) no VA None 38.8822689 None yes yes American_Gut_round 6
000009229.1213064 GAGTACAGTCTA GTGTGCCAGCMGCCGCGGTAA 20 Within the past year None n 12/18/13 yes 72.0 61.0 None UBERON:feces None None no None 133.9732819 None Daily 40 no Caucasian USA 100 Regularly (3-5 times/week) 2191:452334347 None 92242 -114.3613425 None None None None no None UBERON:feces None None None 15 9229 None Stool Within the past month GAZ:United States of America In the past year None human gut metagenome yes None 16S rRNA sequencing by synthesis Not in the last year FWD:GTGCCAGCMGCCGCGGTAA; REV:GGACTACHVGGGTWTCTAAT None 22.62911243 ENVO:urban biome None Daily no None No CCME no years None This analysis was done as in Caporaso et al 2011 Genome research. The PCR primers (F515/R806) were developed against the V4 region of the 16S rRNA (both bacteria and archaea), which we determined would yield optimal community clustering with reads of this length using a procedure similar to that of ref. 15. [For reference, this primer pair amplifies the region 533_786 in the Escherichia coli strain 83972 sequence (greengenes accession no. prokMSA_id:470367).] The reverse PCR primer is barcoded with a 12-base error-correcting Golay code to facilitate multiplexing of up to 1,500 samples per lane, and both PCR primers contain sequencer adapter regions. American Gut Project Stool sample None Regularly (3-5 times/week) 1/7/42 no None ENVO:feces None I do not have a skin condition None no no V4 American Gut Project 65 kidney infection None human None None None female None Both 9/25/13 0.0 None yes Less than 25% 40 None None 9229 None None None .1,g None Never None bed Rarely (few times/month) None CCME UBERON:feces unknown None None no ENVO:human-associated habitat None 7:00 AM yes Filtered None 6-7 hours Omnivore CCME None CCME None 165.0 cipro I do not have IBD no 0 9606 MiSeq 408170 More than 30 None 28 None None None AGP6_rerun_L001 no Illumina I do not use deodorant or antiperspirant None yes cabbage 136 None no 85 MiSeq1 2191 eggs Fecal, oral and skin samples from round 3 MiSeq yes Remained stable vegitables I do not have diabetes big river no Never no CA None 34.1400159 None no yes American_Gut_round 6
000004282.1212961 ATTGAGTGAGTC GTGTGCCAGCMGCCGCGGTAA None More than one year ago yes n 12/18/13 None 1.0 68.0 None UBERON:feces None None no None 298.0795593 Housing... Daily None no Caucasian USA 86 Never 2191:2035538779 no 91104 -118.1181199 Contact... None None None no None UBERON:feces None None None 80 4282 None Stool More than one year ago GAZ:United States of America Not in the last year None human gut metagenome None None 16S rRNA sequencing by synthesis Not in the last year FWD:GTGCCAGCMGCCGCGGTAA; REV:GGACTACHVGGGTWTCTAAT no 19.78795271 ENVO:urban biome None Daily no None None CCME no years None This analysis was done as in Caporaso et al 2011 Genome research. The PCR primers (F515/R806) were developed against the V4 region of the 16S rRNA (both bacteria and archaea), which we determined would yield optimal community clustering with reads of this length using a procedure similar to that of ref. 15. [For reference, this primer pair amplifies the region 533_786 in the Escherichia coli strain 83972 sequence (greengenes accession no. prokMSA_id:470367).] The reverse PCR primer is barcoded with a 12-base error-correcting Golay code to facilitate multiplexing of up to 1,500 samples per lane, and both PCR primers contain sequencer adapter regions. American Gut Project Stool sample None Regularly (3-5 times/week) 4/13/13 no None ENVO:feces None I do not have a skin condition yes no no V4 American Gut Project 73 None no human None Two None male None Outdoors 10/3/13 0.0 None no Less than 25% None yes None 4282 no None None .1,g no Never None None Regularly (3-5 times/week) None CCME UBERON:feces right None no no ENVO:human-associated habitat None 8:45 AM no City no 7-8 hours Vegetarian CCME None CCME no 185.0 None I do not have IBD no 0 9606 MiSeq 408170 11 to 20 None 36 None None no AGP6_rerun_L001 no Illumina I do not use deodorant or antiperspirant Contact..., Housing... yes brocolii 150 None no 20 MiSeq1 2191 Kiwi Fruit Fecal, oral and skin samples from round 3 MiSeq yes Remained stable bread I do not have diabetes pasadena no Rarely (few times/month) no CA no 34.1657707 None yes no American_Gut_round 6
000010710.1213087 GTAGACATGTGT GTGTGCCAGCMGCCGCGGTAA None More than one year ago None n 12/18/13 None 52.0 81.0 None UBERON:feces None None no None 2.610644341 Housing... Occasionally (1-2 times/week) None no Caucasian USA 84 Daily 2191:2556452015 no 94502 -122.2483726 Contact... None None None no None UBERON:feces None None None 55 10710 None Stool More than one year ago GAZ:United States of America In the past week None human gut metagenome None None 16S rRNA sequencing by synthesis Not in the last year FWD:GTGCCAGCMGCCGCGGTAA; REV:GGACTACHVGGGTWTCTAAT no 26.57844991 ENVO:urban biome None Daily no None No CCME no years None This analysis was done as in Caporaso et al 2011 Genome research. The PCR primers (F515/R806) were developed against the V4 region of the 16S rRNA (both bacteria and archaea), which we determined would yield optimal community clustering with reads of this length using a procedure similar to that of ref. 15. [For reference, this primer pair amplifies the region 533_786 in the Escherichia coli strain 83972 sequence (greengenes accession no. prokMSA_id:470367).] The reverse PCR primer is barcoded with a 12-base error-correcting Golay code to facilitate multiplexing of up to 1,500 samples per lane, and both PCR primers contain sequencer adapter regions. American Gut Project Stool sample None Regularly (3-5 times/week) 8/31/61 no None ENVO:feces None Rosacea None None yes V4 American Gut Project 69 None no human None None None female None Both 10/28/13 0.0 None no Less than 25% None no None 10710 yes None None .1,g no Never None None Regularly (3-5 times/week) None CCME UBERON:feces right None no no ENVO:human-associated habitat None 6:55 AM no Bottled None 7-8 hours Omnivore CCME None CCME no 175.0 None I do not have IBD no 0 9606 MiSeq 408170 11 to 20 None 10.3 None None no AGP6_rerun_L001 no Illumina I use an antiperspirant Contact..., Housing... yes edamame 180 None no 45 MiSeq1 2191 None Fecal, oral and skin samples from round 3 MiSeq None Remained stable potato I do not have diabetes alameda no Never no CA None 37.7339032 None yes yes American_Gut_round 6
000010225.1213086 CGCCGGTAATCT GTGTGCCAGCMGCCGCGGTAA None More than one year ago None n 12/18/13 None 40.0 74.0 None UBERON:feces None None None None 5.392939568 Housing... Daily None no Caucasian USA 0 Never 2191:216313603 None 3801 -70.7625532 Contact... None None None no None UBERON:feces None None None None 10225 None Stool More than one year ago GAZ:United States of America Not in the last year None human gut metagenome None None 16S rRNA sequencing by synthesis In the past year FWD:GTGCCAGCMGCCGCGGTAA; REV:GGACTACHVGGGTWTCTAAT no 21.76674798 ENVO:urban biome None Daily no None None CCME no years None This analysis was done as in Caporaso et al 2011 Genome research. The PCR primers (F515/R806) were developed against the V4 region of the 16S rRNA (both bacteria and archaea), which we determined would yield optimal community clustering with reads of this length using a procedure similar to that of ref. 15. [For reference, this primer pair amplifies the region 533_786 in the Escherichia coli strain 83972 sequence (greengenes accession no. prokMSA_id:470367).] The reverse PCR primer is barcoded with a 12-base error-correcting Golay code to facilitate multiplexing of up to 1,500 samples per lane, and both PCR primers contain sequencer adapter regions. American Gut Project Stool sample None Occasionally (1-2 times/week) 4/2/74 no None ENVO:feces None I do not have a skin condition None no no V4 American Gut Project 73 None no human None None None male None Outdoors 11/8/13 0.0 None no Less than 25% None no None 10225 no None None .1,g no Never None None Rarely (few times/month) None CCME UBERON:feces right None no no ENVO:human-associated habitat None 11:30 AM no City None 7-8 hours Omnivore CCME None CCME yes 185.0 None I do not have IBD yes 0 9606 MiSeq 408170 Less than 5 None None None None no AGP6_rerun_L001 no Illumina I do not use deodorant or antiperspirant Contact..., Housing... no None 165 None no None MiSeq1 2191 None Fecal, oral and skin samples from round 3 MiSeq None Remained stable None I do not have diabetes portsmouth no Never no NH None 43.0717552 None yes no American_Gut_round 6
Blank33.H9.1213113 TGTGTGTAACGC GTGTGCCAGCMGCCGCGGTAA None None None n 12/18/13 None None None None None None None None None 1624.1 None None None None None None None None 2191:unknown None 80309 -105.79 None None None None None None None None None None None Blank33.H9 None Blank None GAZ:United States of America None None unclassified metagenome None None 16S rRNA sequencing by synthesis None FWD:GTGCCAGCMGCCGCGGTAA; REV:GGACTACHVGGGTWTCTAAT None None ENVO:aquatic biome None None None None None CCME None years None This analysis was done as in Caporaso et al 2011 Genome research. The PCR primers (F515/R806) were developed against the V4 region of the 16S rRNA (both bacteria and archaea), which we determined would yield optimal community clustering with reads of this length using a procedure similar to that of ref. 15. [For reference, this primer pair amplifies the region 533_786 in the Escherichia coli strain 83972 sequence (greengenes accession no. prokMSA_id:470367).] The reverse PCR primer is barcoded with a 12-base error-correcting Golay code to facilitate multiplexing of up to 1,500 samples per lane, and both PCR primers contain sequencer adapter regions. American Gut Project blank None None None None None ENVO:sterile water None None None None None V4 American Gut Project None None None None None None None unknown None None None 0.0 None None None None None None Blank33.H9 None None None .1,g None None None None None None CCME None unknown None None None ENVO:water None None None None None None None CCME None CCME None None None None None 0 None MiSeq 408169 None None None None None None AGP6_rerun_L001 None Illumina None None None None None None None None MiSeq1 2191 None Fecal, oral and skin samples from round 3 MiSeq None None None None boulder None None None CO None 40.02 None None None American_Gut_round 30
000010298.1213043 CGCTTAGTGCTG GTGTGCCAGCMGCCGCGGTAA 50 Never None n 12/18/13 None 2.0 14.0 None UBERON:feces None None no None 28.61847115 Indoor, Indoor Never 20 no Caucasian USA 100 Never 2191:1378085820 no 20742 -76.9441362 Little, Moderate None None None yes None UBERON:feces None None None 60 10298 None Stool More than one year ago GAZ:United States of America In the past 6 months None human gut metagenome None None 16S rRNA sequencing by synthesis In the past 6 months FWD:GTGCCAGCMGCCGCGGTAA; REV:GGACTACHVGGGTWTCTAAT no 17.35802469 ENVO:urban biome None Regularly (3-5 times/week) no None No CCME yes years None This analysis was done as in Caporaso et al 2011 Genome research. The PCR primers (F515/R806) were developed against the V4 region of the 16S rRNA (both bacteria and archaea), which we determined would yield optimal community clustering with reads of this length using a procedure similar to that of ref. 15. [For reference, this primer pair amplifies the region 533_786 in the Escherichia coli strain 83972 sequence (greengenes accession no. prokMSA_id:470367).] The reverse PCR primer is barcoded with a 12-base error-correcting Golay code to facilitate multiplexing of up to 1,500 samples per lane, and both PCR primers contain sequencer adapter regions. American Gut Project Stool sample None Daily 5/25/12 no None ENVO:feces None I do not have a skin condition None no no V4 American Gut Project 36 Otitis media no human None None None female None Both 11/17/13 0.0 None no 25 to 50% 30 no None 10298 no Mother None .1,g yes Never None None Never None CCME UBERON:feces unknown None yes no ENVO:human-associated habitat 3-4 days/wk = trivisol drops 1cc 2:00 PM no City None 8 or more hours Omnivore but no red meat CCME Chicken only once a week CCME no 91.0 Amoxicillin, Augmentin, TMS I do not have IBD yes 0 9606 MiSeq 408170 11 to 20 None 130 None None no AGP6_rerun_L001 no Illumina I do not use deodorant or antiperspirant Cat, Cat, Little, Moderate, Indoor, Indoor no Spinach 32 None no 40 MiSeq1 2191 None Fecal, oral and skin samples from round 3 MiSeq None Remained stable Wheat I do not have diabetes college park no Rarely (few times/month) no MD None 38.9810284 None no no American_Gut_round 6
000010104.1213053 ACCTGTCCTTTC GTGTGCCAGCMGCCGCGGTAA 24 Never None n 12/18/13 None 41.0 66.0 None UBERON:feces None None no None 626.2399902 Housing... Regularly (3-5 times/week) 49 no Caucasian USA 100 Never 2191:1413722162 no 83860 -116.4346649 Contact... None None None no None UBERON:feces None None None 10 10104 None Stool More than one year ago GAZ:United States of America Not in the last year None human gut metagenome None None 16S rRNA sequencing by synthesis Not in the last year FWD:GTGCCAGCMGCCGCGGTAA; REV:GGACTACHVGGGTWTCTAAT no 22.34883218 ENVO:urban biome None Daily no None None CCME no years None This analysis was done as in Caporaso et al 2011 Genome research. The PCR primers (F515/R806) were developed against the V4 region of the 16S rRNA (both bacteria and archaea), which we determined would yield optimal community clustering with reads of this length using a procedure similar to that of ref. 15. [For reference, this primer pair amplifies the region 533_786 in the Escherichia coli strain 83972 sequence (greengenes accession no. prokMSA_id:470367).] The reverse PCR primer is barcoded with a 12-base error-correcting Golay code to facilitate multiplexing of up to 1,500 samples per lane, and both PCR primers contain sequencer adapter regions. American Gut Project Stool sample None Regularly (3-5 times/week) 6/27/73 no None ENVO:feces None I do not have a skin condition None no no V4 American Gut Project 68 None yes human None None None male None Outdoors 10/12/13 0.0 None no Less than 25% 27 no None 10104 no None None .1,g yes Never None None Never None CCME UBERON:feces right None yes no ENVO:human-associated habitat Maca, Kelp, 2:10 PM no Well None 7-8 hours Omnivore CCME I eat only whole natural foods in the way our anscestors ate them. No exceptions. No processed foods etc. CCME no 173.0 None I do not have IBD yes 0 9606 MiSeq 408170 Less than 5 None 65 None None no AGP6_rerun_L001 no Illumina I do not use deodorant or antiperspirant Contact..., Housing... yes Haven't eaten vegetables in seven days. Otherwise it would be cabbage 147 None no 90 MiSeq1 2191 None Fecal, oral and skin samples from round 3 MiSeq None Remained stable Sprouted Brown rice I do not have diabetes sagle no Never no ID None 48.1862312 None yes no American_Gut_round 6
000010867.1213028 AACTTCACTTCC GTGTGCCAGCMGCCGCGGTAA None Never None n 12/18/13 None 50.0 101.0 None UBERON:feces None None no None 667.2123413 Indoor Daily None no Caucasian USA 0 Never 2191:81035998 no 83814 -116.7804664 Extensive None None None no None UBERON:feces None None None 20 10867 None Stool More than one year ago GAZ:United States of America Not in the last year None human gut metagenome None None 16S rRNA sequencing by synthesis Not in the last year FWD:GTGCCAGCMGCCGCGGTAA; REV:GGACTACHVGGGTWTCTAAT no 23.52394408 ENVO:urban biome None Daily no None None CCME None years None This analysis was done as in Caporaso et al 2011 Genome research. The PCR primers (F515/R806) were developed against the V4 region of the 16S rRNA (both bacteria and archaea), which we determined would yield optimal community clustering with reads of this length using a procedure similar to that of ref. 15. [For reference, this primer pair amplifies the region 533_786 in the Escherichia coli strain 83972 sequence (greengenes accession no. prokMSA_id:470367).] The reverse PCR primer is barcoded with a 12-base error-correcting Golay code to facilitate multiplexing of up to 1,500 samples per lane, and both PCR primers contain sequencer adapter regions. American Gut Project Stool sample None Daily 9/28/63 no yes ENVO:feces None I do not have a skin condition None no no V4 American Gut Project 82 None yes human None None None male None Indoors 11/17/13 0.0 None no 25 to 50% None no None 10867 no None None .1,g yes Never None None Daily None CCME UBERON:feces right None no no ENVO:human-associated habitat B Complex CoQ10 Copper DHEA EFA Evening Gingko Biloba Ginseng Glucosamine HCI w/MSM L-Lysine Milk Thistle Multi-Vitamin Resveratrol Turmeric 11:50 AM no Filtered None 7-8 hours Omnivore CCME None CCME None 208.0 None I do not have IBD no 0 9606 MiSeq 408170 11 to 20 None 120 None None no AGP6_rerun_L001 no Illumina I use an antiperspirant Parrot, Extensive, Indoor yes Spinach 225 None no 80 MiSeq1 2191 None Fecal, oral and skin samples from round 3 MiSeq None Remained stable Crackers I do not have diabetes coeur d alene no Never no ID None 47.6776832 None yes no American_Gut_round 6
000004290.1212971 ACCAATCTCGGC GTGTGCCAGCMGCCGCGGTAA 55 Within the past 6 months None n 12/18/13 None 41.0 56.0 None UBERON:feces Stress Foods; other no Other 298.0795593 Housing... Daily 13 no Caucasian USA 100 Daily 2191:1959307485 yes 91104 -118.1181199 Contact... yes None None no None UBERON:feces None Monthly no 55 4290 None Stool More than one year ago GAZ:United States of America Not in the last year yes human gut metagenome None None 16S rRNA sequencing by synthesis In the past year FWD:GTGCCAGCMGCCGCGGTAA; REV:GGACTACHVGGGTWTCTAAT yes 18.45725688 ENVO:urban biome None Daily no None None CCME no years None This analysis was done as in Caporaso et al 2011 Genome research. The PCR primers (F515/R806) were developed against the V4 region of the 16S rRNA (both bacteria and archaea), which we determined would yield optimal community clustering with reads of this length using a procedure similar to that of ref. 15. [For reference, this primer pair amplifies the region 533_786 in the Escherichia coli strain 83972 sequence (greengenes accession no. prokMSA_id:470367).] The reverse PCR primer is barcoded with a 12-base error-correcting Golay code to facilitate multiplexing of up to 1,500 samples per lane, and both PCR primers contain sequencer adapter regions. American Gut Project Stool sample None Daily 1/20/73 no None ENVO:feces None I do not have a skin condition None no no V4 American Gut Project 69 None no human None None None unknown yes Outdoors 10/2/13 0.0 None no 51 to 75% 32 no None 4290 yes None None .1,g yes Never yes None Rarely (few times/month) None CCME UBERON:feces right None None no ENVO:human-associated habitat calcium, magnesium, vitamin D 10:45 AM no Filtered None 7-8 hours Omnivore CCME None CCME yes 175.0 None I do not have IBD no 0 9606 MiSeq 408170 More than 30 no 166 None menstration no AGP6_rerun_L001 no Illumina I use an antiperspirant Contact..., Housing... yes carrots, lettuce, apples &cranberries 125 None no 45 MiSeq1 2191 shrimp Fecal, oral and skin samples from round 3 MiSeq None Remained stable rice and potatoes I do not have diabetes pasadena no Never no CA None 34.1657707 yes yes no American_Gut_round 6
000010162.1213007 GTCATGCTCCAG GTGTGCCAGCMGCCGCGGTAA 53 More than one year ago None n 12/18/13 None 44.0 54.0 None UBERON:feces None None no None 38.65314865 Indoor Occasionally (1-2 times/week) 14 no Caucasian Finland 97 Rarely (few times/month) 2191:3856253918 no 1985 -70.989778 Extensive None None None no None UBERON:feces None None None 75 10162 None Stool More than one year ago GAZ:United States of America Not in the last year None human gut metagenome None None 16S rRNA sequencing by synthesis In the past month FWD:GTGCCAGCMGCCGCGGTAA; REV:GGACTACHVGGGTWTCTAAT no 19.36639118 ENVO:urban biome None Daily no None No CCME yes years None This analysis was done as in Caporaso et al 2011 Genome research. The PCR primers (F515/R806) were developed against the V4 region of the 16S rRNA (both bacteria and archaea), which we determined would yield optimal community clustering with reads of this length using a procedure similar to that of ref. 15. [For reference, this primer pair amplifies the region 533_786 in the Escherichia coli strain 83972 sequence (greengenes accession no. prokMSA_id:470367).] The reverse PCR primer is barcoded with a 12-base error-correcting Golay code to facilitate multiplexing of up to 1,500 samples per lane, and both PCR primers contain sequencer adapter regions. American Gut Project Stool sample None Daily 11/20/69 no yes ENVO:feces None I do not have a skin condition None no no V4 American Gut Project 66 None yes human None None None female None Both 11/15/13 0.0 None no Less than 25% 30 no None 10162 no Husband None .1,g yes Never None None Occasionally (1-2 times/week) None CCME UBERON:feces right None yes no ENVO:human-associated habitat Vitamin D3 (2000 I.U.) 8:00 AM no Well None 8 or more hours Vegetarian CCME Avoid dairy products including butter, fried foods and wine with sulfites CCME yes 168.0 None I do not have IBD no 0 9606 MiSeq 408170 21 to 30 None 189 None None yes AGP6_rerun_L001 no Illumina Not sure, but I use some form of deodorant/antiperspirant Dog, Extensive, Indoor no onion 120 None no 25 MiSeq1 2191 None Fecal, oral and skin samples from round 3 MiSeq None Remained stable bread I do not have diabetes west newbury no Rarely (few times/month) no MA None 42.8014795 None yes yes American_Gut_round 6
000001271.1213022 CATCGGATCTGA GTGTGCCAGCMGCCGCGGTAA 79 More than one year ago None n 5/20/13 None 0.0 69.0 None UBERON:feces None None no None 6.584047794 None Daily 11 yes Caucasian USA 100 Daily 2191:1419286842 no 34212 -82.3777335 None None None None no None UBERON:feces None None None 75 1271 None Stool More than one year ago GAZ:United States of America Not in the last year None human gut metagenome None None 16S rRNA sequencing by synthesis Not in the last year FWD:GTGCCAGCMGCCGCGGTAA; REV:GGACTACHVGGGTWTCTAAT no 26.08789063 ENVO:urban biome None Daily no None No CCME not_sure years None This analysis was done as in Caporaso et al 2011 Genome research. The PCR primers (F515/R806) were developed against the V4 region of the 16S rRNA (both bacteria and archaea), which we determined would yield optimal community clustering with reads of this length using a procedure similar to that of ref. 15. [For reference, this primer pair amplifies the region 533_786 in the Escherichia coli strain 83972 sequence (greengenes accession no. prokMSA_id:470367).] The reverse PCR primer is barcoded with a 12-base error-correcting Golay code to facilitate multiplexing of up to 1,500 samples per lane, and both PCR primers contain sequencer adapter regions. American Gut Project Stool sample None Rarely (few times/month) 9/15/13 no yes ENVO:feces None I do not have a skin condition None no yes V4 American Gut Project 64 None yes human None One None female None Indoors 5/1/13 0.0 None no 51 to 75% 10 yes None 1271 yes None None .1,g no Never None None Rarely (few times/month) None CCME UBERON:feces right None None no ENVO:human-associated habitat None 4:10 PM no Filtered yes 5-6 hours Omnivore CCME None CCME no 163.0 None I do not have IBD yes 0 9606 MiSeq 408170 11 to 20 None 110 None None no Knight_AFG_16s_w_phiX_NoIndex_L001 None Illumina I use an antiperspirant None no spinach 152 None no 25 MiSeq1 2191 None Fecal, oral and skin samples from round 3 MiSeq None Decreased more than 10 pounds sugar I do not have diabetes bradenton no Never no FL yes 27.4933783 None yes yes American_Gut_round 6
000001249.1213076 GGCTGCATACTC GTGTGCCAGCMGCCGCGGTAA None More than one year ago None n 12/18/13 yes 72.0 72.0 None UBERON:feces None None yes None 31.76734924 Housing... Occasionally (1-2 times/week) None no Hispanic USA 0 Rarely (few times/month) 2191:4041215903 no 32819 -81.460856 Contact... None None None no None UBERON:feces None None None None 1249 None Stool More than one year ago GAZ:United States of America In the past 6 months None human gut metagenome None None 16S rRNA sequencing by synthesis Not in the last year FWD:GTGCCAGCMGCCGCGGTAA; REV:GGACTACHVGGGTWTCTAAT None None ENVO:urban biome None Daily no None No CCME no years None This analysis was done as in Caporaso et al 2011 Genome research. The PCR primers (F515/R806) were developed against the V4 region of the 16S rRNA (both bacteria and archaea), which we determined would yield optimal community clustering with reads of this length using a procedure similar to that of ref. 15. [For reference, this primer pair amplifies the region 533_786 in the Escherichia coli strain 83972 sequence (greengenes accession no. prokMSA_id:470367).] The reverse PCR primer is barcoded with a 12-base error-correcting Golay code to facilitate multiplexing of up to 1,500 samples per lane, and both PCR primers contain sequencer adapter regions. American Gut Project Stool sample None Occasionally (1-2 times/week) 12/15/41 no None ENVO:feces None I do not have a skin condition None no no V4 American Gut Project None diahrrea yes human None None None female None Both 9/28/13 0.0 None no None None no None 1249 yes None None .1,g yes Never None None Rarely (few times/month) None CCME UBERON:feces right None no no ENVO:human-associated habitat Turmeric, Probiotics 11:30 AM no Filtered None 5-6 hours Omnivore CCME None CCME yes None Hospital- do not know I do not have IBD no 0 9606 MiSeq 408170 None None None None None no AGP6_rerun_L001 no Illumina I use an antiperspirant Contact..., Housing... no None 160 None no None MiSeq1 2191 None Fecal, oral and skin samples from round 3 MiSeq None Remained stable None I do not have diabetes orlando no Rarely (few times/month) no FL None 28.4630493 None no no American_Gut_round 6
000009721.1212978 ATGCTAACCACG GTGTGCCAGCMGCCGCGGTAA 25 Within the past 3 months None n 12/18/13 None 38.0 64.0 None UBERON:feces None None yes None 3.951129436 None Occasionally (1-2 times/week) 35 no Caucasian USA 100 Daily 2191:1923473512 yes 33131 -80.1847167 None None None None no None UBERON:feces None None None 10 9721 None Stool More than one year ago GAZ:United States of America In the past year None human gut metagenome None None 16S rRNA sequencing by synthesis Not in the last year FWD:GTGCCAGCMGCCGCGGTAA; REV:GGACTACHVGGGTWTCTAAT no 21.74070069 ENVO:urban biome None Daily no None None CCME no years None This analysis was done as in Caporaso et al 2011 Genome research. The PCR primers (F515/R806) were developed against the V4 region of the 16S rRNA (both bacteria and archaea), which we determined would yield optimal community clustering with reads of this length using a procedure similar to that of ref. 15. [For reference, this primer pair amplifies the region 533_786 in the Escherichia coli strain 83972 sequence (greengenes accession no. prokMSA_id:470367).] The reverse PCR primer is barcoded with a 12-base error-correcting Golay code to facilitate multiplexing of up to 1,500 samples per lane, and both PCR primers contain sequencer adapter regions. American Gut Project Stool sample spray Daily 7/12/76 no None ENVO:feces None I do not have a skin condition None yes no V4 American Gut Project 68 None yes human None None None unknown None Both 9/25/13 0.0 None no Less than 25% 40 None None 9721 yes None None .1,g yes Never None None Rarely (few times/month) None CCME UBERON:feces right None yes no ENVO:human-associated habitat Probiotic 10:00 AM no Filtered None 7-8 hours Omnivore CCME Eggs CCME yes 173.0 None I do not have IBD no 0 9606 MiSeq 408170 11 to 20 None 110 None None no AGP6_rerun_L001 no Illumina I use deodorant None yes Leafy Greens 143 None no 90 MiSeq1 2191 None Fecal, oral and skin samples from round 3 MiSeq None Increased more than 10 pounds Fruit I do not have diabetes miami no Never no FL None 25.76528 None yes no American_Gut_round 6
000010299.1212977 CACGTGACATGT GTGTGCCAGCMGCCGCGGTAA 41 More than one year ago None n 12/18/13 None 36.0 64.0 None UBERON:feces None None yes None 28.61847115 Indoor, Indoor Daily 20 no Caucasian USA 100 Rarely (few times/month) 2191:3377524279 no 20742 -76.9441362 Extensive, Moderate None None None no None UBERON:feces None None None 90 10299 None Stool More than one year ago GAZ:United States of America Not in the last year None human gut metagenome None None 16S rRNA sequencing by synthesis In the past year FWD:GTGCCAGCMGCCGCGGTAA; REV:GGACTACHVGGGTWTCTAAT no 22.2379149 ENVO:urban biome None Daily no None I use some other type of birth control CCME yes years None This analysis was done as in Caporaso et al 2011 Genome research. The PCR primers (F515/R806) were developed against the V4 region of the 16S rRNA (both bacteria and archaea), which we determined would yield optimal community clustering with reads of this length using a procedure similar to that of ref. 15. [For reference, this primer pair amplifies the region 533_786 in the Escherichia coli strain 83972 sequence (greengenes accession no. prokMSA_id:470367).] The reverse PCR primer is barcoded with a 12-base error-correcting Golay code to facilitate multiplexing of up to 1,500 samples per lane, and both PCR primers contain sequencer adapter regions. American Gut Project Stool sample None Regularly (3-5 times/week) 8/25/77 no None ENVO:feces None I do not have a skin condition None no no V4 American Gut Project 67 None no human None None None female None Outdoors 11/7/13 0.0 None no 25 to 50% 39 no None 10299 no Daughter None .1,g yes Never None None Regularly (3-5 times/week) None CCME UBERON:feces left None yes no ENVO:human-associated habitat Fish oil 7:40 AM no City None 6-7 hours Vegetarian but eat seafood CCME Do eat chicken once weekly, no pork or other CCME no 170.0 None I do not have IBD yes 0 9606 MiSeq 408170 11 to 20 None 228 None None no AGP6_rerun_L001 no Illumina Not sure, but I use some form of deodorant/antiperspirant Cat, cat, Extensive, Moderate, Indoor, Indoor yes Broccoli 142 None no 10 MiSeq1 2191 None Fecal, oral and skin samples from round 3 MiSeq None Remained stable pasta (barilla, high protein) I do not have diabetes college park no Rarely (few times/month) no MD None 38.9810284 None yes no American_Gut_round 6
000009400.1213023 CATAGTGATTGG GTGTGCCAGCMGCCGCGGTAA 56 More than one year ago None n 12/18/13 None 67.0 54.0 None UBERON:feces None None no None 31.81302071 Housing... Daily 20 no Caucasian USA 96 Daily 2191:2297487623 no 95003 -121.8994016 Contact... None None None no None UBERON:feces None None None 50 9400 None Stool More than one year ago GAZ:United States of America In the past week None human gut metagenome None None 16S rRNA sequencing by synthesis In the past week FWD:GTGCCAGCMGCCGCGGTAA; REV:GGACTACHVGGGTWTCTAAT no 20.13325444 ENVO:urban biome None Daily no None No CCME no years None This analysis was done as in Caporaso et al 2011 Genome research. The PCR primers (F515/R806) were developed against the V4 region of the 16S rRNA (both bacteria and archaea), which we determined would yield optimal community clustering with reads of this length using a procedure similar to that of ref. 15. [For reference, this primer pair amplifies the region 533_786 in the Escherichia coli strain 83972 sequence (greengenes accession no. prokMSA_id:470367).] The reverse PCR primer is barcoded with a 12-base error-correcting Golay code to facilitate multiplexing of up to 1,500 samples per lane, and both PCR primers contain sequencer adapter regions. American Gut Project Stool sample on Regularly (3-5 times/week) 11/11/46 yes None ENVO:feces None I do not have a skin condition yes yes no V4 American Gut Project 65 prevent bladder infection, cold sore no human None None None female None Indoors 10/7/13 0.0 None no More than 76% 20 no None 9400 on None None .1,g yes Never None None Daily None CCME UBERON:feces right None yes no ENVO:human-associated habitat glucosamine, chondrotin, fish oil, mangosteen, L-glutamine, BCAA, D-ribose, shilajit, lychee, aloe, grape seed and skin extract, beet root, fiber supplements, vegetable protein powder 8:15 AM no Bottled None 7-8 hours Omnivore CCME high fiber CCME yes 165.0 bactrim (generic), valacyclovir I do not have IBD no 0 9606 MiSeq 408170 11 to 20 None 300 None None no AGP6_rerun_L001 None Illumina I use deodorant Contact..., Housing... yes berries 121 None no 50 MiSeq1 2191 None Fecal, oral and skin samples from round 3 MiSeq None Remained stable grains I do not have diabetes aptos no Rarely (few times/month) no CA None 36.9771729 None yes yes American_Gut_round 6
000009373.1213096 AGGCACAGTAGG GTGTGCCAGCMGCCGCGGTAA None Within the past 6 months None n 12/18/13 None 40.0 108.0 None UBERON:feces Lack of sleep Depression no Stress 209.2589111 Housing... Regularly (3-5 times/week) None no Caucasian USA 89 Never 2191:754621548 no 60007 -87.9703461 Contact... yes None None no None UBERON:feces None Monthly yes 100 9373 yes Stool More than one year ago GAZ:United States of America In the past 6 months None human gut metagenome None None 16S rRNA sequencing by synthesis In the past year FWD:GTGCCAGCMGCCGCGGTAA; REV:GGACTACHVGGGTWTCTAAT yes None ENVO:urban biome None Daily no None None CCME no years None This analysis was done as in Caporaso et al 2011 Genome research. The PCR primers (F515/R806) were developed against the V4 region of the 16S rRNA (both bacteria and archaea), which we determined would yield optimal community clustering with reads of this length using a procedure similar to that of ref. 15. [For reference, this primer pair amplifies the region 533_786 in the Escherichia coli strain 83972 sequence (greengenes accession no. prokMSA_id:470367).] The reverse PCR primer is barcoded with a 12-base error-correcting Golay code to facilitate multiplexing of up to 1,500 samples per lane, and both PCR primers contain sequencer adapter regions. American Gut Project Stool sample None Rarely (few times/month) 2/19/74 no None ENVO:feces None I do not have a skin condition None yes no V4 American Gut Project None UTI no human None None None male None Indoors 8/26/13 0.0 None yes Less than 25% None no None 9373 yes None None .1,g no Rarely (few times/month) None None Regularly (3-5 times/week) None CCME UBERON:feces right None no no ENVO:human-associated habitat None 1:25 PM no Filtered None 6-7 hours Omnivore CCME None CCME no None Cipro I do not have IBD no 0 9606 MiSeq 408170 Less than 5 no 21.3 None None no AGP6_rerun_L001 no Illumina I use deodorant Contact..., Housing... no Brocolli 240 None no 0 MiSeq1 2191 None Fecal, oral and skin samples from round 3 MiSeq None Remained stable Pasta I do not have diabetes elk grove village None Never no IL None 42.0039178 None yes None American_Gut_round 6
000010938.1213104 TAGTGTCGGATC GTGTGCCAGCMGCCGCGGTAA 39 More than one year ago None n 12/18/13 None 0.0 80.0 None UBERON:feces None None yes None 157.7642365 Indoor Daily 19 no Caucasian USA 100 Never 2191:2086470646 no 20777 -76.9577073 Moderate None None None no None UBERON:feces None None None 15 10938 None Stool More than one year ago GAZ:United States of America Not in the last year None human gut metagenome None None 16S rRNA sequencing by synthesis In the past 6 months FWD:GTGCCAGCMGCCGCGGTAA; REV:GGACTACHVGGGTWTCTAAT no 24.00289352 ENVO:urban biome None Daily no None None CCME yes years None This analysis was done as in Caporaso et al 2011 Genome research. The PCR primers (F515/R806) were developed against the V4 region of the 16S rRNA (both bacteria and archaea), which we determined would yield optimal community clustering with reads of this length using a procedure similar to that of ref. 15. [For reference, this primer pair amplifies the region 533_786 in the Escherichia coli strain 83972 sequence (greengenes accession no. prokMSA_id:470367).] The reverse PCR primer is barcoded with a 12-base error-correcting Golay code to facilitate multiplexing of up to 1,500 samples per lane, and both PCR primers contain sequencer adapter regions. American Gut Project Stool sample None Regularly (3-5 times/week) 11/5/13 no None ENVO:feces None I do not have a skin condition None no no V4 American Gut Project 72 None yes human None None None male None Indoors 11/5/13 0.0 None no Less than 25% 42 no None 10938 no wife None .1,g yes Never yes None Regularly (3-5 times/week) None CCME UBERON:feces right None yes no ENVO:human-associated habitat Fish Oil (1000 mg/day); DHEA (25 mg x2/day) 6:30 AM no Well None 6-7 hours Omnivore CCME Paleo since about 9 weeks ago CCME no 183.0 None I do not have IBD no 0 9606 MiSeq 408170 6 to 10 None 123 None None no AGP6_rerun_L001 no Illumina I use deodorant 3 poodles, Moderate, Indoor yes leafy greens 177 None no 85 MiSeq1 2191 None Fecal, oral and skin samples from round 3 MiSeq None Decreased more than 10 pounds fruit I do not have diabetes highland no Rarely (few times/month) no MD None 39.1791249 None no yes American_Gut_round 6
000010908.1213091 CATCAAGCATAG GTGTGCCAGCMGCCGCGGTAA 48 More than one year ago None n 12/18/13 None 43.0 58.0 None UBERON:feces None None no None 383.9515686 Housing... Regularly (3-5 times/week) 10 no Caucasian USA 100 Regularly (3-5 times/week) 2191:3204501548 yes 85251 -111.9224398 Contact... None None None yes None UBERON:feces None None None 100 10908 None Stool More than one year ago GAZ:United States of America In the past 6 months None human gut metagenome None None 16S rRNA sequencing by synthesis In the past month FWD:GTGCCAGCMGCCGCGGTAA; REV:GGACTACHVGGGTWTCTAAT no 20.65748393 ENVO:urban biome None Daily no None No CCME no years None This analysis was done as in Caporaso et al 2011 Genome research. The PCR primers (F515/R806) were developed against the V4 region of the 16S rRNA (both bacteria and archaea), which we determined would yield optimal community clustering with reads of this length using a procedure similar to that of ref. 15. [For reference, this primer pair amplifies the region 533_786 in the Escherichia coli strain 83972 sequence (greengenes accession no. prokMSA_id:470367).] The reverse PCR primer is barcoded with a 12-base error-correcting Golay code to facilitate multiplexing of up to 1,500 samples per lane, and both PCR primers contain sequencer adapter regions. American Gut Project Stool sample None Daily 9/14/70 no None ENVO:feces None I do not have a skin condition None no no V4 American Gut Project 66 tooth infections needing root canals no human None None None female None Depends on the season 11/6/13 0.0 None no Less than 25% 42 no None 10908 no None None .1,g yes Never yes None Never None CCME UBERON:feces right None yes no ENVO:human-associated habitat MAP amino acids, Bifera iron, sublingual B12, digestive enzymes, probiotics 12:30 PM no City None Less than 5 hours Omnivore but no red meat CCME Vegan at home since boyfriend is & I follow fat adapted endurance athlete eating protocol CCME yes 168.0 penicillin vk, amoxicillin I do not have IBD no 0 9606 MiSeq 408170 6 to 10 None 546 None None no AGP6_rerun_L001 no Illumina I do not use deodorant or antiperspirant Contact..., Housing... yes carrot 128 None no 0 MiSeq1 2191 None Fecal, oral and skin samples from round 3 MiSeq None Remained stable blueberries I do not have diabetes scottsdale no Regularly (3-5 times/week) no AZ None 33.4986286 None yes yes American_Gut_round 6
Blank28.B4.1212985 GACTGACTCGTC GTGTGCCAGCMGCCGCGGTAA None None None n 12/18/13 None None None None None None None None None 1624.1 None None None None None None None None 2191:unknown None 80309 -105.79 None None None None None None None None None None None Blank28.B4 None Blank None GAZ:United States of America None None unclassified metagenome None None 16S rRNA sequencing by synthesis None FWD:GTGCCAGCMGCCGCGGTAA; REV:GGACTACHVGGGTWTCTAAT None None ENVO:aquatic biome None None None None None CCME None years None This analysis was done as in Caporaso et al 2011 Genome research. The PCR primers (F515/R806) were developed against the V4 region of the 16S rRNA (both bacteria and archaea), which we determined would yield optimal community clustering with reads of this length using a procedure similar to that of ref. 15. [For reference, this primer pair amplifies the region 533_786 in the Escherichia coli strain 83972 sequence (greengenes accession no. prokMSA_id:470367).] The reverse PCR primer is barcoded with a 12-base error-correcting Golay code to facilitate multiplexing of up to 1,500 samples per lane, and both PCR primers contain sequencer adapter regions. American Gut Project blank None None None None None ENVO:sterile water None None None None None V4 American Gut Project None None None None None None None unknown None None None 0.0 None None None None None None Blank28.B4 None None None .1,g None None None None None None CCME None unknown None None None ENVO:water None None None None None None None CCME None CCME None None None None None 0 None MiSeq 408169 None None None None None None AGP6_rerun_L001 None Illumina None None None None None None None None MiSeq1 2191 None Fecal, oral and skin samples from round 3 MiSeq None None None None boulder None None None CO None 40.02 None None None American_Gut_round 10
000003842.1213101 CTAGCTATGGAC GTGTGCCAGCMGCCGCGGTAA 58 Within the past year None n 12/18/13 None 38.0 99.0 None UBERON:feces None None no None 1586.071899 Indoor Regularly (3-5 times/week) 19 no Caucasian USA 100 Never 2191:2120836891 no 80549 -105.0085856 Extensive None None None no None UBERON:feces None None None 25 3842 None Stool More than one year ago GAZ:United States of America Not in the last year None human gut metagenome None None 16S rRNA sequencing by synthesis Not in the last year FWD:GTGCCAGCMGCCGCGGTAA; REV:GGACTACHVGGGTWTCTAAT no 29.02233064 ENVO:urban biome None Daily no None None CCME yes years None This analysis was done as in Caporaso et al 2011 Genome research. The PCR primers (F515/R806) were developed against the V4 region of the 16S rRNA (both bacteria and archaea), which we determined would yield optimal community clustering with reads of this length using a procedure similar to that of ref. 15. [For reference, this primer pair amplifies the region 533_786 in the Escherichia coli strain 83972 sequence (greengenes accession no. prokMSA_id:470367).] The reverse PCR primer is barcoded with a 12-base error-correcting Golay code to facilitate multiplexing of up to 1,500 samples per lane, and both PCR primers contain sequencer adapter regions. American Gut Project Stool sample None Rarely (few times/month) 3/31/76 no yes ENVO:feces None I do not have a skin condition None no no V4 American Gut Project 73 None yes human None None None male None Indoors 10/14/13 0.0 None no Less than 25% 23 no None 3842 no spouse None .1,g no Never None None Never None CCME UBERON:feces right None yes no ENVO:human-associated habitat None 10:00 PM no City None 6-7 hours Omnivore CCME no alchohol, coffee or tea CCME no 185.0 None I do not have IBD no 0 9606 MiSeq 408170 21 to 30 None 203 None None no AGP6_rerun_L001 no Illumina Not sure, but I use some form of deodorant/antiperspirant Yellow Lab Dog, Extensive, Indoor no carrot 220 None no 75 MiSeq1 2191 None Fecal, oral and skin samples from round 3 MiSeq None Remained stable oatmeal I do not have diabetes wellington no Never no CO None 40.7038712 None yes yes American_Gut_round 6
000009675.1213127 ATTATCGTCCCT GTGTGCCAGCMGCCGCGGTAA 55 Never None n 12/18/13 None 50.0 68.0 None UBERON:feces None None None None 2.252920866 Indoor Daily 25 no Caucasian USA 100 Daily 2191:835638159 no 32136 -81.1270035 Extensive None None None no None UBERON:feces None None None 75 9675 None Stool More than one year ago GAZ:United States of America Not in the last year None human gut metagenome None None 16S rRNA sequencing by synthesis Not in the last year FWD:GTGCCAGCMGCCGCGGTAA; REV:GGACTACHVGGGTWTCTAAT no 24.36937557 ENVO:urban biome None Daily no None No CCME no years None This analysis was done as in Caporaso et al 2011 Genome research. The PCR primers (F515/R806) were developed against the V4 region of the 16S rRNA (both bacteria and archaea), which we determined would yield optimal community clustering with reads of this length using a procedure similar to that of ref. 15. [For reference, this primer pair amplifies the region 533_786 in the Escherichia coli strain 83972 sequence (greengenes accession no. prokMSA_id:470367).] The reverse PCR primer is barcoded with a 12-base error-correcting Golay code to facilitate multiplexing of up to 1,500 samples per lane, and both PCR primers contain sequencer adapter regions. American Gut Project Stool sample None Daily 5/1/64 no None ENVO:feces None I do not have a skin condition yes no None V4 American Gut Project 66 None no human None None None female None Outdoors 9/3/13 0.0 None no Less than 25% 20 no None 9675 yes None None .1,g yes Never None None Rarely (few times/month) None CCME UBERON:feces right None no no ENVO:human-associated habitat hemaplex, calcium 4:00 AM no Bottled None 6-7 hours Omnivore CCME None CCME no 168.0 None I do not have IBD yes 0 9606 MiSeq 408170 11 to 20 None 280 None None yes AGP6_rerun_L001 no Illumina Not sure, but I use some form of deodorant/antiperspirant cat, Extensive, Indoor no squash 151 None no 25 MiSeq1 2191 None Fecal, oral and skin samples from round 3 MiSeq None Remained stable brown rice I do not have diabetes flagler beach no Occasionally (1-2 times/week) no FL None 29.4749754 None yes yes American_Gut_round 6
000008976.1212976 CTCTTCTGATCA GTGTGCCAGCMGCCGCGGTAA 34 More than one year ago None n 12/18/13 None 34.0 62.0 None UBERON:feces None None no None 97.69953918 Indoor Daily 30 no Hispanic USA 100 Never 2191:2444917028 no 29204 -81.0036821 Little None None None no None UBERON:feces None None None 58 8976 None Stool More than one year ago GAZ:United States of America In the past year None human gut metagenome None None 16S rRNA sequencing by synthesis Not in the last year FWD:GTGCCAGCMGCCGCGGTAA; REV:GGACTACHVGGGTWTCTAAT no 23.68505859 ENVO:urban biome None Daily no None No CCME no years None This analysis was done as in Caporaso et al 2011 Genome research. The PCR primers (F515/R806) were developed against the V4 region of the 16S rRNA (both bacteria and archaea), which we determined would yield optimal community clustering with reads of this length using a procedure similar to that of ref. 15. [For reference, this primer pair amplifies the region 533_786 in the Escherichia coli strain 83972 sequence (greengenes accession no. prokMSA_id:470367).] The reverse PCR primer is barcoded with a 12-base error-correcting Golay code to facilitate multiplexing of up to 1,500 samples per lane, and both PCR primers contain sequencer adapter regions. American Gut Project Stool sample None Regularly (3-5 times/week) 10/16/79 no yes ENVO:feces None I do not have a skin condition None no no V4 American Gut Project 64 Bronchitis no human None None None female None Both 9/26/13 0.0 None no Less than 25% 36 no None 8976 no None None .1,g yes Never None None Occasionally (1-2 times/week) None CCME UBERON:feces left None yes no ENVO:human-associated habitat Antronex, kelp tablets 6:35 AM no City None 7-8 hours Omnivore CCME no grains CCME no 163.0 Azithromycin Dihydrate (250mg) I do not have IBD no 0 9606 MiSeq 408170 21 to 30 None 213 None None no AGP6_rerun_L001 no Illumina I use deodorant Fish, Little, Indoor no zucchini 138 None no 42 MiSeq1 2191 None Fecal, oral and skin samples from round 3 MiSeq None Remained stable plantain I do not have diabetes columbia no Rarely (few times/month) no SC None 34.0291227 None yes yes American_Gut_round 6
000001626.1212997 GTACGATATGAC GTGTGCCAGCMGCCGCGGTAA 30 Within the past year None n 5/20/13 None 75.0 104.0 None UBERON:feces None None yes None 5.980104923 None Regularly (3-5 times/week) 60 no Caucasian USA 100 Never 2191:2030696252 no 90815 -118.1181199 None None None None no None UBERON:feces None None None 50 1626 None Stool More than one year ago GAZ:United States of America In the past 6 months None human gut metagenome None None 16S rRNA sequencing by synthesis In the past 6 months FWD:GTGCCAGCMGCCGCGGTAA; REV:GGACTACHVGGGTWTCTAAT no 31.19020062 ENVO:urban biome None Daily no None None CCME no years None This analysis was done as in Caporaso et al 2011 Genome research. The PCR primers (F515/R806) were developed against the V4 region of the 16S rRNA (both bacteria and archaea), which we determined would yield optimal community clustering with reads of this length using a procedure similar to that of ref. 15. [For reference, this primer pair amplifies the region 533_786 in the Escherichia coli strain 83972 sequence (greengenes accession no. prokMSA_id:470367).] The reverse PCR primer is barcoded with a 12-base error-correcting Golay code to facilitate multiplexing of up to 1,500 samples per lane, and both PCR primers contain sequencer adapter regions. American Gut Project Stool sample None Occasionally (1-2 times/week) 12/3/38 no yes ENVO:feces None I do not have a skin condition None yes no V4 American Gut Project 72 after surgery no human None None None male None Indoors 8/9/13 0.0 None yes 25 to 50% 10 no None 1626 yes None None .1,g yes Never None None Rarely (few times/month) None CCME UBERON:feces right None no no ENVO:human-associated habitat krill, vit c, multi, beta carotene 9:10 AM no Filtered None 7-8 hours Omnivore CCME None CCME no 183.0 cipro I do not have IBD None 0 9606 MiSeq 408170 6 to 10 None 100 None None no Knight_AFG_16s_w_phiX_NoIndex_L001 no Illumina I use deoderant fish yes lettuce 230 None no 50 MiSeq1 2191 None Fecal, oral and skin samples from round 3 MiSeq None Decreased more than 10 pounds bread I do not have diabetes long beach no Rarely (few times/month) no CA None 33.7963296 None yes yes American_Gut_round 6
000009070.1213136 TATCCAAGCGCA GTGTGCCAGCMGCCGCGGTAA 34 Within the past 6 months None n 12/18/13 None 29.0 79.0 None UBERON:feces Stress None no Other 61.83166885 Housing... Never 18 no Caucasian USA 100 Never 2191:2907824909 yes 98103 -122.3425575 Contact... None None None no None UBERON:feces None Monthly yes 10 9070 None Stool More than one year ago GAZ:United States of America Not in the last year yes human gut metagenome None yes 16S rRNA sequencing by synthesis Not in the last year FWD:GTGCCAGCMGCCGCGGTAA; REV:GGACTACHVGGGTWTCTAAT yes 21.87111111 ENVO:urban biome None Daily no None None CCME no years None This analysis was done as in Caporaso et al 2011 Genome research. The PCR primers (F515/R806) were developed against the V4 region of the 16S rRNA (both bacteria and archaea), which we determined would yield optimal community clustering with reads of this length using a procedure similar to that of ref. 15. [For reference, this primer pair amplifies the region 533_786 in the Escherichia coli strain 83972 sequence (greengenes accession no. prokMSA_id:470367).] The reverse PCR primer is barcoded with a 12-base error-correcting Golay code to facilitate multiplexing of up to 1,500 samples per lane, and both PCR primers contain sequencer adapter regions. American Gut Project Stool sample None Daily 8/28/84 no None ENVO:feces None Eczema None no no V4 American Gut Project 75 None no human None None None male None Both 9/17/13 0.0 None no Less than 25% 48 no None 9070 no None None .1,g yes Never None None Rarely (few times/month) None CCME UBERON:feces right None yes no ENVO:human-associated habitat b6, zinc 8:55 PM no Filtered None 7-8 hours Omnivore CCME Ray Peat diet. no grains, beans, minimal vegetables CCME no 191.0 None I do not have IBD yes 0 9606 MiSeq 408170 11 to 20 no 25 None not sure, may be excess serotonin yes AGP6_rerun_L001 no Illumina I do not use deodorant or antiperspirant Contact..., Housing... no potato 175 None no 90 MiSeq1 2191 None Fecal, oral and skin samples from round 3 MiSeq None Remained stable orange juice, milk I do not have diabetes seattle no Rarely (few times/month) no WA None 47.6600087 None yes no American_Gut_round 6
000007680.1213005 GGCAAATACACT GTGTGCCAGCMGCCGCGGTAA None Never None n 12/18/13 None 3.0 12.0 None UBERON:feces None None no None 218.3718414 Outdoor Never None no Caucasian USA 0 Never 2191:3749289896 yes 78665 -97.6222665 Moderate None None None no None UBERON:feces None None None None 7680 None Stool More than one year ago GAZ:United States of America In the past year None human gut metagenome None None 16S rRNA sequencing by synthesis Not in the last year FWD:GTGCCAGCMGCCGCGGTAA; REV:GGACTACHVGGGTWTCTAAT no 15.49469388 ENVO:urban biome None Regularly (3-5 times/week) no None None CCME yes years None This analysis was done as in Caporaso et al 2011 Genome research. The PCR primers (F515/R806) were developed against the V4 region of the 16S rRNA (both bacteria and archaea), which we determined would yield optimal community clustering with reads of this length using a procedure similar to that of ref. 15. [For reference, this primer pair amplifies the region 533_786 in the Escherichia coli strain 83972 sequence (greengenes accession no. prokMSA_id:470367).] The reverse PCR primer is barcoded with a 12-base error-correcting Golay code to facilitate multiplexing of up to 1,500 samples per lane, and both PCR primers contain sequencer adapter regions. American Gut Project Stool sample None Daily 6/8/11 no None ENVO:feces None I do not have a skin condition None no no V4 American Gut Project 35 Penis Infection no human None None None male None Outdoors 11/12/13 0.0 None no Less than 25% None no None 7680 no Mother, Father None .1,g yes Never None None Never None CCME UBERON:feces right None no no ENVO:human-associated habitat Tummy Tonic, Cod Liver Oil, Wet Cough Syrup, Probiotics 1:50 PM no Bottled None 8 or more hours Omnivore CCME None CCME no 89.0 None I do not have IBD yes 0 9606 MiSeq 408170 21 to 30 None None None None no AGP6_rerun_L001 no Illumina I do not use deodorant or antiperspirant Cat, Moderate, Outdoor yes Sweet Potatoes 27 None no None MiSeq1 2191 None Fecal, oral and skin samples from round 3 MiSeq None Remained stable Rice I do not have diabetes round rock no Rarely (few times/month) no TX None 30.5464236 None no no American_Gut_round 6
000010179.1212981 ACCTCAGTCAAG GTGTGCCAGCMGCCGCGGTAA 60 More than one year ago None n 12/18/13 yes 72.0 88.0 None UBERON:feces Lack of sleep None no Foods; other 233.4643402 Housing... Daily 30 no Caucasian USA 100 Never 2191:1746649926 yes 75025 -96.7601057 Contact... None None None no None UBERON:feces None A few times a year notsure 20 10179 yes Stool More than one year ago GAZ:United States of America Not in the last year None human gut metagenome None yes 16S rRNA sequencing by synthesis In the past month FWD:GTGCCAGCMGCCGCGGTAA; REV:GGACTACHVGGGTWTCTAAT yes 25.16216216 ENVO:urban biome None Daily no imitrex None CCME yes years None This analysis was done as in Caporaso et al 2011 Genome research. The PCR primers (F515/R806) were developed against the V4 region of the 16S rRNA (both bacteria and archaea), which we determined would yield optimal community clustering with reads of this length using a procedure similar to that of ref. 15. [For reference, this primer pair amplifies the region 533_786 in the Escherichia coli strain 83972 sequence (greengenes accession no. prokMSA_id:470367).] The reverse PCR primer is barcoded with a 12-base error-correcting Golay code to facilitate multiplexing of up to 1,500 samples per lane, and both PCR primers contain sequencer adapter regions. American Gut Project Stool sample None Daily 7/5/42 no None ENVO:feces None I do not have a skin condition None no no V4 American Gut Project 74 None no human None None None male None Both 11/11/13 0.0 None no Less than 25% 10 no None 10179 yes None None .1,g no Never None None Never None CCME UBERON:feces left None yes no ENVO:human-associated habitat None 10:25 AM no Filtered None 7-8 hours Omnivore CCME exhaustive list of food intolerances CCME no 188.0 None I do not have IBD no 0 9606 MiSeq 408170 6 to 10 yes 140 None None no AGP6_rerun_L001 no Illumina Not sure, but I use some form of deodorant/antiperspirant Contact..., Housing... no sweet potato 196 None no 80 MiSeq1 2191 None Fecal, oral and skin samples from round 3 MiSeq None Remained stable grains I do not have diabetes plano no Never no TX None 33.0869379 None yes no American_Gut_round 6
000009541.1212994 GACGCACTAACT GTGTGCCAGCMGCCGCGGTAA 50 Within the past 3 months None n 12/18/13 None 59.0 65.0 None UBERON:feces None None no None 185.0700836 Housing... Daily 23 no Caucasian Canada 100 Never 2191:3116402903 no L0S 1E3 -79.2831681 Contact... None None None no None UBERON:feces None None None 50 9541 None Stool More than one year ago GAZ:Canada In the past 6 months None human gut metagenome None None 16S rRNA sequencing by synthesis Not in the last year FWD:GTGCCAGCMGCCGCGGTAA; REV:GGACTACHVGGGTWTCTAAT no 25.68279164 ENVO:urban biome None Daily no None No CCME yes years None This analysis was done as in Caporaso et al 2011 Genome research. The PCR primers (F515/R806) were developed against the V4 region of the 16S rRNA (both bacteria and archaea), which we determined would yield optimal community clustering with reads of this length using a procedure similar to that of ref. 15. [For reference, this primer pair amplifies the region 533_786 in the Escherichia coli strain 83972 sequence (greengenes accession no. prokMSA_id:470367).] The reverse PCR primer is barcoded with a 12-base error-correcting Golay code to facilitate multiplexing of up to 1,500 samples per lane, and both PCR primers contain sequencer adapter regions. American Gut Project Stool sample None Occasionally (1-2 times/week) 4/2/55 no None ENVO:feces None I do not have a skin condition None no no V4 American Gut Project 63 tooth abcess no human None None None female None Depends on the season 9/26/13 0.0 None no Less than 25% 27 no None 9541 no son None .1,g no Never None None Regularly (3-5 times/week) None CCME UBERON:feces right None yes no ENVO:human-associated habitat None 12:30 PM no Filtered None 6-7 hours Omnivore CCME no gmo products; organic dairy and organic meats and veggies CCME no 160.0 can't recall: first time on antibiotics in over 40 years I do not have IBD yes 0 9606 MiSeq 408170 11 to 20 None 250 None None no AGP6_rerun_L001 no Illumina I do not use deodorant or antiperspirant Contact..., Housing... no none; always a variety 145 None no 50 MiSeq1 2191 None Fecal, oral and skin samples from round 3 MiSeq None None brown rice I do not have diabetes fonthill no Never no ONTARIO None 43.0514979 None yes no American_Gut_round 6
000010871.1213068 TTGGATTGAACG GTGTGCCAGCMGCCGCGGTAA 41 More than one year ago None n 12/18/13 None 32.0 52.0 None UBERON:feces None None no None 7.929883003 Indoor Daily 27 no Caucasian USA 100 Daily 2191:1590655850 yes 95834 -121.5255815 Extensive None None None no None UBERON:feces None None None 14 10871 None Stool More than one year ago GAZ:United States of America Not in the last year None human gut metagenome None None 16S rRNA sequencing by synthesis In the past month FWD:GTGCCAGCMGCCGCGGTAA; REV:GGACTACHVGGGTWTCTAAT no None ENVO:urban biome None Daily no None No CCME no years None This analysis was done as in Caporaso et al 2011 Genome research. The PCR primers (F515/R806) were developed against the V4 region of the 16S rRNA (both bacteria and archaea), which we determined would yield optimal community clustering with reads of this length using a procedure similar to that of ref. 15. [For reference, this primer pair amplifies the region 533_786 in the Escherichia coli strain 83972 sequence (greengenes accession no. prokMSA_id:470367).] The reverse PCR primer is barcoded with a 12-base error-correcting Golay code to facilitate multiplexing of up to 1,500 samples per lane, and both PCR primers contain sequencer adapter regions. American Gut Project Stool sample spray Regularly (3-5 times/week) 6/30/82 no yes ENVO:feces None I do not have a skin condition None no no V4 American Gut Project None None no human None None None female None Indoors 11/10/13 0.0 None no 51 to 75% 32 no None 10871 yes None None .1,g yes Never None None Occasionally (1-2 times/week) None CCME UBERON:feces right None no no ENVO:human-associated habitat Greens Supplement (Athletic Greens and similar products), Glutamine, BCAA, Calcium + Vitamin D 1:30 PM no Filtered None 6-7 hours Omnivore CCME None CCME yes None None I do not have IBD yes 0 9606 MiSeq 408170 More than 30 None 125 None None no AGP6_rerun_L001 no Illumina I use an antiperspirant Cats, Extensive, Indoor yes broccoli 116 None no 86 MiSeq1 2191 None Fecal, oral and skin samples from round 3 MiSeq None Remained stable oats I do not have diabetes sacramento no Rarely (few times/month) no CA None 38.6418022 None no no American_Gut_round 6
000002822.1213019 GATGACCCAAAT GTGTGCCAGCMGCCGCGGTAA 46 Within the past year None n 12/18/13 None 36.0 68.0 None UBERON:feces None None no None 17.75139427 Confined Rarely (few times/month) 18 no Caucasian United Kingdom 100 Never 2191:1484361676 no 95616 -121.7405167 Little None None None no None UBERON:feces None None None 80 2822 None Stool More than one year ago GAZ:United States of America Not in the last year None human gut metagenome None None 16S rRNA sequencing by synthesis In the past 6 months FWD:GTGCCAGCMGCCGCGGTAA; REV:GGACTACHVGGGTWTCTAAT no 24.20798898 ENVO:urban biome None Daily no None I use the NuvaRing CCME no years None This analysis was done as in Caporaso et al 2011 Genome research. The PCR primers (F515/R806) were developed against the V4 region of the 16S rRNA (both bacteria and archaea), which we determined would yield optimal community clustering with reads of this length using a procedure similar to that of ref. 15. [For reference, this primer pair amplifies the region 533_786 in the Escherichia coli strain 83972 sequence (greengenes accession no. prokMSA_id:470367).] The reverse PCR primer is barcoded with a 12-base error-correcting Golay code to facilitate multiplexing of up to 1,500 samples per lane, and both PCR primers contain sequencer adapter regions. American Gut Project Stool sample None Occasionally (1-2 times/week) 12/29/77 no None ENVO:feces None I do not have a skin condition None yes no V4 American Gut Project 66 skin rash no human None None None female None Both 11/15/13 0.0 None no 25 to 50% 36 no None 2822 no None None .1,g no Never None None Regularly (3-5 times/week) None CCME UBERON:feces right None no no ENVO:human-associated habitat None 11:10 AM no City None 7-8 hours Omnivore CCME None CCME no 168.0 None I do not have IBD yes 0 9606 MiSeq 408170 6 to 10 None 119 None None yes AGP6_rerun_L001 no Illumina I use deodorant bearded dragon, Little, Confined yes onion 150 None no 20 MiSeq1 2191 None Fecal, oral and skin samples from round 3 MiSeq None Remained stable pasta I do not have diabetes davis no Rarely (few times/month) no CA None 38.5449065 None yes yes American_Gut_round 6
000009593.1212955 AGCGCTCACATC GTGTGCCAGCMGCCGCGGTAA None More than one year ago None n 12/18/13 yes 53.0 83.0 None UBERON:feces None None no None 240.3143158 Outdoor Rarely (few times/month) None no Caucasian USA 15 Never 2191:56075626 no 29625 -82.6501332 Little None None None no None UBERON:feces None None None 20 9593 None Stool More than one year ago GAZ:United States of America Not in the last year None human gut metagenome None None 16S rRNA sequencing by synthesis Not in the last year FWD:GTGCCAGCMGCCGCGGTAA; REV:GGACTACHVGGGTWTCTAAT no 27.31674018 ENVO:urban biome None Daily no None None CCME no years None This analysis was done as in Caporaso et al 2011 Genome research. The PCR primers (F515/R806) were developed against the V4 region of the 16S rRNA (both bacteria and archaea), which we determined would yield optimal community clustering with reads of this length using a procedure similar to that of ref. 15. [For reference, this primer pair amplifies the region 533_786 in the Escherichia coli strain 83972 sequence (greengenes accession no. prokMSA_id:470367).] The reverse PCR primer is barcoded with a 12-base error-correcting Golay code to facilitate multiplexing of up to 1,500 samples per lane, and both PCR primers contain sequencer adapter regions. American Gut Project Stool sample None Regularly (3-5 times/week) 11/12/60 no None ENVO:feces None I do not have a skin condition None no no V4 American Gut Project 69 None yes human None None None male None Outdoors 10/24/13 0.0 yes no Less than 25% None no None 9593 no None None .1,g no Never yes None Daily None CCME UBERON:feces right None no no ENVO:human-associated habitat None 9:45 AM None City None 8 or more hours Omnivore CCME None CCME no 175.0 None I do not have IBD no 0 9606 MiSeq 408170 11 to 20 None 110 None None None AGP6_rerun_L001 no Illumina I use an antiperspirant 1, Little, Outdoor yes apple 185 None no 80 MiSeq1 2191 None Fecal, oral and skin samples from round 3 MiSeq None Remained stable potatoe I do not have diabetes anderson no Rarely (few times/month) no SC None 34.5034394 None yes None American_Gut_round 6
000004284.1213139 AAGACGTAGCGG GTGTGCCAGCMGCCGCGGTAA 51 Within the past month None n 12/18/13 None 28.0 90.0 None UBERON:feces None None no None 298.0795593 Housing... Daily 20 no Caucasian USA 100 Rarely (few times/month) 2191:1703894371 no 91104 -118.1181199 Contact... None None None no None UBERON:feces None None None 50 4284 None Stool Within the past 3 months GAZ:United States of America Not in the last year None human gut metagenome None None 16S rRNA sequencing by synthesis Not in the last year FWD:GTGCCAGCMGCCGCGGTAA; REV:GGACTACHVGGGTWTCTAAT no 30.40657439 ENVO:urban biome None Daily no None I use the NuvaRing CCME no years None This analysis was done as in Caporaso et al 2011 Genome research. The PCR primers (F515/R806) were developed against the V4 region of the 16S rRNA (both bacteria and archaea), which we determined would yield optimal community clustering with reads of this length using a procedure similar to that of ref. 15. [For reference, this primer pair amplifies the region 533_786 in the Escherichia coli strain 83972 sequence (greengenes accession no. prokMSA_id:470367).] The reverse PCR primer is barcoded with a 12-base error-correcting Golay code to facilitate multiplexing of up to 1,500 samples per lane, and both PCR primers contain sequencer adapter regions. American Gut Project Stool sample None Regularly (3-5 times/week) 2/13/86 no yes ENVO:feces None I do not have a skin condition None yes no V4 American Gut Project 68 None no human None More than three None female None Both 10/2/13 0.0 None no 25 to 50% 29 yes None 4284 no None None .1,g no Never None None Regularly (3-5 times/week) None CCME UBERON:feces right None no no ENVO:human-associated habitat None 11:00 PM no Filtered no 7-8 hours Omnivore CCME None CCME no 173.0 None I do not have IBD no 0 9606 MiSeq 408170 21 to 30 None 23 None None no AGP6_rerun_L001 no Illumina I use an antiperspirant Contact..., Housing... no onions 200 None no 50 MiSeq1 2191 None Fecal, oral and skin samples from round 3 MiSeq None Remained stable bread I do not have diabetes pasadena no Occasionally (1-2 times/week) no CA no 34.1657707 None yes yes American_Gut_round 6
000009148.1213122 GCGGACTATTCA GTGTGCCAGCMGCCGCGGTAA 35 Within the past month None n 12/18/13 yes 44.0 70.0 None UBERON:feces None None no None 22.64736938 Indoor Rarely (few times/month) 25 no Caucasian USA 100 Never 2191:436848285 no 21620 -76.0690036 Moderate None None None no None UBERON:feces None None None 10 9148 None Stool More than one year ago GAZ:United States of America Not in the last year None human gut metagenome None None 16S rRNA sequencing by synthesis Not in the last year FWD:GTGCCAGCMGCCGCGGTAA; REV:GGACTACHVGGGTWTCTAAT no None ENVO:urban biome None Daily no None None CCME no years None This analysis was done as in Caporaso et al 2011 Genome research. The PCR primers (F515/R806) were developed against the V4 region of the 16S rRNA (both bacteria and archaea), which we determined would yield optimal community clustering with reads of this length using a procedure similar to that of ref. 15. [For reference, this primer pair amplifies the region 533_786 in the Escherichia coli strain 83972 sequence (greengenes accession no. prokMSA_id:470367).] The reverse PCR primer is barcoded with a 12-base error-correcting Golay code to facilitate multiplexing of up to 1,500 samples per lane, and both PCR primers contain sequencer adapter regions. American Gut Project Stool sample None Occasionally (1-2 times/week) 8/11/70 no None ENVO:feces None I do not have a skin condition None yes no V4 American Gut Project None None no human None None None male None Outdoors 11/15/13 0.0 None no 51 to 75% 40 no None 9148 no None None .1,g yes Never yes None Occasionally (1-2 times/week) None CCME UBERON:feces left None no no ENVO:human-associated habitat fish oil 1:00 PM no Bottled None 6-7 hours Omnivore CCME None CCME yes None None I do not have IBD yes 0 9606 MiSeq 408170 6 to 10 None 23 None None no AGP6_rerun_L001 no Illumina I do not use deodorant or antiperspirant cat, Moderate, Indoor yes spinach 155 None no 90 MiSeq1 2191 eggs Fecal, oral and skin samples from round 3 MiSeq None Remained stable pasta I do not have diabetes chestertown no Rarely (few times/month) no MD None 39.2188663 None yes no American_Gut_round 6
000009678.1213066 TGTGTAGCCATG GTGTGCCAGCMGCCGCGGTAA 45 Within the past year None n 12/18/13 None 68.0 86.0 None UBERON:feces None None yes None 229.4727325 Housing... Daily 23 no Caucasian USA 100 Never 2191:3695473817 no 94705 -122.2341905 Contact... None None None no None UBERON:feces None None None 80 9678 None Stool More than one year ago GAZ:United States of America Not in the last year None human gut metagenome None None 16S rRNA sequencing by synthesis In the past year FWD:GTGCCAGCMGCCGCGGTAA; REV:GGACTACHVGGGTWTCTAAT no 28.35034657 ENVO:urban biome None Daily no None None CCME yes years None This analysis was done as in Caporaso et al 2011 Genome research. The PCR primers (F515/R806) were developed against the V4 region of the 16S rRNA (both bacteria and archaea), which we determined would yield optimal community clustering with reads of this length using a procedure similar to that of ref. 15. [For reference, this primer pair amplifies the region 533_786 in the Escherichia coli strain 83972 sequence (greengenes accession no. prokMSA_id:470367).] The reverse PCR primer is barcoded with a 12-base error-correcting Golay code to facilitate multiplexing of up to 1,500 samples per lane, and both PCR primers contain sequencer adapter regions. American Gut Project Stool sample None Regularly (3-5 times/week) 4/10/46 no None ENVO:feces None Psoriasis None yes no V4 American Gut Project 69 None yes human None None None male None Outdoors 9/13/13 0.0 None no Less than 25% 32 no None 9678 on son None .1,g no Never yes None Regularly (3-5 times/week) None CCME UBERON:feces unknown None yes no ENVO:human-associated habitat None 11:00 AM no City None 6-7 hours Omnivore CCME low carb CCME no 175.0 None I do not have IBD no 0 9606 MiSeq 408170 11 to 20 None 300 None None no AGP6_rerun_L001 no Illumina I use an antiperspirant Contact..., Housing... no brocolli 192 None no 20 MiSeq1 2191 None Fecal, oral and skin samples from round 3 MiSeq None Remained stable friut I do not have diabetes berkeley no Occasionally (1-2 times/week) no CA None 37.8646149 None yes yes American_Gut_round 6
000003285.1213029 TCCATCGACGTG GTGTGCCAGCMGCCGCGGTAA 39 Within the past 3 months None n 12/18/13 None 37.0 61.0 None UBERON:feces Lack of sleep Stress no Foods; other 1575.246948 Indoor Occasionally (1-2 times/week) 19 no Hispanic USA 100 Rarely (few times/month) 2191:1372960439 yes 80301 -105.2077798 Extensive yes yes None no None UBERON:feces None Monthly yes 30 3285 yes Stool More than one year ago GAZ:United States of America Not in the last year yes human gut metagenome None yes 16S rRNA sequencing by synthesis Not in the last year FWD:GTGCCAGCMGCCGCGGTAA; REV:GGACTACHVGGGTWTCTAAT yes 23.91156463 ENVO:urban biome None Daily no None No CCME yes years Novolog This analysis was done as in Caporaso et al 2011 Genome research. The PCR primers (F515/R806) were developed against the V4 region of the 16S rRNA (both bacteria and archaea), which we determined would yield optimal community clustering with reads of this length using a procedure similar to that of ref. 15. [For reference, this primer pair amplifies the region 533_786 in the Escherichia coli strain 83972 sequence (greengenes accession no. prokMSA_id:470367).] The reverse PCR primer is barcoded with a 12-base error-correcting Golay code to facilitate multiplexing of up to 1,500 samples per lane, and both PCR primers contain sequencer adapter regions. American Gut Project Stool sample None Occasionally (1-2 times/week) 3/2/77 no None ENVO:feces None I do not have a skin condition yes yes no V4 American Gut Project 63 None yes human None None None female yes Depends on the season 8/29/13 0.0 None no 25 to 50% 42 no None 3285 no partner None .1,g yes Never yes None Rarely (few times/month) None CCME UBERON:feces right 6/10/99 no no ENVO:human-associated habitat Omega 3, magnesium, zinc 2:30 PM no Bottled None 8 or more hours Omnivore CCME None CCME no 160.0 None I do not have IBD no 0 9606 MiSeq 408170 6 to 10 no 80 None None no AGP6_rerun_L001 no Illumina I use an antiperspirant 1, Extensive, Indoor no corn 135 None no 70 MiSeq1 2191 soy Fecal, oral and skin samples from round 3 MiSeq yes Increased more than 10 pounds corn tortillas Type I boulder no Rarely (few times/month) no CO None 40.0406506 None yes yes American_Gut_round 6
000010941.1213015 TTACCTTACACC GTGTGCCAGCMGCCGCGGTAA 49 More than one year ago None n 12/18/13 None 57.0 63.0 None UBERON:feces None None yes None 70.78269196 Indoor Occasionally (1-2 times/week) 19 yes Caucasian USA 100 Daily 2191:3274592737 no 2072 -71.1027778 Extensive None None None no None UBERON:feces None None None 50 10941 None Stool More than one year ago GAZ:United States of America In the past year None human gut metagenome None None 16S rRNA sequencing by synthesis In the past month FWD:GTGCCAGCMGCCGCGGTAA; REV:GGACTACHVGGGTWTCTAAT no 27.33888889 ENVO:urban biome None Daily no None No CCME no years None This analysis was done as in Caporaso et al 2011 Genome research. The PCR primers (F515/R806) were developed against the V4 region of the 16S rRNA (both bacteria and archaea), which we determined would yield optimal community clustering with reads of this length using a procedure similar to that of ref. 15. [For reference, this primer pair amplifies the region 533_786 in the Escherichia coli strain 83972 sequence (greengenes accession no. prokMSA_id:470367).] The reverse PCR primer is barcoded with a 12-base error-correcting Golay code to facilitate multiplexing of up to 1,500 samples per lane, and both PCR primers contain sequencer adapter regions. American Gut Project Stool sample None Occasionally (1-2 times/week) 10/13/56 no yes ENVO:feces None I do not have a skin condition None yes no V4 American Gut Project 60 None no human None None None female None Indoors 11/4/13 0.0 None no Less than 25% 32 no None 10941 no None None .1,g yes Never None None Occasionally (1-2 times/week) None CCME UBERON:feces ambidextrous None yes no ENVO:human-associated habitat VSL3, Digestive Advantage for lactose intolerance, vitamin D 2000 iu, Biotin 2500 mcgs 8:35 AM yes Well None 6-7 hours Omnivore CCME FODMPA diet CCME yes 152.0 None I do not have IBD yes 0 9606 MiSeq 408170 None None 145 None None no AGP6_rerun_L001 no Illumina I use deodorant tuxedo, Extensive, Indoor no carrots 140 None no 50 MiSeq1 2191 maybe shellfish, not sure, first alergic reaction two nights ago but not sure to what Fecal, oral and skin samples from round 3 MiSeq None Remained stable breads I do not have diabetes stoughton yes Never no MA None 42.125 None yes no American_Gut_round 6
000006915.1213116 AAGTGGCTATCC GTGTGCCAGCMGCCGCGGTAA 42 Within the past month None n 12/18/13 None 49.0 67.0 None UBERON:feces None None no None 33.25356674 Indoor Rarely (few times/month) 20 no Caucasian USA 100 Regularly (3-5 times/week) 2191:699351296 yes 7921 -74.6751731 Extensive None None None no None UBERON:feces None None None 80 6915 None Stool More than one year ago GAZ:United States of America Not in the last year None human gut metagenome None None 16S rRNA sequencing by synthesis Not in the last year FWD:GTGCCAGCMGCCGCGGTAA; REV:GGACTACHVGGGTWTCTAAT no 24.04660239 ENVO:urban biome None Regularly (3-5 times/week) no None None CCME yes years None This analysis was done as in Caporaso et al 2011 Genome research. The PCR primers (F515/R806) were developed against the V4 region of the 16S rRNA (both bacteria and archaea), which we determined would yield optimal community clustering with reads of this length using a procedure similar to that of ref. 15. [For reference, this primer pair amplifies the region 533_786 in the Escherichia coli strain 83972 sequence (greengenes accession no. prokMSA_id:470367).] The reverse PCR primer is barcoded with a 12-base error-correcting Golay code to facilitate multiplexing of up to 1,500 samples per lane, and both PCR primers contain sequencer adapter regions. American Gut Project Stool sample spray Rarely (few times/month) 8/1/65 no None ENVO:feces None I do not have a skin condition None no no V4 American Gut Project 66 None yes human None None None unknown None Outdoors 10/11/13 0.0 None no Less than 25% 38 no None 6915 no parent, dog None .1,g yes Never yes None Rarely (few times/month) None CCME UBERON:feces right None None no ENVO:human-associated habitat Green Coffee Bean Extract, Flax Seed Oil 11:00 AM no Filtered None 5-6 hours Omnivore CCME None CCME yes 168.0 None I do not have IBD no 0 9606 MiSeq 408170 11 to 20 None 21 None None no AGP6_rerun_L001 no Illumina I use deodorant Extensive, Indoor yes Spinach 149 None no 20 MiSeq1 2191 Anything with pollen (Honey, Chamomile, Saffron,) Fecal, oral and skin samples from round 3 MiSeq yes Remained stable Rice I do not have diabetes bedminster no Rarely (few times/month) no NJ None 40.6431955 None yes yes American_Gut_round 6
000002322.1213016 AGGGAAAGGATC GTGTGCCAGCMGCCGCGGTAA 36 More than one year ago None n 5/20/13 None 72.0 65.0 None UBERON:feces None None yes None 238.0722656 None Daily 27 no Hispanic USA 100 Never 2191:3615971002 no 52556 -91.9658333 None None None None no None UBERON:feces None None None 40 2322 None Stool More than one year ago GAZ:United States of America Not in the last year None human gut metagenome None None 16S rRNA sequencing by synthesis Not in the last year FWD:GTGCCAGCMGCCGCGGTAA; REV:GGACTACHVGGGTWTCTAAT no 24.88647461 ENVO:urban biome None Daily no None None CCME no years None This analysis was done as in Caporaso et al 2011 Genome research. The PCR primers (F515/R806) were developed against the V4 region of the 16S rRNA (both bacteria and archaea), which we determined would yield optimal community clustering with reads of this length using a procedure similar to that of ref. 15. [For reference, this primer pair amplifies the region 533_786 in the Escherichia coli strain 83972 sequence (greengenes accession no. prokMSA_id:470367).] The reverse PCR primer is barcoded with a 12-base error-correcting Golay code to facilitate multiplexing of up to 1,500 samples per lane, and both PCR primers contain sequencer adapter regions. American Gut Project Stool sample None Occasionally (1-2 times/week) 5/2/42 no yes ENVO:feces None I do not have a skin condition None no no V4 American Gut Project 64 None no human None None None male None Indoors 3/3/13 0.0 None no 51 to 75% 37 no None 2322 no None None .1,g yes Never None None Never None CCME UBERON:feces right None no no ENVO:human-associated habitat Vit A, Fish oil, Juvenon (Acetyl L-Carnitine, Alpha Lipoic Acid, Biotin, Calcium, Phosphorus), Longevinex (resveratrol, rice bran phytate, quercetin, ferulic acid, nucleotides), Vit B Complex, Vit C, Vit D3, Vit E, Co Q-10, Chondrotin, Glucosamine, MSM 6:30 AM no Bottled None 8 or more hours Omnivore CCME None CCME no 163.0 None I do not have IBD no 0 9606 MiSeq 408170 More than 30 None 30 None None yes Knight_AFG_16s_w_phiX_NoIndex_L001 no Illumina I do not use deoderant or antiperspirant None no Spinich 145 None no 60 MiSeq1 2191 None Fecal, oral and skin samples from round 3 MiSeq None Increased more than 10 pounds Beans I do not have diabetes fairfield no Never None IA None 41.0072222 None no no American_Gut_round 6
000001780.1213073 GCTGTGATTCGA GTGTGCCAGCMGCCGCGGTAA 50 More than one year ago None n 12/18/13 None 61.0 95.0 None UBERON:feces None None no None 23.11036301 None Daily 25 no Caucasian USA 100 Never 2191:1532130940 no 97209 -122.6880503 None None yes None no None UBERON:feces None None None 75 1780 None Stool More than one year ago GAZ:United States of America Not in the last year None human gut metagenome None None 16S rRNA sequencing by synthesis In the past year FWD:GTGCCAGCMGCCGCGGTAA; REV:GGACTACHVGGGTWTCTAAT no 26.95945946 ENVO:urban biome None Daily no None None CCME no years Metformin, Insulin, Actos This analysis was done as in Caporaso et al 2011 Genome research. The PCR primers (F515/R806) were developed against the V4 region of the 16S rRNA (both bacteria and archaea), which we determined would yield optimal community clustering with reads of this length using a procedure similar to that of ref. 15. [For reference, this primer pair amplifies the region 533_786 in the Escherichia coli strain 83972 sequence (greengenes accession no. prokMSA_id:470367).] The reverse PCR primer is barcoded with a 12-base error-correcting Golay code to facilitate multiplexing of up to 1,500 samples per lane, and both PCR primers contain sequencer adapter regions. American Gut Project Stool sample None Regularly (3-5 times/week) 10/14/52 no None ENVO:feces None I do not have a skin condition None yes no V4 American Gut Project 74 None yes human None None None male None Outdoors 10/9/13 0.0 None no 51 to 75% 25 no None 1780 no None None .1,g yes Never None None Daily None CCME UBERON:feces right 4/15/92 yes no ENVO:human-associated habitat Grape seed extract 10:15 AM no Bottled None 7-8 hours Omnivore CCME Diabetic CCME no 188.0 None I do not have IBD no 0 9606 MiSeq 408170 Less than 5 None 32.5 None None no AGP6_rerun_L001 no Illumina I do not use deodorant or antiperspirant dogs yes greens 210 None no 25 MiSeq1 2191 None Fecal, oral and skin samples from round 3 MiSeq None Remained stable bread/pasta Type II portland no Never no OR None 45.5266975 None yes yes American_Gut_round 6
000007650.1213058 GAGGACCAGCAA GTGTGCCAGCMGCCGCGGTAA 50 More than one year ago None n 12/18/13 None 44.0 68.0 None UBERON:feces None None None None 67.53837585 Indoor, Outdoor Daily 16 no Caucasian USA 100 Never 2191:233449747 no 92009 -117.2499749 Extensive, Moderate None None None no None UBERON:feces None None None 90 7650 None Stool More than one year ago GAZ:United States of America In the past year None human gut metagenome None None 16S rRNA sequencing by synthesis In the past year FWD:GTGCCAGCMGCCGCGGTAA; REV:GGACTACHVGGGTWTCTAAT no 20.91846856 ENVO:urban biome None Daily no None None CCME yes years None This analysis was done as in Caporaso et al 2011 Genome research. The PCR primers (F515/R806) were developed against the V4 region of the 16S rRNA (both bacteria and archaea), which we determined would yield optimal community clustering with reads of this length using a procedure similar to that of ref. 15. [For reference, this primer pair amplifies the region 533_786 in the Escherichia coli strain 83972 sequence (greengenes accession no. prokMSA_id:470367).] The reverse PCR primer is barcoded with a 12-base error-correcting Golay code to facilitate multiplexing of up to 1,500 samples per lane, and both PCR primers contain sequencer adapter regions. American Gut Project Stool sample None Daily 10/11/69 no yes ENVO:feces None I do not have a skin condition None no no V4 American Gut Project 71 None no human None None None male None Both 10/2/13 0.0 None no 51 to 75% 34 no None 7650 None spouse None .1,g no Never None None Regularly (3-5 times/week) None CCME UBERON:feces right None no no ENVO:human-associated habitat None 11:00 AM None Filtered None 6-7 hours Vegetarian but eat seafood CCME None CCME no 180.0 None I do not have IBD yes 0 9606 MiSeq 408170 11 to 20 None 230 None None yes AGP6_rerun_L001 no Illumina I use deodorant cat, cat, Extensive, Moderate, Indoor, Outdoor no greens 150 None no 10 MiSeq1 2191 None Fecal, oral and skin samples from round 3 MiSeq None Remained stable wheat I do not have diabetes carlsbad None Occasionally (1-2 times/week) no CA None 33.095442 None yes no American_Gut_round 6
000001646.1213145 CAGCCGCATATC GTGTGCCAGCMGCCGCGGTAA 30 Never None n 5/20/13 None 63.0 83.0 None UBERON:not_feces None None yes None 99.74677277 None Regularly (3-5 times/week) 60 no Caucasian USA 100 Never 2191:1946244162 no 92084 -117.2425355 None None None None no None UBERON:not_feces None None None 25 1646 None Stool More than one year ago GAZ:United States of America Not in the last year None human gut metagenome None None 16S rRNA sequencing by synthesis Not in the last year FWD:GTGCCAGCMGCCGCGGTAA; REV:GGACTACHVGGGTWTCTAAT no None ENVO:urban biome None Regularly (3-5 times/week) no None None CCME no years None This analysis was done as in Caporaso et al 2011 Genome research. The PCR primers (F515/R806) were developed against the V4 region of the 16S rRNA (both bacteria and archaea), which we determined would yield optimal community clustering with reads of this length using a procedure similar to that of ref. 15. [For reference, this primer pair amplifies the region 533_786 in the Escherichia coli strain 83972 sequence (greengenes accession no. prokMSA_id:470367).] The reverse PCR primer is barcoded with a 12-base error-correcting Golay code to facilitate multiplexing of up to 1,500 samples per lane, and both PCR primers contain sequencer adapter regions. American Gut Project Stool sample None Daily 10/25/50 no None ENVO:feces None I do not have a skin condition None no no V4 American Gut Project None None yes human None None None male None Outdoors 3/25/13 0.0 None no Less than 25% 10 no None 1646 no None None .1,g yes Never None None Daily None CCME UBERON:not_feces right None no no ENVO:human-associated habitat Cayenne Pepper, Ginger, Turmeric 8:00 AM no Filtered None 7-8 hours Omnivore CCME None CCME no None None I do not have IBD no 0 9606 MiSeq 408170 6 to 10 None 140 None None no Knight_AFG_16s_w_phiX_NoIndex_L001 no Illumina I do not use deoderant or antiperspirant None no Cabbage 185 None no 75 MiSeq1 2191 None Fecal, oral and skin samples from round 3 MiSeq None Decreased more than 10 pounds Beans I do not have diabetes vista no Never no CA None 33.2000368 None yes no American_Gut_round 6
000010723.1213082 TCATTCCACTCA GTGTGCCAGCMGCCGCGGTAA 41 More than one year ago None n 12/18/13 None 56.0 99.0 None UBERON:feces None None yes None 314.2067261 Housing... Occasionally (1-2 times/week) 17 no Caucasian USA 100 Never 2191:3692484587 no 45429 -84.1540659 Contact... None None None no None UBERON:feces None None None 70 10723 None Stool Within the past year GAZ:United States of America Not in the last year None human gut metagenome None None 16S rRNA sequencing by synthesis In the past month FWD:GTGCCAGCMGCCGCGGTAA; REV:GGACTACHVGGGTWTCTAAT no 30.68042055 ENVO:urban biome None Daily no None None CCME no years None This analysis was done as in Caporaso et al 2011 Genome research. The PCR primers (F515/R806) were developed against the V4 region of the 16S rRNA (both bacteria and archaea), which we determined would yield optimal community clustering with reads of this length using a procedure similar to that of ref. 15. [For reference, this primer pair amplifies the region 533_786 in the Escherichia coli strain 83972 sequence (greengenes accession no. prokMSA_id:470367).] The reverse PCR primer is barcoded with a 12-base error-correcting Golay code to facilitate multiplexing of up to 1,500 samples per lane, and both PCR primers contain sequencer adapter regions. American Gut Project Stool sample None Regularly (3-5 times/week) 6/4/58 no None ENVO:feces None I do not have a skin condition None no None V4 American Gut Project 71 None no human None None None male None Indoors 11/4/13 0.0 None no More than 76% 42 no None 10723 no None None .1,g no Never yes None Never None CCME UBERON:feces right None no no ENVO:human-associated habitat None 6:45 AM no City None 6-7 hours Omnivore CCME None CCME no 180.0 None I do not have IBD no 0 9606 MiSeq 408170 6 to 10 None 134 None None yes AGP6_rerun_L001 no Illumina I use an antiperspirant Contact..., Housing... no leafy greens 220 None no 30 MiSeq1 2191 None Fecal, oral and skin samples from round 3 MiSeq None Remained stable bread I do not have diabetes kettering no Occasionally (1-2 times/week) no OH None 39.6801641 None yes yes American_Gut_round 6
000010936.1213013 GGCCTATAAGTC GTGTGCCAGCMGCCGCGGTAA 55 More than one year ago None n 12/18/13 None 61.0 95.0 None UBERON:feces None None None None 0.386727333 Housing... Daily 24 no Caucasian USA 100 Never 2191:2363046042 no 33702 -82.6321376 Contact... None None None no None UBERON:feces None None None 78 10936 None Stool More than one year ago GAZ:United States of America Not in the last year None human gut metagenome None None 16S rRNA sequencing by synthesis In the past week FWD:GTGCCAGCMGCCGCGGTAA; REV:GGACTACHVGGGTWTCTAAT no 36.04248047 ENVO:urban biome None Daily no None No CCME no years None This analysis was done as in Caporaso et al 2011 Genome research. The PCR primers (F515/R806) were developed against the V4 region of the 16S rRNA (both bacteria and archaea), which we determined would yield optimal community clustering with reads of this length using a procedure similar to that of ref. 15. [For reference, this primer pair amplifies the region 533_786 in the Escherichia coli strain 83972 sequence (greengenes accession no. prokMSA_id:470367).] The reverse PCR primer is barcoded with a 12-base error-correcting Golay code to facilitate multiplexing of up to 1,500 samples per lane, and both PCR primers contain sequencer adapter regions. American Gut Project Stool sample None Occasionally (1-2 times/week) 2/8/53 no None ENVO:feces None I do not have a skin condition None no no V4 American Gut Project 64 None no human None None None female None Outdoors 11/6/13 0.0 None no Less than 25% 21 no None 10936 no None None .1,g no Never None None Never None CCME UBERON:feces right None yes no ENVO:human-associated habitat None 5:45 AM no Filtered None 7-8 hours Omnivore CCME no processed sugar, flour or wheat CCME no 163.0 None I do not have IBD no 0 9606 MiSeq 408170 11 to 20 None 24 None None None AGP6_rerun_L001 no Illumina I do not use deodorant or antiperspirant Contact..., Housing... no kale 210 None no 22 MiSeq1 2191 None Fecal, oral and skin samples from round 3 MiSeq None Decreased more than 10 pounds brown rice I do not have diabetes saint petersburg no Occasionally (1-2 times/week) no FL None 27.8512042 None None no American_Gut_round 6
000007679.1212996 CGTAGAGCTCTC GTGTGCCAGCMGCCGCGGTAA None More than one year ago None n 12/18/13 yes 30.0 40.0 None UBERON:feces None None no None 218.3718414 Outdoor Rarely (few times/month) None no None USA 0 Daily 2191:973325923 yes 78665 -97.6222665 Extensive None None None no None UBERON:feces None None None None 7679 None Stool More than one year ago GAZ:United States of America In the past year None human gut metagenome None None 16S rRNA sequencing by synthesis Not in the last year FWD:GTGCCAGCMGCCGCGGTAA; REV:GGACTACHVGGGTWTCTAAT no None ENVO:urban biome None Daily no None No CCME yes years None This analysis was done as in Caporaso et al 2011 Genome research. The PCR primers (F515/R806) were developed against the V4 region of the 16S rRNA (both bacteria and archaea), which we determined would yield optimal community clustering with reads of this length using a procedure similar to that of ref. 15. [For reference, this primer pair amplifies the region 533_786 in the Escherichia coli strain 83972 sequence (greengenes accession no. prokMSA_id:470367).] The reverse PCR primer is barcoded with a 12-base error-correcting Golay code to facilitate multiplexing of up to 1,500 samples per lane, and both PCR primers contain sequencer adapter regions. American Gut Project Stool sample None Regularly (3-5 times/week) 11/1/83 no None ENVO:feces None I do not have a skin condition None no no V4 American Gut Project None Sinus Infection no human None None None female None Outdoors 11/12/13 0.0 None no Less than 25% None no None 7679 no Spouse, Son None .1,g yes Never None None Never None CCME UBERON:feces right None no no ENVO:human-associated habitat None 8:10 AM no Bottled None 6-7 hours Omnivore CCME None CCME no None None I do not have IBD yes 0 9606 MiSeq 408170 More than 30 None None None None no AGP6_rerun_L001 no Illumina I use deodorant Cat, Extensive, Outdoor yes Sweet Potatoes 89 None no None MiSeq1 2191 None Fecal, oral and skin samples from round 3 MiSeq None Remained stable Rice I do not have diabetes round rock no Rarely (few times/month) no TX None 30.5464236 None yes no American_Gut_round 6
000004216.1212989 CGCCATTGTGCA GTGTGCCAGCMGCCGCGGTAA 50 Within the past 3 months None n 12/18/13 yes 30.0 74.0 None UBERON:feces None None no None 1619.837158 Outdoor, Outdoor Regularly (3-5 times/week) 10 no Caucasian USA 100 Never 2191:4095514450 no 80303 -105.2077798 Moderate, Moderate None None None no None UBERON:feces None None None 90 4216 None Stool More than one year ago GAZ:United States of America Not in the last year None human gut metagenome yes None 16S rRNA sequencing by synthesis Not in the last year FWD:GTGCCAGCMGCCGCGGTAA; REV:GGACTACHVGGGTWTCTAAT no 23.01031541 ENVO:urban biome None Daily no None None CCME yes years None This analysis was done as in Caporaso et al 2011 Genome research. The PCR primers (F515/R806) were developed against the V4 region of the 16S rRNA (both bacteria and archaea), which we determined would yield optimal community clustering with reads of this length using a procedure similar to that of ref. 15. [For reference, this primer pair amplifies the region 533_786 in the Escherichia coli strain 83972 sequence (greengenes accession no. prokMSA_id:470367).] The reverse PCR primer is barcoded with a 12-base error-correcting Golay code to facilitate multiplexing of up to 1,500 samples per lane, and both PCR primers contain sequencer adapter regions. American Gut Project Stool sample None Regularly (3-5 times/week) 5/4/84 no None ENVO:feces None Eczema None no no V4 American Gut Project 71 None yes human None Three None unknown None Outdoors 10/15/13 0.0 None no Less than 25% 40 yes None 4216 no roommate None .1,g no Rarely (few times/month) None None Daily None CCME UBERON:feces right None no no ENVO:human-associated habitat None 9:30 AM no City no 6-7 hours Omnivore CCME None CCME no 180.0 None I do not have IBD no 0 9606 MiSeq 408170 11 to 20 None 267 None None yes AGP6_rerun_L001 no Illumina I use deodorant dog, dog, Moderate, Moderate, Outdoor, Outdoor no tomato 165 None no 10 MiSeq1 2191 None Fecal, oral and skin samples from round 3 MiSeq None Remained stable beer I do not have diabetes boulder no Rarely (few times/month) no CO no 40.0005378 None yes yes American_Gut_round 6
000010896.1213075 TAGCAGTTGCGT GTGTGCCAGCMGCCGCGGTAA None More than one year ago None n 12/18/13 None 56.0 65.0 None UBERON:feces None None yes None 70.64073944 Housing... Occasionally (1-2 times/week) None no Caucasian USA 0 Rarely (few times/month) 2191:2823808986 no 93109 -119.7252297 Contact... None None None yes None UBERON:feces None None None 40 10896 None Stool More than one year ago GAZ:United States of America In the past year None human gut metagenome None None 16S rRNA sequencing by synthesis In the past month FWD:GTGCCAGCMGCCGCGGTAA; REV:GGACTACHVGGGTWTCTAAT no 22.70773001 ENVO:urban biome None Daily no None No CCME no years None This analysis was done as in Caporaso et al 2011 Genome research. The PCR primers (F515/R806) were developed against the V4 region of the 16S rRNA (both bacteria and archaea), which we determined would yield optimal community clustering with reads of this length using a procedure similar to that of ref. 15. [For reference, this primer pair amplifies the region 533_786 in the Escherichia coli strain 83972 sequence (greengenes accession no. prokMSA_id:470367).] The reverse PCR primer is barcoded with a 12-base error-correcting Golay code to facilitate multiplexing of up to 1,500 samples per lane, and both PCR primers contain sequencer adapter regions. American Gut Project Stool sample None Regularly (3-5 times/week) 7/27/58 no None ENVO:feces None None None yes no V4 American Gut Project 67 mouth sore yes human None None None female None Depends on the season 11/13/13 0.0 None no Less than 25% None no None 10896 no None None .1,g no Never yes None Regularly (3-5 times/week) None CCME UBERON:feces ambidextrous None no no ENVO:human-associated habitat None 7:00 AM no Filtered None 8 or more hours Omnivore CCME None CCME no 170.0 amoxicillin None no 0 9606 MiSeq 408170 6 to 10 None 165 None None no AGP6_rerun_L001 no Illumina I use deodorant Contact..., Housing... no tomatoe 145 None no 60 MiSeq1 2191 None Fecal, oral and skin samples from round 3 MiSeq None Remained stable bread None santa barbara no Occasionally (1-2 times/week) no CA None 34.4038383 None yes no American_Gut_round 6
Blank33.C9.1212951 TACAGTTACGCG GTGTGCCAGCMGCCGCGGTAA None None None n 12/18/13 None None None None None None None None None 1624.1 None None None None None None None None 2191:unknown None 80309 -105.79 None None None None None None None None None None None Blank33.C9 None Blank None GAZ:United States of America None None unclassified metagenome None None 16S rRNA sequencing by synthesis None FWD:GTGCCAGCMGCCGCGGTAA; REV:GGACTACHVGGGTWTCTAAT None None ENVO:aquatic biome None None None None None CCME None years None This analysis was done as in Caporaso et al 2011 Genome research. The PCR primers (F515/R806) were developed against the V4 region of the 16S rRNA (both bacteria and archaea), which we determined would yield optimal community clustering with reads of this length using a procedure similar to that of ref. 15. [For reference, this primer pair amplifies the region 533_786 in the Escherichia coli strain 83972 sequence (greengenes accession no. prokMSA_id:470367).] The reverse PCR primer is barcoded with a 12-base error-correcting Golay code to facilitate multiplexing of up to 1,500 samples per lane, and both PCR primers contain sequencer adapter regions. American Gut Project blank None None None None None ENVO:sterile water None None None None None V4 American Gut Project None None None None None None None unknown None None None 0.0 None None None None None None Blank33.C9 None None None .1,g None None None None None None CCME None unknown None None None ENVO:water None None None None None None None CCME None CCME None None None None None 0 None MiSeq 408169 None None None None None None AGP6_rerun_L001 None Illumina None None None None None None None None MiSeq1 2191 None Fecal, oral and skin samples from round 3 MiSeq None None None None boulder None None None CO None 40.02 None None None American_Gut_round 20
000010178.1212990 TGAGGACTACCT GTGTGCCAGCMGCCGCGGTAA 30 More than one year ago None n 12/18/13 None 46.0 105.0 None UBERON:feces None None no None 265.861908 Housing... Daily 40 no Caucasian USA 100 Daily 2191:2368954623 yes 55408 -93.2935778 Contact... None None None no None UBERON:feces None None None 20 10178 None Stool More than one year ago GAZ:United States of America Not in the last year None human gut metagenome None None 16S rRNA sequencing by synthesis Not in the last year FWD:GTGCCAGCMGCCGCGGTAA; REV:GGACTACHVGGGTWTCTAAT no 38.76899408 ENVO:urban biome None Daily no None No CCME no years None This analysis was done as in Caporaso et al 2011 Genome research. The PCR primers (F515/R806) were developed against the V4 region of the 16S rRNA (both bacteria and archaea), which we determined would yield optimal community clustering with reads of this length using a procedure similar to that of ref. 15. [For reference, this primer pair amplifies the region 533_786 in the Escherichia coli strain 83972 sequence (greengenes accession no. prokMSA_id:470367).] The reverse PCR primer is barcoded with a 12-base error-correcting Golay code to facilitate multiplexing of up to 1,500 samples per lane, and both PCR primers contain sequencer adapter regions. American Gut Project Stool sample None Occasionally (1-2 times/week) 5/6/68 no yes ENVO:feces None I do not have a skin condition None yes no V4 American Gut Project 65 None None human None None None female None Indoors 11/1/13 0.0 None no Less than 25% 30 no None 10178 yes None None .1,g yes Never None None Occasionally (1-2 times/week) None CCME UBERON:feces unknown None no no ENVO:human-associated habitat Probiotic, Fish Oil 2:00 PM None City None 7-8 hours Omnivore CCME None CCME None 165.0 None I do not have IBD no 0 9606 MiSeq 408170 21 to 30 None 250 None None no AGP6_rerun_L001 no Illumina I use deodorant Contact..., Housing... yes leafy greens 233 None no 80 MiSeq1 2191 None Fecal, oral and skin samples from round 3 MiSeq None Remained stable Bread I do not have diabetes minneapolis no Never no MN None 44.9479791 None yes yes American_Gut_round 6
000006806.1212944 TCGTGGATAGCT GTGTGCCAGCMGCCGCGGTAA None More than one year ago None n 12/18/13 yes 35.0 51.0 None UBERON:feces None None no None 70.80503082 Housing... Daily None no Asian or Pacific Islander USA 0 Rarely (few times/month) 2191:2830528025 no 6611 -73.2006639 Contact... None None None no None UBERON:feces None None None 70 6806 None Stool More than one year ago GAZ:United States of America Not in the last year None human gut metagenome None None 16S rRNA sequencing by synthesis In the past month FWD:GTGCCAGCMGCCGCGGTAA; REV:GGACTACHVGGGTWTCTAAT no 20.84859521 ENVO:urban biome None Daily no None None CCME yes years None This analysis was done as in Caporaso et al 2011 Genome research. The PCR primers (F515/R806) were developed against the V4 region of the 16S rRNA (both bacteria and archaea), which we determined would yield optimal community clustering with reads of this length using a procedure similar to that of ref. 15. [For reference, this primer pair amplifies the region 533_786 in the Escherichia coli strain 83972 sequence (greengenes accession no. prokMSA_id:470367).] The reverse PCR primer is barcoded with a 12-base error-correcting Golay code to facilitate multiplexing of up to 1,500 samples per lane, and both PCR primers contain sequencer adapter regions. American Gut Project Stool sample None Rarely (few times/month) 5/22/79 no None ENVO:feces None Eczema None no no V4 American Gut Project 62 None no human None None None unknown None Depends on the season 9/27/13 0.0 None no None None no None 6806 yes daughter None .1,g yes Never None None Regularly (3-5 times/week) None CCME UBERON:feces right None no no ENVO:human-associated habitat DHA 10:00 AM no City None 7-8 hours Omnivore CCME None CCME no 157.0 None I do not have IBD no 0 9606 MiSeq 408170 11 to 20 None None None None no AGP6_rerun_L001 no Illumina I do not use deodorant or antiperspirant Contact..., Housing... yes Broccoli 114 None no 30 MiSeq1 2191 None Fecal, oral and skin samples from round 3 MiSeq None Decreased more than 10 pounds None I do not have diabetes trumbull no Never no CT None 41.2428563 None yes no American_Gut_round 6
000002321.1213070 GGTATGGCTACT GTGTGCCAGCMGCCGCGGTAA 49 None None n 5/20/13 None 72.0 61.0 None UBERON:feces None None yes None 238.0722656 None Daily 16 no Hispanic USA 100 Never 2191:1849354066 no 52556 -91.9658333 None None None None no None UBERON:feces None None None 35 2321 None Stool More than one year ago GAZ:United States of America Not in the last year None human gut metagenome None None 16S rRNA sequencing by synthesis Not in the last year FWD:GTGCCAGCMGCCGCGGTAA; REV:GGACTACHVGGGTWTCTAAT no None ENVO:urban biome None Daily no None None CCME no years None This analysis was done as in Caporaso et al 2011 Genome research. The PCR primers (F515/R806) were developed against the V4 region of the 16S rRNA (both bacteria and archaea), which we determined would yield optimal community clustering with reads of this length using a procedure similar to that of ref. 15. [For reference, this primer pair amplifies the region 533_786 in the Escherichia coli strain 83972 sequence (greengenes accession no. prokMSA_id:470367).] The reverse PCR primer is barcoded with a 12-base error-correcting Golay code to facilitate multiplexing of up to 1,500 samples per lane, and both PCR primers contain sequencer adapter regions. American Gut Project Stool sample None Daily 5/2/42 no yes ENVO:feces None I do not have a skin condition None no no V4 American Gut Project None None no human None None None male None Outdoors 1/28/13 0.0 None no 51 to 75% 35 no None 2321 no None None .1,g yes Never None None Never None CCME UBERON:feces right None no no ENVO:human-associated habitat Vit A, MSM, Co Q-10, Asprin, Juvenon (Acetyl L-Carnitine & Alpha Lipoic Acid), Longevinex (Resveratrol + other), Vit B Complex, B12, Vit C, Vit D (in other supplements), Vit E, Fish Oil, Glucosamine, Chondrotoin 6:30 AM no Bottled None 8 or more hours Omnivore CCME None CCME no None None I do not have IBD no 0 9606 MiSeq 408170 21 to 30 None 264 None None yes Knight_AFG_16s_w_phiX_NoIndex_L001 no Illumina I do not use deoderant or antiperspirant None no Spinich 135 None no 65 MiSeq1 2191 n/a Fecal, oral and skin samples from round 3 MiSeq None Remained stable Grains I do not have diabetes fairfield no Never no IA None 41.0072222 None no no American_Gut_round 6
000004285.1213110 TCTACGGCACGT GTGTGCCAGCMGCCGCGGTAA 37 Within the past 3 months None n 12/18/13 None 42.0 79.0 None UBERON:feces None None no None 298.0795593 Confined Daily 23 no Caucasian USA 100 Regularly (3-5 times/week) 2191:2798061244 no 91104 -118.1181199 Little None None None no None UBERON:feces None None None 40 4285 None Stool More than one year ago GAZ:United States of America In the past year None human gut metagenome None None 16S rRNA sequencing by synthesis In the past year FWD:GTGCCAGCMGCCGCGGTAA; REV:GGACTACHVGGGTWTCTAAT no 28.24265381 ENVO:urban biome None Daily no None No CCME no years None This analysis was done as in Caporaso et al 2011 Genome research. The PCR primers (F515/R806) were developed against the V4 region of the 16S rRNA (both bacteria and archaea), which we determined would yield optimal community clustering with reads of this length using a procedure similar to that of ref. 15. [For reference, this primer pair amplifies the region 533_786 in the Escherichia coli strain 83972 sequence (greengenes accession no. prokMSA_id:470367).] The reverse PCR primer is barcoded with a 12-base error-correcting Golay code to facilitate multiplexing of up to 1,500 samples per lane, and both PCR primers contain sequencer adapter regions. American Gut Project Stool sample None Daily 3/10/72 no yes ENVO:feces None I do not have a skin condition None no no V4 American Gut Project 66 bronchitis yes human None None None female None Both 10/3/13 0.0 None no Less than 25% 40 no None 4285 yes None None .1,g no Never None None Regularly (3-5 times/week) None CCME UBERON:feces left None no no ENVO:human-associated habitat None 7:30 AM no Filtered None 6-7 hours Omnivore CCME None CCME no 168.0 None I do not have IBD no 0 9606 MiSeq 408170 21 to 30 None 95 None None no AGP6_rerun_L001 no Illumina I use an antiperspirant frog, Little, Confined yes greens 175 None no 60 MiSeq1 2191 None Fecal, oral and skin samples from round 3 MiSeq None Remained stable rice I do not have diabetes pasadena no Rarely (few times/month) no CA None 34.1657707 None yes no American_Gut_round 6
000009592.1213114 TGACCGGCTGTT GTGTGCCAGCMGCCGCGGTAA None More than one year ago None n 12/18/13 None 60.0 63.0 None UBERON:feces None None no None 240.3143158 Outdoor Regularly (3-5 times/week) None no Caucasian USA 37 Daily 2191:973838022 no 29625 -82.6501332 Little None None None no None UBERON:feces None None None 60 9592 None Stool More than one year ago GAZ:United States of America Not in the last year None human gut metagenome None None 16S rRNA sequencing by synthesis In the past month FWD:GTGCCAGCMGCCGCGGTAA; REV:GGACTACHVGGGTWTCTAAT no 23.29467456 ENVO:urban biome None Daily no None No CCME yes years None This analysis was done as in Caporaso et al 2011 Genome research. The PCR primers (F515/R806) were developed against the V4 region of the 16S rRNA (both bacteria and archaea), which we determined would yield optimal community clustering with reads of this length using a procedure similar to that of ref. 15. [For reference, this primer pair amplifies the region 533_786 in the Escherichia coli strain 83972 sequence (greengenes accession no. prokMSA_id:470367).] The reverse PCR primer is barcoded with a 12-base error-correcting Golay code to facilitate multiplexing of up to 1,500 samples per lane, and both PCR primers contain sequencer adapter regions. American Gut Project Stool sample spray Regularly (3-5 times/week) 12/19/53 no None ENVO:feces None I do not have a skin condition None no no V4 American Gut Project 65 None yes human None None None female None Outdoors 10/22/13 0.0 None no Less than 25% None no None 9592 no Spouse None .1,g yes Never yes None Rarely (few times/month) None CCME UBERON:feces right None no no ENVO:human-associated habitat CoQ10, Fish Oil, Psyllium 9:00 AM no City None 7-8 hours Omnivore CCME None CCME no 165.0 None I do not have IBD no 0 9606 MiSeq 408170 More than 30 None 160 None None yes AGP6_rerun_L001 no Illumina I use an antiperspirant Dog, Little, Outdoor yes Kale 140 None no 40 MiSeq1 2191 None Fecal, oral and skin samples from round 3 MiSeq None Remained stable chocolate bar I do not have diabetes anderson no Rarely (few times/month) no SC None 34.5034394 None yes no American_Gut_round 6
000010880.1213133 TCCATTTCATGC GTGTGCCAGCMGCCGCGGTAA 42 Within the past 6 months None n 12/18/13 yes 47.0 76.0 None UBERON:feces None None no None 89.4965744 Housing... Daily 21 no Caucasian USA 100 Never 2191:575412172 no 90038 -118.3315838 Contact... None None None no None UBERON:feces None None None 60 10880 None Stool Within the past year GAZ:United States of America Not in the last year None human gut metagenome None None 16S rRNA sequencing by synthesis Not in the last year FWD:GTGCCAGCMGCCGCGGTAA; REV:GGACTACHVGGGTWTCTAAT no 22.16250704 ENVO:urban biome None Daily no None None CCME no years None This analysis was done as in Caporaso et al 2011 Genome research. The PCR primers (F515/R806) were developed against the V4 region of the 16S rRNA (both bacteria and archaea), which we determined would yield optimal community clustering with reads of this length using a procedure similar to that of ref. 15. [For reference, this primer pair amplifies the region 533_786 in the Escherichia coli strain 83972 sequence (greengenes accession no. prokMSA_id:470367).] The reverse PCR primer is barcoded with a 12-base error-correcting Golay code to facilitate multiplexing of up to 1,500 samples per lane, and both PCR primers contain sequencer adapter regions. American Gut Project Stool sample None Daily 9/16/66 no None ENVO:feces None I do not have a skin condition None no no V4 American Gut Project 73 None yes human None None None male None Both 11/12/13 0.0 None no 25 to 50% 37 no None 10880 yes None None .1,g no Never None None Occasionally (1-2 times/week) None CCME UBERON:feces right None no no ENVO:human-associated habitat None 7:00 AM no City None 7-8 hours Omnivore CCME None CCME no 185.0 None I do not have IBD no 0 9606 MiSeq 408170 21 to 30 None 238 None None yes AGP6_rerun_L001 no Illumina I use deodorant Contact..., Housing... yes kale 168 None yes 40 MiSeq1 2191 None Fecal, oral and skin samples from round 3 MiSeq None Remained stable oats I do not have diabetes los angeles no Regularly (3-5 times/week) no CA None 34.0895186 None yes no American_Gut_round 6
000010121.1213032 CATACACGCACC GTGTGCCAGCMGCCGCGGTAA 40 Within the past year None n 12/18/13 None 61.0 64.0 None UBERON:feces None None yes None 102.8708496 Outdoor Daily 30 no Caucasian USA 100 Never 2191:1229812273 no 4349 -70.0336654 Extensive None None None no None UBERON:feces None None None 80 10121 None Stool More than one year ago GAZ:United States of America Not in the last year None human gut metagenome None None 16S rRNA sequencing by synthesis In the past year FWD:GTGCCAGCMGCCGCGGTAA; REV:GGACTACHVGGGTWTCTAAT no 22.39451994 ENVO:urban biome None Daily no None None CCME no years None This analysis was done as in Caporaso et al 2011 Genome research. The PCR primers (F515/R806) were developed against the V4 region of the 16S rRNA (both bacteria and archaea), which we determined would yield optimal community clustering with reads of this length using a procedure similar to that of ref. 15. [For reference, this primer pair amplifies the region 533_786 in the Escherichia coli strain 83972 sequence (greengenes accession no. prokMSA_id:470367).] The reverse PCR primer is barcoded with a 12-base error-correcting Golay code to facilitate multiplexing of up to 1,500 samples per lane, and both PCR primers contain sequencer adapter regions. American Gut Project Stool sample None Regularly (3-5 times/week) 3/3/53 no None ENVO:feces None I do not have a skin condition None no no V4 American Gut Project 67 None yes human None None None male None Outdoors 10/21/13 0.0 None no Less than 25% 30 no None 10121 no None None .1,g yes Never None None Daily None CCME UBERON:feces right None no no ENVO:human-associated habitat fishoil 6:00 AM no Well None 7-8 hours Omnivore CCME None CCME no 170.0 None I do not have IBD yes 0 9606 MiSeq 408170 11 to 20 None 250 None None no AGP6_rerun_L001 no Illumina I use an antiperspirant chickens, cows, horses, Extensive, Outdoor no cabbage 143 None no 20 MiSeq1 2191 None Fecal, oral and skin samples from round 3 MiSeq None Remained stable wheat I do not have diabetes fayette no Never no ME None 44.4089558 None yes no American_Gut_round 6
000001734.1213036 TGTTAAGCAGCA GTGTGCCAGCMGCCGCGGTAA 49 Within the past 3 months None n 12/18/13 None 44.0 52.0 None UBERON:feces None None no None 6.93894577 Indoor Daily 29 no Caucasian USA 100 Daily 2191:576439122 no 95060 -122.0307963 Little None None None no None UBERON:feces None None None 30 1734 None Stool More than one year ago GAZ:United States of America Not in the last year None human gut metagenome None None 16S rRNA sequencing by synthesis Not in the last year FWD:GTGCCAGCMGCCGCGGTAA; REV:GGACTACHVGGGTWTCTAAT no 19.73754883 ENVO:urban biome None Daily no None No CCME no years None This analysis was done as in Caporaso et al 2011 Genome research. The PCR primers (F515/R806) were developed against the V4 region of the 16S rRNA (both bacteria and archaea), which we determined would yield optimal community clustering with reads of this length using a procedure similar to that of ref. 15. [For reference, this primer pair amplifies the region 533_786 in the Escherichia coli strain 83972 sequence (greengenes accession no. prokMSA_id:470367).] The reverse PCR primer is barcoded with a 12-base error-correcting Golay code to facilitate multiplexing of up to 1,500 samples per lane, and both PCR primers contain sequencer adapter regions. American Gut Project Stool sample None Regularly (3-5 times/week) 4/9/70 no None ENVO:feces None I do not have a skin condition None no no V4 American Gut Project 64 None yes human None None None female None Outdoors 8/19/13 0.0 None no Less than 25% 22 no None 1734 no None None .1,g yes Never None None Regularly (3-5 times/week) None CCME UBERON:feces left None no no ENVO:human-associated habitat Vit D, DHA, Fish Oil - Omega 3, 6, 9 1:10 PM no Filtered None 7-8 hours Omnivore CCME None CCME yes None None I do not have IBD yes 0 9606 MiSeq 408170 11 to 20 None 250 None None None AGP6_rerun_L001 no Illumina I do not use deodorant or antiperspirant Lizard, Little, Indoor no Leafy greens 115 None no 70 MiSeq1 2191 None Fecal, oral and skin samples from round 3 MiSeq None Remained stable Quinao I do not have diabetes santa cruz no Rarely (few times/month) no CA None 36.9741171 None no no American_Gut_round 6
000010139.1213031 GCTAGACACTAC GTGTGCCAGCMGCCGCGGTAA 30 Within the past 6 months None n 12/18/13 None 52.0 59.0 None UBERON:feces None None no None 31.0247345 Housing... Daily 60 no Asian or Pacific Islander USA 100 Occasionally (1-2 times/week) 2191:4263570946 no 11050 -73.6981858 Contact... None None None no None UBERON:feces None None None 80 10139 None Stool More than one year ago GAZ:United States of America Not in the last year None human gut metagenome None None 16S rRNA sequencing by synthesis In the past month FWD:GTGCCAGCMGCCGCGGTAA; REV:GGACTACHVGGGTWTCTAAT no 24.14047867 ENVO:urban biome None Daily no None No CCME yes years None This analysis was done as in Caporaso et al 2011 Genome research. The PCR primers (F515/R806) were developed against the V4 region of the 16S rRNA (both bacteria and archaea), which we determined would yield optimal community clustering with reads of this length using a procedure similar to that of ref. 15. [For reference, this primer pair amplifies the region 533_786 in the Escherichia coli strain 83972 sequence (greengenes accession no. prokMSA_id:470367).] The reverse PCR primer is barcoded with a 12-base error-correcting Golay code to facilitate multiplexing of up to 1,500 samples per lane, and both PCR primers contain sequencer adapter regions. American Gut Project Stool sample None Daily 1/28/62 no None ENVO:feces None I do not have a skin condition None no no V4 American Gut Project 62 None no human None None None female None None 11/10/13 0.0 None no Less than 25% 10 no None 10139 no husband None .1,g no Never None None Occasionally (1-2 times/week) None CCME UBERON:feces right None no no ENVO:human-associated habitat None 6:00 PM no City None 7-8 hours Omnivore CCME None CCME no 157.0 None I do not have IBD no 0 9606 MiSeq 408170 6 to 10 None 50 None None no AGP6_rerun_L001 no Illumina I use deodorant Contact..., Housing... yes leafy greens, carrots, onions 132 None no 20 MiSeq1 2191 None Fecal, oral and skin samples from round 3 MiSeq None Remained stable wheat I do not have diabetes port washington no Never no NY None 40.8256561 None yes no American_Gut_round 6
000008974.1212967 ACTTTGCTTTGC GTGTGCCAGCMGCCGCGGTAA None More than one year ago None n 12/18/13 None 60.0 98.0 None UBERON:feces None None no None 148.5522461 Housing... Never None no Caucasian USA 78 Never 2191:158470069 yes 27516 -79.0558445 Contact... None None None no None UBERON:feces None None None 5 8974 None Stool More than one year ago GAZ:United States of America Not in the last year None human gut metagenome None None 16S rRNA sequencing by synthesis Not in the last year FWD:GTGCCAGCMGCCGCGGTAA; REV:GGACTACHVGGGTWTCTAAT no 30.40150764 ENVO:urban biome None Regularly (3-5 times/week) no None None CCME no years None This analysis was done as in Caporaso et al 2011 Genome research. The PCR primers (F515/R806) were developed against the V4 region of the 16S rRNA (both bacteria and archaea), which we determined would yield optimal community clustering with reads of this length using a procedure similar to that of ref. 15. [For reference, this primer pair amplifies the region 533_786 in the Escherichia coli strain 83972 sequence (greengenes accession no. prokMSA_id:470367).] The reverse PCR primer is barcoded with a 12-base error-correcting Golay code to facilitate multiplexing of up to 1,500 samples per lane, and both PCR primers contain sequencer adapter regions. American Gut Project Stool sample None Occasionally (1-2 times/week) 9/9/53 no None ENVO:feces None I do not have a skin condition None no no V4 American Gut Project 71 None yes human None None None male None None 9/26/13 0.0 None no Less than 25% None no None 8974 no None None .1,g no Never None None Regularly (3-5 times/week) None CCME UBERON:feces right None no no ENVO:human-associated habitat None 11:55 AM no Filtered None 6-7 hours Omnivore CCME None CCME no 180.0 None I do not have IBD yes 0 9606 MiSeq 408170 6 to 10 None 64.4 None None no AGP6_rerun_L001 no Illumina I do not use deodorant or antiperspirant Contact..., Housing... yes Broccoli 218 None no 95 MiSeq1 2191 None Fecal, oral and skin samples from round 3 MiSeq None Remained stable beer I do not have diabetes chapel hill no Never no NC None 35.9131996 None yes no American_Gut_round 6
000010807A.1213077 TGGAAGAACGGC GTGTGCCAGCMGCCGCGGTAA None More than one year ago yes n 12/18/13 None 49.0 72.0 None UBERON:feces None None no None 19.26420975 Housing... Regularly (3-5 times/week) None no Caucasian USA 61 Occasionally (1-2 times/week) 2191:1963962429 no 11201 -73.9859414 Contact... None None None no None UBERON:feces None None None 20 10807A None Stool More than one year ago GAZ:United States of America Not in the last year None human gut metagenome None None 16S rRNA sequencing by synthesis Not in the last year FWD:GTGCCAGCMGCCGCGGTAA; REV:GGACTACHVGGGTWTCTAAT no 25.05680552 ENVO:urban biome None Daily no None No CCME no years None This analysis was done as in Caporaso et al 2011 Genome research. The PCR primers (F515/R806) were developed against the V4 region of the 16S rRNA (both bacteria and archaea), which we determined would yield optimal community clustering with reads of this length using a procedure similar to that of ref. 15. [For reference, this primer pair amplifies the region 533_786 in the Escherichia coli strain 83972 sequence (greengenes accession no. prokMSA_id:470367).] The reverse PCR primer is barcoded with a 12-base error-correcting Golay code to facilitate multiplexing of up to 1,500 samples per lane, and both PCR primers contain sequencer adapter regions. American Gut Project Stool sample None Regularly (3-5 times/week) 7/1/65 no None ENVO:feces None Rosacea None no no V4 American Gut Project 67 None yes human None None None female None Depends on the season 11/7/13 0.0 None no 25 to 50% None no None 10807 no None None .1,g no Rarely (few times/month) yes None Regularly (3-5 times/week) None CCME UBERON:feces right None no no ENVO:human-associated habitat None 2:27 PM no Bottled None 7-8 hours Omnivore CCME None CCME no 170.0 None I do not have IBD no 0 9606 MiSeq 408170 6 to 10 None 105 None None no AGP6_rerun_L001 no Illumina Not sure, but I use some form of deoderant/antiperspirant Contact..., Housing... no carrot 160 None no 80 MiSeq1 2191 None Fecal, oral and skin samples from round 3 MiSeq None Remained stable bread I do not have diabetes brooklyn no Regularly (3-5 times/week) no NY None 40.6986772 None no yes American_Gut_round 6
000006004.1213093 ACAAGAACCTTG GTGTGCCAGCMGCCGCGGTAA None Within the past 6 months None n 12/18/13 yes 54.0 68.0 None UBERON:feces None None no None 201.0117188 Housing... Rarely (few times/month) None no Caucasian USA 0 Never 2191:2358226097 no 63132 -90.3795438 Contact... None None None no None UBERON:feces None None None None 6004 None Stool More than one year ago GAZ:United States of America In the past 6 months None human gut metagenome None None 16S rRNA sequencing by synthesis In the past month FWD:GTGCCAGCMGCCGCGGTAA; REV:GGACTACHVGGGTWTCTAAT no None ENVO:urban biome None Daily no None None CCME not_sure years None This analysis was done as in Caporaso et al 2011 Genome research. The PCR primers (F515/R806) were developed against the V4 region of the 16S rRNA (both bacteria and archaea), which we determined would yield optimal community clustering with reads of this length using a procedure similar to that of ref. 15. [For reference, this primer pair amplifies the region 533_786 in the Escherichia coli strain 83972 sequence (greengenes accession no. prokMSA_id:470367).] The reverse PCR primer is barcoded with a 12-base error-correcting Golay code to facilitate multiplexing of up to 1,500 samples per lane, and both PCR primers contain sequencer adapter regions. American Gut Project Stool sample None Daily 6/23/60 no None ENVO:feces None Eczema None yes no V4 American Gut Project None tooth ache no human None None None male None Indoors 11/18/13 0.0 None no 51 to 75% None no None 6004 no None None .1,g no Never yes None Daily None CCME UBERON:feces right None no no ENVO:human-associated habitat None 8:30 AM no Filtered None 6-7 hours Omnivore CCME None CCME no None clindamycin I do not have IBD no 0 9606 MiSeq 408170 6 to 10 None None None None yes AGP6_rerun_L001 no Illumina I do not use deodorant or antiperspirant Contact..., Housing... no cauliflower 150 None no None MiSeq1 2191 None Fecal, oral and skin samples from round 3 MiSeq None Remained stable bread I do not have diabetes st. louis no Regularly (3-5 times/week) no MO None 38.6785807 None yes yes American_Gut_round 6
000007033.1212963 GTTCCTCCATTA GTGTGCCAGCMGCCGCGGTAA 31 More than one year ago yes n 12/18/13 yes 42.0 81.0 None UBERON:feces None None no None 51.64722061 Housing... Daily 19 no Caucasian USA 100 Never 2191:1426910650 yes 95340 -120.4829677 Contact... None None None no None UBERON:feces None None None 20 7033 None Stool More than one year ago GAZ:United States of America Not in the last year None human gut metagenome None None 16S rRNA sequencing by synthesis Not in the last year FWD:GTGCCAGCMGCCGCGGTAA; REV:GGACTACHVGGGTWTCTAAT no 23.74554325 ENVO:urban biome None Daily no None None CCME no years None This analysis was done as in Caporaso et al 2011 Genome research. The PCR primers (F515/R806) were developed against the V4 region of the 16S rRNA (both bacteria and archaea), which we determined would yield optimal community clustering with reads of this length using a procedure similar to that of ref. 15. [For reference, this primer pair amplifies the region 533_786 in the Escherichia coli strain 83972 sequence (greengenes accession no. prokMSA_id:470367).] The reverse PCR primer is barcoded with a 12-base error-correcting Golay code to facilitate multiplexing of up to 1,500 samples per lane, and both PCR primers contain sequencer adapter regions. American Gut Project Stool sample None Regularly (3-5 times/week) 1/5/72 no None ENVO:feces None I do not have a skin condition None no no V4 American Gut Project 73 None no human None None None male None Both 9/25/13 0.0 None no Less than 25% 50 no None 7033 no None None .1,g yes Never yes None Rarely (few times/month) None CCME UBERON:feces right None yes no ENVO:human-associated habitat l-methylfolate, vitamin D, kelp 12:00 PM no Filtered None 7-8 hours Omnivore CCME limited starch, limited sugar CCME no 185.0 None I do not have IBD no 0 9606 MiSeq 408170 More than 30 None 164 None None None AGP6_rerun_L001 no Illumina Not sure, but I use some form of deodorant/antiperspirant Contact..., Housing... yes broccoli 180 None no 80 MiSeq1 2191 None Fecal, oral and skin samples from round 3 MiSeq None Remained stable white rice I do not have diabetes merced no Occasionally (1-2 times/week) no CA None 37.3021632 None yes yes American_Gut_round 6
000004283.1213125 GGCGATTTACGT GTGTGCCAGCMGCCGCGGTAA 43 Within the past month None n 12/18/13 None 26.0 70.0 None UBERON:feces None None no None 298.0795593 Housing... Never 25 no Caucasian USA 100 Never 2191:2094493132 no 91104 -118.1181199 Contact... None None None no None UBERON:feces None None None 22 4283 None Stool More than one year ago GAZ:United States of America In the past 6 months None human gut metagenome None None 16S rRNA sequencing by synthesis In the past week FWD:GTGCCAGCMGCCGCGGTAA; REV:GGACTACHVGGGTWTCTAAT no 21.01948302 ENVO:urban biome None Daily no None None CCME no years None This analysis was done as in Caporaso et al 2011 Genome research. The PCR primers (F515/R806) were developed against the V4 region of the 16S rRNA (both bacteria and archaea), which we determined would yield optimal community clustering with reads of this length using a procedure similar to that of ref. 15. [For reference, this primer pair amplifies the region 533_786 in the Escherichia coli strain 83972 sequence (greengenes accession no. prokMSA_id:470367).] The reverse PCR primer is barcoded with a 12-base error-correcting Golay code to facilitate multiplexing of up to 1,500 samples per lane, and both PCR primers contain sequencer adapter regions. American Gut Project Stool sample None Rarely (few times/month) 10/22/87 no None ENVO:feces None I do not have a skin condition yes no no V4 American Gut Project 72 Campylobacter jejuni food poisoning no human None Two None male None Both 10/2/13 0.0 None no Less than 25% 32 yes None 4283 no None None .1,g yes Never None None Rarely (few times/month) None CCME UBERON:feces right None no no ENVO:human-associated habitat echinacea 10:30 PM no City yes 7-8 hours Omnivore CCME None CCME no 183.0 None I do not have IBD no 0 9606 MiSeq 408170 6 to 10 None 115 None None yes AGP6_rerun_L001 no Illumina I use deodorant Contact..., Housing... no potatoes 155 None no 78 MiSeq1 2191 None Fecal, oral and skin samples from round 3 MiSeq None Decreased more than 10 pounds bread I do not have diabetes pasadena no Never no CA no 34.1657707 None yes no American_Gut_round 6
000004671.1212965 CTACGAAAGCCT GTGTGCCAGCMGCCGCGGTAA 29 None None n 12/18/13 yes 64.0 92.0 None UBERON:feces None None yes None 22.65641403 Housing... Daily 24 no Caucasian USA 93 Never 2191:3275176712 yes 93101 -119.7107494 Contact... None None None no None UBERON:feces None None None 22 4671 None Stool More than one year ago GAZ:United States of America Not in the last year None human gut metagenome None None 16S rRNA sequencing by synthesis In the past year FWD:GTGCCAGCMGCCGCGGTAA; REV:GGACTACHVGGGTWTCTAAT no 40.03194444 ENVO:urban biome None Daily no None None CCME no years None This analysis was done as in Caporaso et al 2011 Genome research. The PCR primers (F515/R806) were developed against the V4 region of the 16S rRNA (both bacteria and archaea), which we determined would yield optimal community clustering with reads of this length using a procedure similar to that of ref. 15. [For reference, this primer pair amplifies the region 533_786 in the Escherichia coli strain 83972 sequence (greengenes accession no. prokMSA_id:470367).] The reverse PCR primer is barcoded with a 12-base error-correcting Golay code to facilitate multiplexing of up to 1,500 samples per lane, and both PCR primers contain sequencer adapter regions. American Gut Project Stool sample None Regularly (3-5 times/week) 6/3/50 no None ENVO:feces None I do not have a skin condition None no no V4 American Gut Project 60 None no human None None None male None Both 10/12/13 0.0 None no Less than 25% 40 no None 4671 no None None .1,g yes Never None None Daily None CCME UBERON:feces right None yes no ENVO:human-associated habitat vitamin C 1000mg, pantethine 450mg weekly, chromium picolinate 200mcg weekly, taurine 500mg weekly, boron 3mg weekly, aspirin 81mg, magnesium (oxide) 250mg, vitamin D3 5000IU, vitamin K2 90mcg, lithium 2.5mg, vitamin B12 500mcg weekly, super B complex weekly, biotin 5000mcg weekly 11:25 AM no Filtered None 6-7 hours Omnivore CCME I try to follow the paleo diet CCME no 155.0 None I do not have IBD no 0 9606 MiSeq 408170 11 to 20 None 168 None None no AGP6_rerun_L001 no Illumina I use an antiperspirant Contact..., Housing... no green beans 205 None no 78 MiSeq1 2191 garlic (the sulfur I think) -- more of a sensitivity than an allergy: I feel hungover the following day. Fecal, oral and skin samples from round 3 MiSeq yes Remained stable fruit I do not have diabetes santa barbara no Never no CA None 34.420334 None yes None American_Gut_round 6
000004213.1213120 CTTCCAACTCAT GTGTGCCAGCMGCCGCGGTAA 50 Within the past 3 months None n 12/18/13 yes 30.0 74.0 None UBERON:feces None None no None 1619.837158 Outdoor, Outdoor Regularly (3-5 times/week) 10 no Caucasian USA 100 Never 2191:4095514450 no 80303 -105.2077798 Moderate, Moderate None None None no None UBERON:feces None None None 90 4213 None Stool More than one year ago GAZ:United States of America Not in the last year None human gut metagenome yes None 16S rRNA sequencing by synthesis Not in the last year FWD:GTGCCAGCMGCCGCGGTAA; REV:GGACTACHVGGGTWTCTAAT no 23.01031541 ENVO:urban biome None Daily no None None CCME yes years None This analysis was done as in Caporaso et al 2011 Genome research. The PCR primers (F515/R806) were developed against the V4 region of the 16S rRNA (both bacteria and archaea), which we determined would yield optimal community clustering with reads of this length using a procedure similar to that of ref. 15. [For reference, this primer pair amplifies the region 533_786 in the Escherichia coli strain 83972 sequence (greengenes accession no. prokMSA_id:470367).] The reverse PCR primer is barcoded with a 12-base error-correcting Golay code to facilitate multiplexing of up to 1,500 samples per lane, and both PCR primers contain sequencer adapter regions. American Gut Project Stool sample None Regularly (3-5 times/week) 5/4/84 no None ENVO:feces None Eczema None no no V4 American Gut Project 71 None yes human None Three None unknown None Outdoors 10/16/13 0.0 None no Less than 25% 40 yes None 4213 no roommate None .1,g no Rarely (few times/month) None None Daily None CCME UBERON:feces right None no no ENVO:human-associated habitat None 10:20 AM no City no 6-7 hours Omnivore CCME None CCME no 180.0 None I do not have IBD no 0 9606 MiSeq 408170 11 to 20 None 267 None None yes AGP6_rerun_L001 no Illumina I use deodorant dog, dog, Moderate, Moderate, Outdoor, Outdoor no tomato 165 None no 10 MiSeq1 2191 None Fecal, oral and skin samples from round 3 MiSeq None Remained stable beer I do not have diabetes boulder no Rarely (few times/month) no CO no 40.0005378 None yes yes American_Gut_round 6
000009710.1213079 ACCGGAGTAGGA GTGTGCCAGCMGCCGCGGTAA 40 None None n 12/18/13 yes 73.0 72.0 None UBERON:feces None None yes None 20.71105576 Indoor Daily 40 no Caucasian USA 100 Regularly (3-5 times/week) 2191:2338566044 no 90814 -118.1429889 Extensive None None None no None UBERON:feces None None None None 9710 None Stool More than one year ago GAZ:United States of America In the past 6 months None human gut metagenome None None 16S rRNA sequencing by synthesis In the past 6 months FWD:GTGCCAGCMGCCGCGGTAA; REV:GGACTACHVGGGTWTCTAAT no 26.62248521 ENVO:urban biome None Daily no None No CCME no years None This analysis was done as in Caporaso et al 2011 Genome research. The PCR primers (F515/R806) were developed against the V4 region of the 16S rRNA (both bacteria and archaea), which we determined would yield optimal community clustering with reads of this length using a procedure similar to that of ref. 15. [For reference, this primer pair amplifies the region 533_786 in the Escherichia coli strain 83972 sequence (greengenes accession no. prokMSA_id:470367).] The reverse PCR primer is barcoded with a 12-base error-correcting Golay code to facilitate multiplexing of up to 1,500 samples per lane, and both PCR primers contain sequencer adapter regions. American Gut Project Stool sample spray Daily 7/10/41 no None ENVO:feces None Psoriasis None yes yes V4 American Gut Project 65 Back surgery yes human None None None female None Outdoors 11/18/13 0.0 None no Less than 25% 20 no None 9710 no None None .1,g yes Never None None Daily None CCME UBERON:feces right None no no ENVO:human-associated habitat metamuscile 8:30 AM no Filtered None 6-7 hours Omnivore CCME None CCME no 165.0 None I do not have IBD no 0 9606 MiSeq 408170 11 to 20 None 150 None None no AGP6_rerun_L001 no Illumina I use deodorant dogs, Extensive, Indoor no broccoli 160 None no None MiSeq1 2191 None Fecal, oral and skin samples from round 3 MiSeq None Increased more than 10 pounds fruits None long beach no Regularly (3-5 times/week) no CA None 33.7709051 None no yes American_Gut_round 6
000005973.1213047 CTCTGCCTAATT GTGTGCCAGCMGCCGCGGTAA None More than one year ago yes n 12/18/13 None 55.0 50.0 None UBERON:feces None None no None 15.82565117 Indoor Daily None no Caucasian Australia 73 Never 2191:1931650810 no 3032 144.9961291 Extensive None None None no None UBERON:feces None None None 40 5973 None Stool More than one year ago GAZ:Australia In the past year None human gut metagenome None None 16S rRNA sequencing by synthesis Not in the last year FWD:GTGCCAGCMGCCGCGGTAA; REV:GGACTACHVGGGTWTCTAAT no 20.78204784 ENVO:urban biome None Daily no None None CCME no years None This analysis was done as in Caporaso et al 2011 Genome research. The PCR primers (F515/R806) were developed against the V4 region of the 16S rRNA (both bacteria and archaea), which we determined would yield optimal community clustering with reads of this length using a procedure similar to that of ref. 15. [For reference, this primer pair amplifies the region 533_786 in the Escherichia coli strain 83972 sequence (greengenes accession no. prokMSA_id:470367).] The reverse PCR primer is barcoded with a 12-base error-correcting Golay code to facilitate multiplexing of up to 1,500 samples per lane, and both PCR primers contain sequencer adapter regions. American Gut Project Stool sample None Daily 6/9/59 no None ENVO:feces None I do not have a skin condition None no no V4 American Gut Project 61 inner ear infection no human None None None unknown None Outdoors 9/26/13 0.0 None no Less than 25% None no None 5973 no None None .1,g yes Never yes None Regularly (3-5 times/week) None CCME UBERON:feces right None yes no ENVO:human-associated habitat fish oil, glucasamine, probiotics 7:00 AM no City None 6-7 hours Omnivore CCME Minimal sugars, limited grains CCME no 157.0 ? I do not have IBD yes 0 9606 MiSeq 408170 11 to 20 None 175 None None yes AGP6_rerun_L001 no Illumina I use deodorant cat, Extensive, Indoor yes leafy greens 110 None no 60 MiSeq1 2191 None Fecal, oral and skin samples from round 3 MiSeq None Remained stable rice I do not have diabetes melbourne no Never no None None -37.837542 None yes yes American_Gut_round 6
Blank28.F4.1213085 ATATGACCCAGC GTGTGCCAGCMGCCGCGGTAA None None None n 12/18/13 None None None None None None None None None 1624.1 None None None None None None None None 2191:unknown None 80309 -105.79 None None None None None None None None None None None Blank28.F4 None Blank None GAZ:United States of America None None unclassified metagenome None None 16S rRNA sequencing by synthesis None FWD:GTGCCAGCMGCCGCGGTAA; REV:GGACTACHVGGGTWTCTAAT None None ENVO:aquatic biome None None None None None CCME None years None This analysis was done as in Caporaso et al 2011 Genome research. The PCR primers (F515/R806) were developed against the V4 region of the 16S rRNA (both bacteria and archaea), which we determined would yield optimal community clustering with reads of this length using a procedure similar to that of ref. 15. [For reference, this primer pair amplifies the region 533_786 in the Escherichia coli strain 83972 sequence (greengenes accession no. prokMSA_id:470367).] The reverse PCR primer is barcoded with a 12-base error-correcting Golay code to facilitate multiplexing of up to 1,500 samples per lane, and both PCR primers contain sequencer adapter regions. American Gut Project blank None None None None None ENVO:sterile water None None None None None V4 American Gut Project None None None None None None None unknown None None None 0.0 None None None None None None Blank28.F4 None None None .1,g None None None None None None CCME None unknown None None None ENVO:water None None None None None None None CCME None CCME None None None None None 0 None MiSeq 408169 None None None None None None AGP6_rerun_L001 None Illumina None None None None None None None None MiSeq1 2191 None Fecal, oral and skin samples from round 3 MiSeq None None None None boulder None None None CO None 40.02 None None None American_Gut_round 14
000008964.1213057 TGAGTGGTCTGT GTGTGCCAGCMGCCGCGGTAA 20 More than one year ago None n 12/18/13 None 34.0 59.0 None UBERON:feces None None no None 120.1622162 Housing... Daily 19 yes Caucasian USA 100 Never 2191:567878132 no 14850 -76.5018807 Contact... None None None no None UBERON:feces None None None 4 8964 None Stool More than one year ago GAZ:United States of America Not in the last year None human gut metagenome None None 16S rRNA sequencing by synthesis Not in the last year FWD:GTGCCAGCMGCCGCGGTAA; REV:GGACTACHVGGGTWTCTAAT no 20.35865449 ENVO:urban biome None Daily no None No CCME no years None This analysis was done as in Caporaso et al 2011 Genome research. The PCR primers (F515/R806) were developed against the V4 region of the 16S rRNA (both bacteria and archaea), which we determined would yield optimal community clustering with reads of this length using a procedure similar to that of ref. 15. [For reference, this primer pair amplifies the region 533_786 in the Escherichia coli strain 83972 sequence (greengenes accession no. prokMSA_id:470367).] The reverse PCR primer is barcoded with a 12-base error-correcting Golay code to facilitate multiplexing of up to 1,500 samples per lane, and both PCR primers contain sequencer adapter regions. American Gut Project Stool sample None Rarely (few times/month) 11/12/79 no None ENVO:feces None I do not have a skin condition None no no V4 American Gut Project 67 None no human None None None female None Outdoors 11/19/13 0.0 None no Less than 25% 61 no None 8964 no None None .1,g yes Never None None Never None CCME UBERON:feces right None yes no ENVO:human-associated habitat cod liver oil, magnesium, probiotic 7:00 AM no Filtered None 6-7 hours Omnivore CCME no grains, no sugars (except minimal fruit and honey), and no starchy vegetables CCME no 170.0 None I do not have IBD no 0 9606 MiSeq 408170 21 to 30 None 203 None None no AGP6_rerun_L001 no Illumina I do not use deodorant or antiperspirant Contact..., Housing... no squash, greens, onion family 130 None no 96 MiSeq1 2191 None Fecal, oral and skin samples from round 3 MiSeq None Remained stable vegetables (non-starchy) and some fruit I do not have diabetes ithaca no Never no NY None 42.4439614 None yes no American_Gut_round 6
000009612.1213134 TCCAACTGCAGA GTGTGCCAGCMGCCGCGGTAA 70 More than one year ago None n 12/18/13 yes None 63.0 None UBERON:feces None None no None 120.4650574 Indoor Daily 20 no Caucasian USA 100 Daily 2191:4175391391 no 94517 -121.9357925 Extensive None None None no None UBERON:feces None None None 95 9612 None Stool More than one year ago GAZ:United States of America Not in the last year None human gut metagenome None None 16S rRNA sequencing by synthesis Not in the last year FWD:GTGCCAGCMGCCGCGGTAA; REV:GGACTACHVGGGTWTCTAAT no 22.59412305 ENVO:urban biome None Daily no None None CCME yes years None This analysis was done as in Caporaso et al 2011 Genome research. The PCR primers (F515/R806) were developed against the V4 region of the 16S rRNA (both bacteria and archaea), which we determined would yield optimal community clustering with reads of this length using a procedure similar to that of ref. 15. [For reference, this primer pair amplifies the region 533_786 in the Escherichia coli strain 83972 sequence (greengenes accession no. prokMSA_id:470367).] The reverse PCR primer is barcoded with a 12-base error-correcting Golay code to facilitate multiplexing of up to 1,500 samples per lane, and both PCR primers contain sequencer adapter regions. American Gut Project Stool sample None Daily None no None ENVO:feces None I do not have a skin condition None no no V4 American Gut Project 66 None no human None None None male None Both 9/22/13 0.0 yes no 51 to 75% 10 no None 9612 yes Spouse None .1,g yes Never yes None Regularly (3-5 times/week) None CCME UBERON:feces right None no no ENVO:human-associated habitat Vitamins C, D, E, Ginkgo, COQ10 7:30 AM no Bottled None 6-7 hours Vegetarian CCME None CCME no 168.0 None I do not have IBD yes 0 9606 MiSeq 408170 11 to 20 None 30 None None no AGP6_rerun_L001 no Illumina I use deodorant Cats, Extensive, Indoor yes Tomato 140 None no 5 MiSeq1 2191 None Fecal, oral and skin samples from round 3 MiSeq None Remained stable None I do not have diabetes clayton no Occasionally (1-2 times/week) no CA None 37.9410341 None yes yes American_Gut_round 6
000001804.1212968 AGCTGTCAAGCT GTGTGCCAGCMGCCGCGGTAA 50 More than one year ago None n 5/20/13 None 84.0 45.0 None UBERON:feces None None no None 1104.929321 None Never 13 no Caucasian USA 100 Rarely (few times/month) 2191:850007650 no 97702 -121.3153096 None None None None no None UBERON:feces None None None 20 1804 None Stool More than one year ago GAZ:United States of America Not in the last year None human gut metagenome None None 16S rRNA sequencing by synthesis Not in the last year FWD:GTGCCAGCMGCCGCGGTAA; REV:GGACTACHVGGGTWTCTAAT no 14.34693878 ENVO:urban biome None Occasionally (1-2 times/week) no None No CCME not_sure years None This analysis was done as in Caporaso et al 2011 Genome research. The PCR primers (F515/R806) were developed against the V4 region of the 16S rRNA (both bacteria and archaea), which we determined would yield optimal community clustering with reads of this length using a procedure similar to that of ref. 15. [For reference, this primer pair amplifies the region 533_786 in the Escherichia coli strain 83972 sequence (greengenes accession no. prokMSA_id:470367).] The reverse PCR primer is barcoded with a 12-base error-correcting Golay code to facilitate multiplexing of up to 1,500 samples per lane, and both PCR primers contain sequencer adapter regions. American Gut Project Stool sample None Never 1/6/30 no yes ENVO:feces None Psoriasis None no no V4 American Gut Project 70 None yes human None None None female None None 4/7/13 0.0 None no Less than 25% 37 no None 1804 yes None None .1,g yes Never None None Never None CCME UBERON:feces right None no no ENVO:human-associated habitat niacinamide 250mg 9:55 AM no City None 8 or more hours Omnivore CCME None CCME no 178.0 None I do not have IBD yes 0 9606 MiSeq 408170 6 to 10 None 70 None None no Knight_AFG_16s_w_phiX_NoIndex_L001 None Illumina I do not use deoderant or antiperspirant None no avocado 100 None no 80 MiSeq1 2191 None Fecal, oral and skin samples from round 3 MiSeq None Remained stable yogurt I do not have diabetes bend no Never no OR None 44.0581728 None yes yes American_Gut_round 6
000003496.1213035 GTCACATCACGA GTGTGCCAGCMGCCGCGGTAA 35 More than one year ago None n 12/18/13 None 4.0 16.0 None UBERON:feces None None no None 4.185313702 Housing... Never 30 yes Caucasian USA 100 Never 2191:2133724597 no 33073 -80.1819268 Contact... None None None no None UBERON:feces None None None 60 3496 None Stool More than one year ago GAZ:United States of America None None human gut metagenome None None 16S rRNA sequencing by synthesis In the past year FWD:GTGCCAGCMGCCGCGGTAA; REV:GGACTACHVGGGTWTCTAAT None None ENVO:urban biome None Daily no None None CCME yes years None This analysis was done as in Caporaso et al 2011 Genome research. The PCR primers (F515/R806) were developed against the V4 region of the 16S rRNA (both bacteria and archaea), which we determined would yield optimal community clustering with reads of this length using a procedure similar to that of ref. 15. [For reference, this primer pair amplifies the region 533_786 in the Escherichia coli strain 83972 sequence (greengenes accession no. prokMSA_id:470367).] The reverse PCR primer is barcoded with a 12-base error-correcting Golay code to facilitate multiplexing of up to 1,500 samples per lane, and both PCR primers contain sequencer adapter regions. American Gut Project Stool sample None Daily 6/16/10 no None ENVO:feces None I do not have a skin condition None no no V4 American Gut Project None None no human None None None male None None 11/9/13 0.0 None no 51 to 75% 35 no None 3496 None Mother, Father, Sister None .1,g no Never None None Never None CCME UBERON:feces unknown None yes no ENVO:human-associated habitat None 8:50 AM no Filtered None 8 or more hours Omnivore CCME mostly gluten free CCME None None None I do not have IBD yes 0 9606 MiSeq 408170 6 to 10 None 40 None None no AGP6_rerun_L001 no Illumina I do not use deodorant or antiperspirant Contact..., Housing... yes cucumbers 36 None no 40 MiSeq1 2191 None Fecal, oral and skin samples from round 3 MiSeq None Remained stable goldfish I do not have diabetes coconut creek no Never no FL None 26.3003637 None no no American_Gut_round 6
000001028.1213128 GAATATACCTGG GTGTGCCAGCMGCCGCGGTAA 48 Within the past year None n 5/20/13 None 49.0 68.0 None UBERON:feces None None no None 90.29508209 None Daily 20 no Caucasian USA 100 Rarely (few times/month) 2191:619982090 yes 2476 -71.1745579 None None None None no None UBERON:feces None None None 40 1028 None Stool More than one year ago GAZ:United States of America Not in the last year None human gut metagenome None None 16S rRNA sequencing by synthesis Not in the last year FWD:GTGCCAGCMGCCGCGGTAA; REV:GGACTACHVGGGTWTCTAAT no None ENVO:urban biome None Daily no None No CCME no years None This analysis was done as in Caporaso et al 2011 Genome research. The PCR primers (F515/R806) were developed against the V4 region of the 16S rRNA (both bacteria and archaea), which we determined would yield optimal community clustering with reads of this length using a procedure similar to that of ref. 15. [For reference, this primer pair amplifies the region 533_786 in the Escherichia coli strain 83972 sequence (greengenes accession no. prokMSA_id:470367).] The reverse PCR primer is barcoded with a 12-base error-correcting Golay code to facilitate multiplexing of up to 1,500 samples per lane, and both PCR primers contain sequencer adapter regions. American Gut Project Stool sample None Regularly (3-5 times/week) 1/25/65 no None ENVO:feces None Eczema yes no no V4 American Gut Project None None yes human None None None female None Both 4/1/13 0.0 None no Less than 25% 32 no None 1028 on None None .1,g yes Never None None Occasionally (1-2 times/week) None CCME UBERON:feces left None no no ENVO:human-associated habitat reversatral 7:00 AM None City None 6-7 hours Omnivore but no red meat CCME None CCME no None None I do not have IBD no 0 9606 MiSeq 408170 6 to 10 None 14.5 None None no Knight_AFG_16s_w_phiX_NoIndex_L001 no Illumina I do not use deoderant or antiperspirant None yes raw carrots 150 None None 60 MiSeq1 2191 tomato Fecal, oral and skin samples from round 3 MiSeq None Remained stable rice I do not have diabetes arlington no Rarely (few times/month) no MA None 42.4148798 None yes yes American_Gut_round 6
000010776.1213099 CATCGCGTTGAC GTGTGCCAGCMGCCGCGGTAA 55 More than one year ago None n 12/18/13 None 51.0 73.0 None UBERON:feces None None no None 42.88465881 Indoor Regularly (3-5 times/week) 20 no Caucasian Canada 100 Rarely (few times/month) 2191:2624116735 no 95128 -121.9416226 Extensive None None None no None UBERON:feces None None None 99 10776 None Stool Within the past year GAZ:United States of America In the past 6 months None human gut metagenome None None 16S rRNA sequencing by synthesis Not in the last year FWD:GTGCCAGCMGCCGCGGTAA; REV:GGACTACHVGGGTWTCTAAT no 26.30601469 ENVO:urban biome None Daily no None No CCME no years None This analysis was done as in Caporaso et al 2011 Genome research. The PCR primers (F515/R806) were developed against the V4 region of the 16S rRNA (both bacteria and archaea), which we determined would yield optimal community clustering with reads of this length using a procedure similar to that of ref. 15. [For reference, this primer pair amplifies the region 533_786 in the Escherichia coli strain 83972 sequence (greengenes accession no. prokMSA_id:470367).] The reverse PCR primer is barcoded with a 12-base error-correcting Golay code to facilitate multiplexing of up to 1,500 samples per lane, and both PCR primers contain sequencer adapter regions. American Gut Project Stool sample None Never 12/9/62 no None ENVO:feces None I do not have a skin condition None no no V4 American Gut Project 66 Swollen wrist no human None None None female None None 11/6/13 0.0 None no Less than 25% 25 no None 10776 no None None .1,g yes Never None None Rarely (few times/month) None CCME UBERON:feces right None no no ENVO:human-associated habitat Probiotics, creatine 8:45 AM no Bottled None 8 or more hours Vegetarian CCME None CCME no 168.0 Penicillan I do not have IBD yes 0 9606 MiSeq 408170 21 to 30 None 217 None None no AGP6_rerun_L001 no Illumina I do not use deodorant or antiperspirant Cats, Extensive, Indoor no tomato 163 None no 1 MiSeq1 2191 None Fecal, oral and skin samples from round 3 MiSeq None Decreased more than 10 pounds bread I do not have diabetes san jose no Never no CA None 37.3189149 None yes no American_Gut_round 6
000009475.1212952 ACCCATACAGCC GTGTGCCAGCMGCCGCGGTAA 43 More than one year ago None n 12/18/13 None 35.0 50.0 None UBERON:feces None None no None 399.9625244 Indoor Regularly (3-5 times/week) 17 None Caucasian USA 100 Never 2191:1863491419 no 92082 -117.0341967 Extensive None None None no None UBERON:feces None None None 48 9475 None Stool More than one year ago GAZ:United States of America Not in the last year None human gut metagenome None None 16S rRNA sequencing by synthesis Not in the last year FWD:GTGCCAGCMGCCGCGGTAA; REV:GGACTACHVGGGTWTCTAAT no 20.48283039 ENVO:urban biome None Daily no None No CCME not_sure years None This analysis was done as in Caporaso et al 2011 Genome research. The PCR primers (F515/R806) were developed against the V4 region of the 16S rRNA (both bacteria and archaea), which we determined would yield optimal community clustering with reads of this length using a procedure similar to that of ref. 15. [For reference, this primer pair amplifies the region 533_786 in the Escherichia coli strain 83972 sequence (greengenes accession no. prokMSA_id:470367).] The reverse PCR primer is barcoded with a 12-base error-correcting Golay code to facilitate multiplexing of up to 1,500 samples per lane, and both PCR primers contain sequencer adapter regions. American Gut Project Stool sample None Regularly (3-5 times/week) 7/17/79 no yes ENVO:feces None I do not have a skin condition None no no V4 American Gut Project 62 None yes human None None None female None Both 10/4/13 0.0 None no 25 to 50% 40 no None 9475 None None None .1,g yes Never None None Regularly (3-5 times/week) None CCME UBERON:feces right None None no ENVO:human-associated habitat garlic, kefir 8:45 AM yes Filtered None 5-6 hours Omnivore CCME None CCME no 157.0 None I do not have IBD no 0 9606 MiSeq 408170 More than 30 None 250 None None None AGP6_rerun_L001 no Illumina I use deodorant Dogs, Extensive, Indoor yes Kale 112 None no 52 MiSeq1 2191 None Fecal, oral and skin samples from round 3 MiSeq None Remained stable oats I do not have diabetes valley center no Occasionally (1-2 times/week) no CA None 33.2183701 None yes yes American_Gut_round 6
000007171.1213119 AAGGGCGCTGAA GTGTGCCAGCMGCCGCGGTAA 48 Within the past month None n 12/18/13 None 59.0 70.0 None UBERON:feces None None no None 3.074560881 Housing... Daily 23 no Caucasian Finland 100 Never 2191:1699551263 no 101 24.9410248 Contact... None None None no None UBERON:feces None None None 70 7171 None Stool Within the past 6 months GAZ:Finland In the past year None human gut metagenome None None 16S rRNA sequencing by synthesis In the past year FWD:GTGCCAGCMGCCGCGGTAA; REV:GGACTACHVGGGTWTCTAAT no 22.73934047 ENVO:urban biome None Daily no None None CCME yes years None This analysis was done as in Caporaso et al 2011 Genome research. The PCR primers (F515/R806) were developed against the V4 region of the 16S rRNA (both bacteria and archaea), which we determined would yield optimal community clustering with reads of this length using a procedure similar to that of ref. 15. [For reference, this primer pair amplifies the region 533_786 in the Escherichia coli strain 83972 sequence (greengenes accession no. prokMSA_id:470367).] The reverse PCR primer is barcoded with a 12-base error-correcting Golay code to facilitate multiplexing of up to 1,500 samples per lane, and both PCR primers contain sequencer adapter regions. American Gut Project Stool sample None Daily 8/5/55 no None ENVO:feces None None yes no no V4 American Gut Project 69 bronchitis no human None None None unknown None Outdoors 9/27/13 0.0 None no Less than 25% 29 no None 7171 yes grandchild None .1,g yes Never None None Daily None CCME UBERON:feces right None no no ENVO:human-associated habitat calcium plus vitamine D supplement 10:00 AM no City None 7-8 hours Omnivore CCME None CCME yes 178.0 None None no 0 9606 MiSeq 408170 6 to 10 None 175 None None no AGP6_rerun_L001 no Illumina I do not use deodorant or antiperspirant Contact..., Housing... no tomato, salad 154 None no 30 MiSeq1 2191 None Fecal, oral and skin samples from round 3 MiSeq None Decreased more than 10 pounds rye bread I do not have diabetes helsinki yes Rarely (few times/month) no None None 60.1733244 None yes yes American_Gut_round 6
000009533.1212983 CAAAGTTTGCGA GTGTGCCAGCMGCCGCGGTAA 38 More than one year ago None n 12/18/13 yes 22.0 104.0 None UBERON:feces None None no None 234.3610229 Indoor Rarely (few times/month) 16 no Caucasian USA 100 Regularly (3-5 times/week) 2191:816649219 no 61530 -89.2728627 Extensive None None None no None UBERON:feces None None None 70 9533 None Stool More than one year ago GAZ:United States of America In the past 6 months None human gut metagenome None None 16S rRNA sequencing by synthesis Not in the last year FWD:GTGCCAGCMGCCGCGGTAA; REV:GGACTACHVGGGTWTCTAAT no 39.47509766 ENVO:urban biome None Daily no None No CCME no years None This analysis was done as in Caporaso et al 2011 Genome research. The PCR primers (F515/R806) were developed against the V4 region of the 16S rRNA (both bacteria and archaea), which we determined would yield optimal community clustering with reads of this length using a procedure similar to that of ref. 15. [For reference, this primer pair amplifies the region 533_786 in the Escherichia coli strain 83972 sequence (greengenes accession no. prokMSA_id:470367).] The reverse PCR primer is barcoded with a 12-base error-correcting Golay code to facilitate multiplexing of up to 1,500 samples per lane, and both PCR primers contain sequencer adapter regions. American Gut Project Stool sample None Occasionally (1-2 times/week) 3/25/92 no None ENVO:feces None I do not have a skin condition None no no V4 American Gut Project 64 UTI yes human None None None female None Indoors 9/5/13 0.0 None no 51 to 75% 46 no 8/31/13 9533 yes None None .1,g yes Never None None Rarely (few times/month) None CCME UBERON:feces right None no no ENVO:human-associated habitat prenatal vitamin 10:45 AM no Filtered None 5-6 hours Omnivore CCME None CCME no 163.0 erythromycin Ulcerative colitis no 0 9606 MiSeq 408170 Less than 5 None 15.1 None None yes AGP6_rerun_L001 yes Illumina I use deodorant dog, Extensive, Indoor yes lettuce 230 None yes 30 MiSeq1 2191 None Fecal, oral and skin samples from round 3 MiSeq None Increased more than 10 pounds bread I do not have diabetes eureka no Regularly (3-5 times/week) no IL None 40.7214251 None no no American_Gut_round 6
000004815.1213107 GCATTCGGCGTT GTGTGCCAGCMGCCGCGGTAA 48 Within the past 3 months None n 12/18/13 None 71.0 63.0 None UBERON:feces None None yes None 310.1638489 Outdoor None 15 no Caucasian USA 97 Daily 2191:3689543116 no 78737 -97.9701846 Little None None None no None UBERON:feces None None None 80 4815 None Stool More than one year ago GAZ:United States of America Not in the last year None human gut metagenome None None 16S rRNA sequencing by synthesis Not in the last year FWD:GTGCCAGCMGCCGCGGTAA; REV:GGACTACHVGGGTWTCTAAT no 21.7680998 ENVO:urban biome None Daily no None No CCME no years None This analysis was done as in Caporaso et al 2011 Genome research. The PCR primers (F515/R806) were developed against the V4 region of the 16S rRNA (both bacteria and archaea), which we determined would yield optimal community clustering with reads of this length using a procedure similar to that of ref. 15. [For reference, this primer pair amplifies the region 533_786 in the Escherichia coli strain 83972 sequence (greengenes accession no. prokMSA_id:470367).] The reverse PCR primer is barcoded with a 12-base error-correcting Golay code to facilitate multiplexing of up to 1,500 samples per lane, and both PCR primers contain sequencer adapter regions. American Gut Project Stool sample spray Regularly (3-5 times/week) 3/15/43 no None ENVO:feces None I do not have a skin condition yes no no V4 American Gut Project 67 None no human None None None female None Both 10/3/13 0.0 None no Less than 25% 34 no None 4815 no None None .1,g yes Never yes None Rarely (few times/month) None CCME UBERON:feces right None no no ENVO:human-associated habitat CQ10, probiotics, borage seed oil, Vit D, algal oil, targeted amino acid therapy, Protandim 9:00 AM no Filtered None 7-8 hours Vegetarian CCME None CCME no 170.0 None I do not have IBD no 0 9606 MiSeq 408170 11 to 20 None 25 None None no AGP6_rerun_L001 no Illumina I use deodorant horse, Little, Outdoor yes spinach/argula 139 None no 20 MiSeq1 2191 None Fecal, oral and skin samples from round 3 MiSeq None Remained stable wheat I do not have diabetes austin no Rarely (few times/month) no TX None 30.181965 None yes yes American_Gut_round 6
000004287.1213049 GCCAAGGATAGG GTGTGCCAGCMGCCGCGGTAA 57 Within the past 3 months None n 12/18/13 None None 61.0 None UBERON:feces None None no None 298.0795593 Housing... Never 24 no Caucasian Austria 94 Regularly (3-5 times/week) 2191:3485683940 no 91104 -118.1181199 Contact... None None None no None UBERON:feces None None None 100 4287 None Stool More than one year ago GAZ:United States of America Not in the last year None human gut metagenome None None 16S rRNA sequencing by synthesis In the past year FWD:GTGCCAGCMGCCGCGGTAA; REV:GGACTACHVGGGTWTCTAAT no 17.67723776 ENVO:urban biome None Daily no None None CCME no years None This analysis was done as in Caporaso et al 2011 Genome research. The PCR primers (F515/R806) were developed against the V4 region of the 16S rRNA (both bacteria and archaea), which we determined would yield optimal community clustering with reads of this length using a procedure similar to that of ref. 15. [For reference, this primer pair amplifies the region 533_786 in the Escherichia coli strain 83972 sequence (greengenes accession no. prokMSA_id:470367).] The reverse PCR primer is barcoded with a 12-base error-correcting Golay code to facilitate multiplexing of up to 1,500 samples per lane, and both PCR primers contain sequencer adapter regions. American Gut Project Stool sample None Daily None no yes ENVO:feces None I do not have a skin condition None no no V4 American Gut Project 73 None no human None None None male None Outdoors 10/3/13 0.0 None no 51 to 75% 13 no None 4287 no None None .1,g yes Never None None Occasionally (1-2 times/week) None CCME UBERON:feces right None yes no ENVO:human-associated habitat Phenylade MTE amino acid mix 8:00 AM no City None 7-8 hours Vegetarian CCME Phenylketonuria CCME no 186.0 None I do not have IBD no 0 9606 MiSeq 408170 More than 30 None 126 None None yes AGP6_rerun_L001 no Illumina I use deodorant Contact..., Housing... yes Peppers 134 None no 0 MiSeq1 2191 None Fecal, oral and skin samples from round 3 MiSeq None Remained stable Rice I do not have diabetes pasadena no Rarely (few times/month) yes CA None 34.1657707 None yes no American_Gut_round 6
000009075.1212960 CCACATTGGGTC GTGTGCCAGCMGCCGCGGTAA 34 Within the past 6 months None n 12/18/13 None 29.0 79.0 None UBERON:feces Stress None no Other 61.83166885 Housing... Never 18 no Caucasian USA 100 Never 2191:2907824909 yes 98103 -122.3425575 Contact... None None None no None UBERON:feces None Monthly yes 10 9075 None Stool More than one year ago GAZ:United States of America Not in the last year yes human gut metagenome None yes 16S rRNA sequencing by synthesis Not in the last year FWD:GTGCCAGCMGCCGCGGTAA; REV:GGACTACHVGGGTWTCTAAT yes 21.87111111 ENVO:urban biome None Daily no None None CCME no years None This analysis was done as in Caporaso et al 2011 Genome research. The PCR primers (F515/R806) were developed against the V4 region of the 16S rRNA (both bacteria and archaea), which we determined would yield optimal community clustering with reads of this length using a procedure similar to that of ref. 15. [For reference, this primer pair amplifies the region 533_786 in the Escherichia coli strain 83972 sequence (greengenes accession no. prokMSA_id:470367).] The reverse PCR primer is barcoded with a 12-base error-correcting Golay code to facilitate multiplexing of up to 1,500 samples per lane, and both PCR primers contain sequencer adapter regions. American Gut Project Stool sample None Daily 8/28/84 no None ENVO:feces None Eczema None no no V4 American Gut Project 75 None no human None None None male None Both 9/26/13 0.0 None no Less than 25% 48 no None 9075 no None None .1,g yes Never None None Rarely (few times/month) None CCME UBERON:feces right None yes no ENVO:human-associated habitat b6, zinc 10:05 AM no Filtered None 7-8 hours Omnivore CCME Ray Peat diet. no grains, beans, minimal vegetables CCME no 191.0 None I do not have IBD yes 0 9606 MiSeq 408170 11 to 20 no 25 None not sure, may be excess serotonin yes AGP6_rerun_L001 no Illumina I do not use deodorant or antiperspirant Contact..., Housing... no potato 175 None no 90 MiSeq1 2191 None Fecal, oral and skin samples from round 3 MiSeq None Remained stable orange juice, milk I do not have diabetes seattle no Rarely (few times/month) no WA None 47.6600087 None yes no American_Gut_round 6
000003800.1213089 CAAGCCCTAGTA GTGTGCCAGCMGCCGCGGTAA 49 More than one year ago None n 12/18/13 yes 41.0 53.0 None UBERON:feces None None None None 1940.734375 Housing... Occasionally (1-2 times/week) 21 no Caucasian USA 100 Rarely (few times/month) 2191:1726898099 no 80108 -104.8948347 Contact... None None None no None UBERON:feces None None None 25 3800 None Stool More than one year ago GAZ:United States of America Not in the last year None human gut metagenome None None 16S rRNA sequencing by synthesis Not in the last year FWD:GTGCCAGCMGCCGCGGTAA; REV:GGACTACHVGGGTWTCTAAT no 20.25244141 ENVO:urban biome None Daily no None No CCME yes years None This analysis was done as in Caporaso et al 2011 Genome research. The PCR primers (F515/R806) were developed against the V4 region of the 16S rRNA (both bacteria and archaea), which we determined would yield optimal community clustering with reads of this length using a procedure similar to that of ref. 15. [For reference, this primer pair amplifies the region 533_786 in the Escherichia coli strain 83972 sequence (greengenes accession no. prokMSA_id:470367).] The reverse PCR primer is barcoded with a 12-base error-correcting Golay code to facilitate multiplexing of up to 1,500 samples per lane, and both PCR primers contain sequencer adapter regions. American Gut Project Stool sample None Rarely (few times/month) 8/19/72 no None ENVO:feces None I do not have a skin condition yes no no V4 American Gut Project 64 None no human None None None female None Both 11/6/13 0.0 None no Less than 25% 30 no None 3800 no son, son, daughter, husband None .1,g yes Never yes None Rarely (few times/month) None CCME UBERON:feces right None yes no ENVO:human-associated habitat salmon & krill oil, Vitamin D 2:00 PM no Filtered None 6-7 hours Omnivore CCME reduced carbohydrates CCME no 163.0 None I do not have IBD no 0 9606 MiSeq 408170 21 to 30 None 245 None None yes AGP6_rerun_L001 no Illumina I use deodorant Contact..., Housing... no spinach 118 None no 75 MiSeq1 2191 None Fecal, oral and skin samples from round 3 MiSeq None Remained stable sugar None castle pines north no Never no CO None 39.4717664 None yes no American_Gut_round 6
000007651.1213004 TAAGGCATCGCT GTGTGCCAGCMGCCGCGGTAA 52 More than one year ago None n 12/18/13 yes 41.0 88.0 None UBERON:feces Other Lack of sleep yes Other 67.53837585 Indoor Occasionally (1-2 times/week) 32 no Caucasian USA 100 Regularly (3-5 times/week) 2191:581756429 no 92009 -117.2499749 None yes None None no None UBERON:feces None A few times a year yes 38 7651 yes Stool More than one year ago GAZ:United States of America In the past 6 months yes human gut metagenome None yes 16S rRNA sequencing by synthesis Not in the last year FWD:GTGCCAGCMGCCGCGGTAA; REV:GGACTACHVGGGTWTCTAAT yes 43.71332908 ENVO:urban biome None Daily no None I use some other type of birth control CCME yes years None This analysis was done as in Caporaso et al 2011 Genome research. The PCR primers (F515/R806) were developed against the V4 region of the 16S rRNA (both bacteria and archaea), which we determined would yield optimal community clustering with reads of this length using a procedure similar to that of ref. 15. [For reference, this primer pair amplifies the region 533_786 in the Escherichia coli strain 83972 sequence (greengenes accession no. prokMSA_id:470367).] The reverse PCR primer is barcoded with a 12-base error-correcting Golay code to facilitate multiplexing of up to 1,500 samples per lane, and both PCR primers contain sequencer adapter regions. American Gut Project Stool sample None Regularly (3-5 times/week) 8/24/72 no None ENVO:feces None Eczema yes yes no V4 American Gut Project 56 None no human None None None female yes Indoors 10/2/13 0.0 None no 51 to 75% 16 no None 7651 yes Husband yes .1,g yes Never None None Occasionally (1-2 times/week) None CCME UBERON:feces right None no no ENVO:human-associated habitat FRS- Vit B 7:45 AM no City None 7-8 hours Omnivore CCME None CCME no 142.0 None I do not have IBD yes 0 9606 MiSeq 408170 More than 30 no 301 None SLE Lupus related or can be by flashing lights yes AGP6_rerun_L001 no Illumina I use deodorant Fish, None, Indoor no Brocoli and lettuce 195 Seasonal allergies no 62 MiSeq1 2191 None Fecal, oral and skin samples from round 3 MiSeq None Decreased more than 10 pounds Rice I do not have diabetes carlsbad no Occasionally (1-2 times/week) no CA None 33.095442 None no yes American_Gut_round 6
000010807B.1212956 GTCCGCAAGTTA GTGTGCCAGCMGCCGCGGTAA None More than one year ago yes n 12/18/13 None 49.0 72.0 None UBERON:feces None None no None 19.26420975 Housing... Regularly (3-5 times/week) None no Caucasian USA 61 Occasionally (1-2 times/week) 2191:1963962429 no 11201 -73.9859414 Contact... None None None no None UBERON:feces None None None 20 10807B None Stool More than one year ago GAZ:United States of America Not in the last year None human gut metagenome None None 16S rRNA sequencing by synthesis Not in the last year FWD:GTGCCAGCMGCCGCGGTAA; REV:GGACTACHVGGGTWTCTAAT no 25.05680552 ENVO:urban biome None Daily no None No CCME no years None This analysis was done as in Caporaso et al 2011 Genome research. The PCR primers (F515/R806) were developed against the V4 region of the 16S rRNA (both bacteria and archaea), which we determined would yield optimal community clustering with reads of this length using a procedure similar to that of ref. 15. [For reference, this primer pair amplifies the region 533_786 in the Escherichia coli strain 83972 sequence (greengenes accession no. prokMSA_id:470367).] The reverse PCR primer is barcoded with a 12-base error-correcting Golay code to facilitate multiplexing of up to 1,500 samples per lane, and both PCR primers contain sequencer adapter regions. American Gut Project Stool sample None Regularly (3-5 times/week) 7/1/65 no None ENVO:feces None Rosacea None no no V4 American Gut Project 67 None yes human None None None female None Depends on the season 11/7/13 0.0 None no 25 to 50% None no None 10807 no None None .1,g no Rarely (few times/month) yes None Regularly (3-5 times/week) None CCME UBERON:feces right None no no ENVO:human-associated habitat None 2:27 PM no Bottled None 7-8 hours Omnivore CCME None CCME no 170.0 None I do not have IBD no 0 9606 MiSeq 408170 6 to 10 None 105 None None no AGP6_rerun_L001 no Illumina Not sure, but I use some form of deoderant/antiperspirant Contact..., Housing... no carrot 160 None no 80 MiSeq1 2191 None Fecal, oral and skin samples from round 3 MiSeq None Remained stable bread I do not have diabetes brooklyn no Regularly (3-5 times/week) no NY None 40.6986772 None no yes American_Gut_round 6
000003494.1213142 CAAGGCACAAGG GTGTGCCAGCMGCCGCGGTAA 35 Within the past year None n 12/18/13 None 43.0 60.0 None UBERON:feces Lack of sleep Caffeine yes Foods; red wine 4.185313702 Housing... Rarely (few times/month) 40 no Other USA 100 Rarely (few times/month) 2191:1722032144 no 33073 -80.1819268 Contact... None None None no None UBERON:feces None Monthly no 0 3494 yes Stool None GAZ:United States of America Not in the last year None human gut metagenome None yes 16S rRNA sequencing by synthesis In the past year FWD:GTGCCAGCMGCCGCGGTAA; REV:GGACTACHVGGGTWTCTAAT yes None ENVO:urban biome None Daily no None No CCME yes years None This analysis was done as in Caporaso et al 2011 Genome research. The PCR primers (F515/R806) were developed against the V4 region of the 16S rRNA (both bacteria and archaea), which we determined would yield optimal community clustering with reads of this length using a procedure similar to that of ref. 15. [For reference, this primer pair amplifies the region 533_786 in the Escherichia coli strain 83972 sequence (greengenes accession no. prokMSA_id:470367).] The reverse PCR primer is barcoded with a 12-base error-correcting Golay code to facilitate multiplexing of up to 1,500 samples per lane, and both PCR primers contain sequencer adapter regions. American Gut Project Stool sample None Regularly (3-5 times/week) 9/30/70 no None ENVO:feces South American Indian Rosacea yes no no V4 American Gut Project None None no human None None None female yes Indoors 11/9/13 0.0 yes no 51 to 75% 25 no None 3494 yes Husband, Daughter, Son yes .1,g yes Never None None Occasionally (1-2 times/week) None CCME UBERON:feces right None yes no ENVO:human-associated habitat Vit D 9:30 AM no Filtered None 6-7 hours Omnivore CCME mostly gluten free CCME no None None I do not have IBD yes 0 9606 MiSeq 408170 6 to 10 no 155 None None no AGP6_rerun_L001 no Illumina I use an antiperspirant Contact..., Housing... no leafy greens 134 None no 100 MiSeq1 2191 None Fecal, oral and skin samples from round 3 MiSeq None Remained stable bread I do not have diabetes coconut creek no Rarely (few times/month) no FL None 26.3003637 None yes no American_Gut_round 6
000001613.1213143 AGGAACCAGACG GTGTGCCAGCMGCCGCGGTAA 60 Within the past 6 months None n 12/18/13 None 29.0 79.0 None UBERON:feces None None no None 111.6498184 Indoor Occasionally (1-2 times/week) 15 no Caucasian USA 100 Never 2191:394367686 no 90024 -118.4367551 Little None None None no None UBERON:feces None None None 100 1613 None Stool More than one year ago GAZ:United States of America Not in the last year None human gut metagenome None None 16S rRNA sequencing by synthesis In the past year FWD:GTGCCAGCMGCCGCGGTAA; REV:GGACTACHVGGGTWTCTAAT no 28.24265381 ENVO:urban biome None Daily no None None CCME no years None This analysis was done as in Caporaso et al 2011 Genome research. The PCR primers (F515/R806) were developed against the V4 region of the 16S rRNA (both bacteria and archaea), which we determined would yield optimal community clustering with reads of this length using a procedure similar to that of ref. 15. [For reference, this primer pair amplifies the region 533_786 in the Escherichia coli strain 83972 sequence (greengenes accession no. prokMSA_id:470367).] The reverse PCR primer is barcoded with a 12-base error-correcting Golay code to facilitate multiplexing of up to 1,500 samples per lane, and both PCR primers contain sequencer adapter regions. American Gut Project Stool sample None Daily 6/27/85 no yes ENVO:feces None I do not have a skin condition None no no V4 American Gut Project 66 None yes human None None None male None Both 9/25/13 0.0 None no Less than 25% 25 no None 1613 yes None None .1,g yes Never None None Rarely (few times/month) None CCME UBERON:feces right None no no ENVO:human-associated habitat calcium, B12 11:45 PM no Filtered None 7-8 hours Vegan CCME None CCME no 168.0 None I do not have IBD no 0 9606 MiSeq 408170 More than 30 None 465 None None yes AGP6_rerun_L001 no Illumina I use deodorant Dog, Little, Indoor no leafy greens 175 None no 0 MiSeq1 2191 None Fecal, oral and skin samples from round 3 MiSeq None Remained stable fruit I do not have diabetes los angeles no Never no CA None 34.0631451 None yes no American_Gut_round 6
Blank33.G12.1213069 TCAGGTTGCCCA GTGTGCCAGCMGCCGCGGTAA None None None n 12/18/13 None None None None None None None None None 1624.1 None None None None None None None None 2191:unknown None 80309 -105.79 None None None None None None None None None None None Blank33.G12 None Blank None GAZ:United States of America None None unclassified metagenome None None 16S rRNA sequencing by synthesis None FWD:GTGCCAGCMGCCGCGGTAA; REV:GGACTACHVGGGTWTCTAAT None None ENVO:aquatic biome None None None None None CCME None years None This analysis was done as in Caporaso et al 2011 Genome research. The PCR primers (F515/R806) were developed against the V4 region of the 16S rRNA (both bacteria and archaea), which we determined would yield optimal community clustering with reads of this length using a procedure similar to that of ref. 15. [For reference, this primer pair amplifies the region 533_786 in the Escherichia coli strain 83972 sequence (greengenes accession no. prokMSA_id:470367).] The reverse PCR primer is barcoded with a 12-base error-correcting Golay code to facilitate multiplexing of up to 1,500 samples per lane, and both PCR primers contain sequencer adapter regions. American Gut Project blank None None None None None ENVO:sterile water None None None None None V4 American Gut Project None None None None None None None unknown None None None 0.0 None None None None None None Blank33.G12 None None None .1,g None None None None None None CCME None unknown None None None ENVO:water None None None None None None None CCME None CCME None None None None None 0 None MiSeq 408169 None None None None None None AGP6_rerun_L001 None Illumina None None None None None None None None MiSeq1 2191 None Fecal, oral and skin samples from round 3 MiSeq None None None None boulder None None None CO None 40.02 None None None American_Gut_round 27
000010136.1212950 TACTCTCTTAGC GTGTGCCAGCMGCCGCGGTAA 35 Within the past year None n 12/18/13 yes 57.0 83.0 None UBERON:feces None None no None 198.0540009 Housing... Never 14 no Caucasian USA 90 Never 2191:972215834 no 13078 -76.0623979 Contact... None None None no None UBERON:feces None None None 33 10136 None Stool More than one year ago GAZ:United States of America Not in the last year None human gut metagenome None None 16S rRNA sequencing by synthesis Not in the last year FWD:GTGCCAGCMGCCGCGGTAA; REV:GGACTACHVGGGTWTCTAAT no 28.12608131 ENVO:urban biome None Daily no None None CCME yes years None This analysis was done as in Caporaso et al 2011 Genome research. The PCR primers (F515/R806) were developed against the V4 region of the 16S rRNA (both bacteria and archaea), which we determined would yield optimal community clustering with reads of this length using a procedure similar to that of ref. 15. [For reference, this primer pair amplifies the region 533_786 in the Escherichia coli strain 83972 sequence (greengenes accession no. prokMSA_id:470367).] The reverse PCR primer is barcoded with a 12-base error-correcting Golay code to facilitate multiplexing of up to 1,500 samples per lane, and both PCR primers contain sequencer adapter regions. American Gut Project Stool sample None Occasionally (1-2 times/week) 11/17/56 no None ENVO:feces None I do not have a skin condition yes yes no V4 American Gut Project 68 None no human None None None male None Outdoors 11/4/13 0.0 None no 51 to 75% 41 no None 10136 no Wife None .1,g yes Never yes None Daily None CCME UBERON:feces right None no no ENVO:human-associated habitat Calcium Citrate w/ Vitamin D, Vitamin C, Fish Oil w. Omega 3 6:50 AM no Well None 5-6 hours Omnivore CCME None CCME no 173.0 None I do not have IBD yes 0 9606 MiSeq 408170 21 to 30 None 140 None None no AGP6_rerun_L001 no Illumina I use deodorant Contact..., Housing... yes Leafy Greens 185 None no 67 MiSeq1 2191 Penicillin Fecal, oral and skin samples from round 3 MiSeq None Remained stable Bread, beer I do not have diabetes jamesville yes Rarely (few times/month) no NY None 42.955273 None yes yes American_Gut_round 6
000009425.1213094 AAGTCACACACA GTGTGCCAGCMGCCGCGGTAA 51 More than one year ago None n 12/18/13 None 58.0 93.0 None UBERON:feces None None yes None 80.93725586 Housing... Rarely (few times/month) 17 no Caucasian USA 100 Daily 2191:429198988 no 39272 -90.2453671 Contact... None None None no None UBERON:feces None None None 27 9425 None Stool More than one year ago GAZ:United States of America Not in the last year None human gut metagenome None None 16S rRNA sequencing by synthesis Not in the last year FWD:GTGCCAGCMGCCGCGGTAA; REV:GGACTACHVGGGTWTCTAAT no 36.66439909 ENVO:urban biome None Daily no None No CCME no years None This analysis was done as in Caporaso et al 2011 Genome research. The PCR primers (F515/R806) were developed against the V4 region of the 16S rRNA (both bacteria and archaea), which we determined would yield optimal community clustering with reads of this length using a procedure similar to that of ref. 15. [For reference, this primer pair amplifies the region 533_786 in the Escherichia coli strain 83972 sequence (greengenes accession no. prokMSA_id:470367).] The reverse PCR primer is barcoded with a 12-base error-correcting Golay code to facilitate multiplexing of up to 1,500 samples per lane, and both PCR primers contain sequencer adapter regions. American Gut Project Stool sample None Regularly (3-5 times/week) 7/13/56 no yes ENVO:feces None I do not have a skin condition None yes no V4 American Gut Project 63 None no human None None None female None Indoors 9/26/13 0.0 None no 51 to 75% 32 no None 9425 no None None .1,g yes Never None None Regularly (3-5 times/week) None CCME UBERON:feces right None no no ENVO:human-associated habitat Mg, Ca, Zn, biotin,Vitamin C, Vitamin D 6:45 AM no Bottled None 7-8 hours Omnivore CCME None CCME no 160.0 None I do not have IBD no 0 9606 MiSeq 408170 11 to 20 None 119 None None no AGP6_rerun_L001 no Illumina I use an antiperspirant Contact..., Housing... yes green beans 207 None no 73 MiSeq1 2191 None Fecal, oral and skin samples from round 3 MiSeq None Remained stable bread I do not have diabetes byram no Regularly (3-5 times/week) no MS None 32.1793163 None yes yes American_Gut_round 6
000010181.1213135 GTTCACGCCCAA GTGTGCCAGCMGCCGCGGTAA 4 Within the past 3 months None n 12/18/13 yes 49.0 52.0 None UBERON:feces None None no None 1575.246948 Housing... Daily 45 no Caucasian USA 91 Rarely (few times/month) 2191:1012678920 no 80301-3170 -105.2077798 Contact... None None None no None UBERON:feces None None None 10 10181 None Stool More than one year ago GAZ:United States of America Not in the last year None human gut metagenome None None 16S rRNA sequencing by synthesis Not in the last year FWD:GTGCCAGCMGCCGCGGTAA; REV:GGACTACHVGGGTWTCTAAT no None ENVO:urban biome None Daily no None No CCME no years None This analysis was done as in Caporaso et al 2011 Genome research. The PCR primers (F515/R806) were developed against the V4 region of the 16S rRNA (both bacteria and archaea), which we determined would yield optimal community clustering with reads of this length using a procedure similar to that of ref. 15. [For reference, this primer pair amplifies the region 533_786 in the Escherichia coli strain 83972 sequence (greengenes accession no. prokMSA_id:470367).] The reverse PCR primer is barcoded with a 12-base error-correcting Golay code to facilitate multiplexing of up to 1,500 samples per lane, and both PCR primers contain sequencer adapter regions. American Gut Project Stool sample None Daily 11/11/64 no None ENVO:feces None I do not have a skin condition None no no V4 American Gut Project None None no human None None None female None Outdoors 10/16/13 0.0 None no Less than 25% 42 no None 10181 no None None .1,g yes Never None None Rarely (few times/month) None CCME UBERON:feces right None yes no ENVO:human-associated habitat iodine, 2 drops per day, spruce bark, 500 mg, three times a day with meals, cranActin, 400 mg, one per day, psyllium, 60 gm/ day (1-2 tbs b4 ea meal) 9:00 AM no City None 8 or more hours Omnivore but no red meat CCME very low carb / low acidic / high alkaline CCME no None None I do not have IBD no 0 9606 MiSeq 408170 11 to 20 None 560 None None no AGP6_rerun_L001 no Illumina I do not use deodorant or antiperspirant Contact..., Housing... no greens (kale) 115 None no 90 MiSeq1 2191 None Fecal, oral and skin samples from round 3 MiSeq None Remained stable from vegetables (mostly green) I do not have diabetes boulder yes Never no CO None 40.0406506 None yes no American_Gut_round 6
000006643.1213112 TTACCGACGAGT GTGTGCCAGCMGCCGCGGTAA 50 Within the past year None n 12/18/13 yes 55.0 52.0 None UBERON:feces None None yes None 312.8041687 Outdoor Daily 18 no Caucasian USA 100 Never 2191:20619573 no 3224 -71.5486562 Moderate None None None no None UBERON:feces None None None 50 6643 None Stool More than one year ago GAZ:United States of America In the past 6 months None human gut metagenome None None 16S rRNA sequencing by synthesis Not in the last year FWD:GTGCCAGCMGCCGCGGTAA; REV:GGACTACHVGGGTWTCTAAT no 20.36911061 ENVO:urban biome None Daily no None No CCME no years None This analysis was done as in Caporaso et al 2011 Genome research. The PCR primers (F515/R806) were developed against the V4 region of the 16S rRNA (both bacteria and archaea), which we determined would yield optimal community clustering with reads of this length using a procedure similar to that of ref. 15. [For reference, this primer pair amplifies the region 533_786 in the Escherichia coli strain 83972 sequence (greengenes accession no. prokMSA_id:470367).] The reverse PCR primer is barcoded with a 12-base error-correcting Golay code to facilitate multiplexing of up to 1,500 samples per lane, and both PCR primers contain sequencer adapter regions. American Gut Project Stool sample None Daily 11/12/58 no None ENVO:feces None Rosacea None yes no V4 American Gut Project 63 cellulitis yes human None None None female None Outdoors 11/11/13 0.0 None no 25 to 50% 32 no None 6643 no None None .1,g no Never yes None Regularly (3-5 times/week) None CCME UBERON:feces unknown None no no ENVO:human-associated habitat None 11:40 AM no Well None 8 or more hours Omnivore CCME None CCME no 160.0 don't recall I do not have IBD yes 0 9606 MiSeq 408170 21 to 30 None 98 None None yes AGP6_rerun_L001 no Illumina I use deodorant chickens, Moderate, Outdoor no brocolli 115 None no 50 MiSeq1 2191 None Fecal, oral and skin samples from round 3 MiSeq None Remained stable fruit and vegetables I do not have diabetes canterbury no Never no NH None 43.3582442 None yes yes American_Gut_round 6
000009127.1212993 GATCATTCTCTC GTGTGCCAGCMGCCGCGGTAA None Within the past 6 months None n 12/18/13 None 9.0 23.0 None UBERON:feces None None no None 25.51987648 Indoor Rarely (few times/month) None yes Caucasian USA 0 Never 2191:167648365 no 11238 -73.9624327 Little None None None no None UBERON:feces None None None 50 9127 None Stool More than one year ago GAZ:United States of America Not in the last year None human gut metagenome None None 16S rRNA sequencing by synthesis Not in the last year FWD:GTGCCAGCMGCCGCGGTAA; REV:GGACTACHVGGGTWTCTAAT no 14.06 ENVO:urban biome None Daily no None No CCME yes years None This analysis was done as in Caporaso et al 2011 Genome research. The PCR primers (F515/R806) were developed against the V4 region of the 16S rRNA (both bacteria and archaea), which we determined would yield optimal community clustering with reads of this length using a procedure similar to that of ref. 15. [For reference, this primer pair amplifies the region 533_786 in the Escherichia coli strain 83972 sequence (greengenes accession no. prokMSA_id:470367).] The reverse PCR primer is barcoded with a 12-base error-correcting Golay code to facilitate multiplexing of up to 1,500 samples per lane, and both PCR primers contain sequencer adapter regions. American Gut Project Stool sample None Daily 7/25/05 no None ENVO:feces None I do not have a skin condition None no no V4 American Gut Project 50 None no human None None None female None Outdoors 9/20/13 0.0 None no Less than 25% None no None 9127 no Mom, dad, Brother None .1,g no Never None None Never None CCME UBERON:feces right None no no ENVO:human-associated habitat None 7:25 PM None Filtered None 8 or more hours Omnivore CCME None CCME no 127.0 None I do not have IBD yes 0 9606 MiSeq 408170 11 to 20 None 141 None None yes AGP6_rerun_L001 no Illumina I do not use deodorant or antiperspirant fish, Little, Indoor no lettuce 50 None no 50 MiSeq1 2191 None Fecal, oral and skin samples from round 3 MiSeq None Decreased more than 10 pounds cookies I do not have diabetes brooklyn no Never no NY None 40.6805029 None no no American_Gut_round 6
000009432.1213083 CGATCGAACACT GTGTGCCAGCMGCCGCGGTAA 51 Never yes n 12/18/13 None 67.0 63.0 None UBERON:feces None None yes None 201.5665436 Indoor, Housing... Daily 15 no Caucasian USA 100 Occasionally (1-2 times/week) 2191:2579760184 no 78634 -97.5466702 Extensive, Contact... None None None no None UBERON:feces None None None None 9432 None Stool More than one year ago GAZ:United States of America Not in the last year None human gut metagenome None None 16S rRNA sequencing by synthesis In the past year FWD:GTGCCAGCMGCCGCGGTAA; REV:GGACTACHVGGGTWTCTAAT no 24.97430083 ENVO:urban biome None Daily no None No CCME no years None This analysis was done as in Caporaso et al 2011 Genome research. The PCR primers (F515/R806) were developed against the V4 region of the 16S rRNA (both bacteria and archaea), which we determined would yield optimal community clustering with reads of this length using a procedure similar to that of ref. 15. [For reference, this primer pair amplifies the region 533_786 in the Escherichia coli strain 83972 sequence (greengenes accession no. prokMSA_id:470367).] The reverse PCR primer is barcoded with a 12-base error-correcting Golay code to facilitate multiplexing of up to 1,500 samples per lane, and both PCR primers contain sequencer adapter regions. American Gut Project Stool sample None Rarely (few times/month) 3/31/47 no None ENVO:feces None I do not have a skin condition None no no V4 American Gut Project 63 None yes human None None None female None Indoors 9/10/13 0.0 None no Less than 25% 34 no None 9432 yes None None .1,g no Never None None Regularly (3-5 times/week) None CCME UBERON:feces ambidextrous None no no ENVO:human-associated habitat probiotic 7:55 AM no City None 6-7 hours Omnivore CCME None CCME no 160.0 None I do not have IBD no 0 9606 MiSeq 408170 11 to 20 None 104.3 None None no AGP6_rerun_L001 no Illumina I use an antiperspirant Extensive, Contact..., Indoor, Housing... no leafy greens 141 None no None MiSeq1 2191 None Fecal, oral and skin samples from round 3 MiSeq None Remained stable bread I do not have diabetes hutto no Never no TX None 30.5426995 None yes yes American_Gut_round 6
000009175.1213072 TTCTCATGGAGG GTGTGCCAGCMGCCGCGGTAA 44 More than one year ago None n 12/18/13 yes 60.0 57.0 None UBERON:feces None None yes None 177.6651611 Indoor Never 18 no Caucasian USA 100 Regularly (3-5 times/week) 2191:2481236867 yes 17225 -77.7277714 Moderate None None None no None UBERON:feces None None None 60 9175 None Stool More than one year ago GAZ:United States of America In the past year None human gut metagenome None None 16S rRNA sequencing by synthesis Not in the last year FWD:GTGCCAGCMGCCGCGGTAA; REV:GGACTACHVGGGTWTCTAAT no 20.9652071 ENVO:urban biome None Daily no None No CCME no years None This analysis was done as in Caporaso et al 2011 Genome research. The PCR primers (F515/R806) were developed against the V4 region of the 16S rRNA (both bacteria and archaea), which we determined would yield optimal community clustering with reads of this length using a procedure similar to that of ref. 15. [For reference, this primer pair amplifies the region 533_786 in the Escherichia coli strain 83972 sequence (greengenes accession no. prokMSA_id:470367).] The reverse PCR primer is barcoded with a 12-base error-correcting Golay code to facilitate multiplexing of up to 1,500 samples per lane, and both PCR primers contain sequencer adapter regions. American Gut Project Stool sample None Regularly (3-5 times/week) 7/16/54 no None ENVO:feces None I do not have a skin condition None yes no V4 American Gut Project 65 Lyme Disease yes human None None None female None Depends on the season 10/3/13 0.0 None no Less than 25% 38 no None 9175 no None None .1,g yes Never None None Daily None CCME UBERON:feces right None no no ENVO:human-associated habitat CoQ 10 400mg, Vit C 500mg bid, Milk Thistle 750mg qd, Resveratrol 500mg, Pyloricil (Orthomolecular), NT Factor Energy (Researched Nutritionals), Enhansa Repair (Lee Silsby), Iodoral 37.5 mg, DHEA 5 mg, Grapefruit Seed Extract, Maca (2 caps daily), Magnesium Taurate 250mg, N-Acetyl Cysteine 500mg bid 7:00 AM no Well None 7-8 hours Omnivore CCME None CCME yes 165.0 Doxycycline I do not have IBD no 0 9606 MiSeq 408170 21 to 30 None 168.5 None None no AGP6_rerun_L001 no Illumina I use deodorant Scottish Terrier, Moderate, Indoor no leafy greens (kale, chard) 126 None no 40 MiSeq1 2191 I have delayed hypersensitivity reactions to potassium sorbate, carob, rosemary, phenols, cherries, cane sugar, aloe Fecal, oral and skin samples from round 3 MiSeq None Remained stable grains (gluten-free, organic) I do not have diabetes greencastle no Rarely (few times/month) no PA None 39.790371 None yes no American_Gut_round 6
000010914.1212995 GTTTGGCCACAC GTGTGCCAGCMGCCGCGGTAA 55 More than one year ago None n 12/18/13 None 59.0 88.0 None UBERON:feces None None yes None 275.3244629 Housing... Daily 26 no Caucasian USA 100 Never 2191:1141720791 no 58103 -96.8262901 Contact... None None None no None UBERON:feces None None None 53 10914 None Stool More than one year ago GAZ:United States of America Not in the last year None human gut metagenome None None 16S rRNA sequencing by synthesis In the past month FWD:GTGCCAGCMGCCGCGGTAA; REV:GGACTACHVGGGTWTCTAAT no 29.64641003 ENVO:urban biome None Daily no None None CCME no years None This analysis was done as in Caporaso et al 2011 Genome research. The PCR primers (F515/R806) were developed against the V4 region of the 16S rRNA (both bacteria and archaea), which we determined would yield optimal community clustering with reads of this length using a procedure similar to that of ref. 15. [For reference, this primer pair amplifies the region 533_786 in the Escherichia coli strain 83972 sequence (greengenes accession no. prokMSA_id:470367).] The reverse PCR primer is barcoded with a 12-base error-correcting Golay code to facilitate multiplexing of up to 1,500 samples per lane, and both PCR primers contain sequencer adapter regions. American Gut Project Stool sample None Regularly (3-5 times/week) 4/21/55 no None ENVO:feces None I do not have a skin condition None no no V4 American Gut Project 68 None None human None None None male None Both 11/5/13 0.0 yes no 51 to 75% 19 no None 10914 no None None .1,g no Never None None Never None CCME UBERON:feces right None no no ENVO:human-associated habitat None 6:15 AM no City None 6-7 hours Omnivore CCME None CCME no 173.0 None Crohn's disease yes 0 9606 MiSeq 408170 6 to 10 None 46 None None no AGP6_rerun_L001 no Illumina Not sure, but I use some form of deodorant/antiperspirant Contact..., Housing... yes sweet potato 195 None no 47 MiSeq1 2191 None Fecal, oral and skin samples from round 3 MiSeq None Remained stable starch I do not have diabetes fargo None Rarely (few times/month) no ND None 46.8647086 None yes yes American_Gut_round 6
000010777.1213117 AGCAGGCACGAA GTGTGCCAGCMGCCGCGGTAA 55 More than one year ago None n 12/18/13 None 27.0 54.0 None UBERON:feces None None no None 298.0795593 Housing... Occasionally (1-2 times/week) 26 no Caucasian USA 100 Rarely (few times/month) 2191:879837438 no 91104 -118.1181199 Contact... None None None no None UBERON:feces None None None 90 10777 None Stool More than one year ago GAZ:United States of America Not in the last year None human gut metagenome None None 16S rRNA sequencing by synthesis In the past year FWD:GTGCCAGCMGCCGCGGTAA; REV:GGACTACHVGGGTWTCTAAT no 21.25472411 ENVO:urban biome None Daily no None I take the pill CCME no years None This analysis was done as in Caporaso et al 2011 Genome research. The PCR primers (F515/R806) were developed against the V4 region of the 16S rRNA (both bacteria and archaea), which we determined would yield optimal community clustering with reads of this length using a procedure similar to that of ref. 15. [For reference, this primer pair amplifies the region 533_786 in the Escherichia coli strain 83972 sequence (greengenes accession no. prokMSA_id:470367).] The reverse PCR primer is barcoded with a 12-base error-correcting Golay code to facilitate multiplexing of up to 1,500 samples per lane, and both PCR primers contain sequencer adapter regions. American Gut Project Stool sample None Occasionally (1-2 times/week) 7/13/87 no None ENVO:feces None I do not have a skin condition None yes no V4 American Gut Project 63 None no human None One None female None Outdoors 11/10/13 0.0 None no 25 to 50% 19 yes None 10777 no None None .1,g no Never yes None Regularly (3-5 times/week) None CCME UBERON:feces right None yes no ENVO:human-associated habitat None 10:40 AM yes City no 7-8 hours Omnivore CCME bell pepper intolerance, beer intolerance, generally stay away from garlic and beans as they also affect my digestion CCME no 160.0 None I do not have IBD no 0 9606 MiSeq 408170 6 to 10 None 108 None None no AGP6_rerun_L001 no Illumina I use an antiperspirant Contact..., Housing... no zucchini 120 None yes 10 MiSeq1 2191 None Fecal, oral and skin samples from round 3 MiSeq None Remained stable rice or pasta I do not have diabetes pasadena no Rarely (few times/month) no CA no 34.1657707 None yes yes American_Gut_round 6
000010135.1213026 CCGATGCCTTGA GTGTGCCAGCMGCCGCGGTAA 50 More than one year ago None n 12/18/13 None 59.0 68.0 None UBERON:feces None None no None 71.08123016 Indoor Daily 30 no Caucasian USA 100 Daily 2191:1519269051 no 4963 -69.721995 Extensive None None None no None UBERON:feces None None None 75 10135 None Stool More than one year ago GAZ:United States of America In the past year None human gut metagenome None None 16S rRNA sequencing by synthesis Not in the last year FWD:GTGCCAGCMGCCGCGGTAA; REV:GGACTACHVGGGTWTCTAAT no 24.20798898 ENVO:urban biome None Daily no None No CCME no years None This analysis was done as in Caporaso et al 2011 Genome research. The PCR primers (F515/R806) were developed against the V4 region of the 16S rRNA (both bacteria and archaea), which we determined would yield optimal community clustering with reads of this length using a procedure similar to that of ref. 15. [For reference, this primer pair amplifies the region 533_786 in the Escherichia coli strain 83972 sequence (greengenes accession no. prokMSA_id:470367).] The reverse PCR primer is barcoded with a 12-base error-correcting Golay code to facilitate multiplexing of up to 1,500 samples per lane, and both PCR primers contain sequencer adapter regions. American Gut Project Stool sample None Regularly (3-5 times/week) 3/14/55 no None ENVO:feces None I do not have a skin condition None yes no V4 American Gut Project 66 appendectomy yes human None None None female None Both 11/11/13 0.0 None no Less than 25% 20 no None 10135 yes None None .1,g yes Never None None Never None CCME UBERON:feces right None no no ENVO:human-associated habitat Cal/mag, Coq10, gcell, bind, ester c, Fiber Gluccomannan 7:20 AM yes Filtered None 6-7 hours Vegetarian but eat seafood CCME None CCME no 168.0 amoxicillan I do not have IBD None 0 9606 MiSeq 408170 6 to 10 None 140 None None no AGP6_rerun_L001 no Illumina Not sure, but I use some form of deodorant/antiperspirant dog, Extensive, Indoor yes leafy green veggies 150 None no 25 MiSeq1 2191 None Fecal, oral and skin samples from round 3 MiSeq None Remained stable veggies I do not have diabetes oakland no Rarely (few times/month) no ME None 44.5402221 None yes yes American_Gut_round 6
000010901.1213102 CTGAGCTCTGCA GTGTGCCAGCMGCCGCGGTAA 49 Within the past year None n 12/18/13 yes 32.0 47.0 None UBERON:feces None None no None 298.0219116 Housing... Occasionally (1-2 times/week) 14 no Caucasian USA 100 Occasionally (1-2 times/week) 2191:1344700119 no 15202 -80.0517215 Contact... None None None no None UBERON:feces None None None 31 10901 None Stool More than one year ago GAZ:United States of America Not in the last year None human gut metagenome None None 16S rRNA sequencing by synthesis None FWD:GTGCCAGCMGCCGCGGTAA; REV:GGACTACHVGGGTWTCTAAT no 18.5978836 ENVO:urban biome None Daily no None No CCME no years None This analysis was done as in Caporaso et al 2011 Genome research. The PCR primers (F515/R806) were developed against the V4 region of the 16S rRNA (both bacteria and archaea), which we determined would yield optimal community clustering with reads of this length using a procedure similar to that of ref. 15. [For reference, this primer pair amplifies the region 533_786 in the Escherichia coli strain 83972 sequence (greengenes accession no. prokMSA_id:470367).] The reverse PCR primer is barcoded with a 12-base error-correcting Golay code to facilitate multiplexing of up to 1,500 samples per lane, and both PCR primers contain sequencer adapter regions. American Gut Project Stool sample None Regularly (3-5 times/week) 2/17/82 no None ENVO:feces None I do not have a skin condition None no no V4 American Gut Project 63 None no human None None None female None Outdoors 11/6/13 0.0 None no 51 to 75% 37 no None 10901 no None None .1,g yes Never None None Rarely (few times/month) None CCME UBERON:feces left None no no ENVO:human-associated habitat Fish oil and magnesium 11:50 AM no Filtered None 6-7 hours Omnivore CCME None CCME no 160.0 Not sure I do not have IBD no 0 9606 MiSeq 408170 More than 30 None 163 None None no AGP6_rerun_L001 no Illumina Not sure, but I use some form of deodorant/antiperspirant Contact..., Housing... yes Sweet potato 105 None no 69 MiSeq1 2191 Penicillin Fecal, oral and skin samples from round 3 MiSeq yes Remained stable Bread I do not have diabetes bellevue no Rarely (few times/month) no PA None 40.4939576 None yes yes American_Gut_round 6
000010297.1213071 CACAGTTGAAGT GTGTGCCAGCMGCCGCGGTAA 21 More than one year ago None n 12/18/13 None 71.0 110.0 None UBERON:feces None None yes None 12.95450211 Housing... Daily 56 no Caucasian USA , Vitamin D 2000IU daily, Nordic Naturals Ultimate Omega + CoQ10 2 tablets daily Never 2191:3661282803 no 2559 -70.616142 Contact... None None None no None UBERON:feces None None None 40 10297 None Stool More than one year ago GAZ:United States of America Not in the last year None human gut metagenome None None 16S rRNA sequencing by synthesis In the past 6 months FWD:GTGCCAGCMGCCGCGGTAA; REV:GGACTACHVGGGTWTCTAAT no 35.00653061 ENVO:urban biome None Daily no None None CCME yes years None This analysis was done as in Caporaso et al 2011 Genome research. The PCR primers (F515/R806) were developed against the V4 region of the 16S rRNA (both bacteria and archaea), which we determined would yield optimal community clustering with reads of this length using a procedure similar to that of ref. 15. [For reference, this primer pair amplifies the region 533_786 in the Escherichia coli strain 83972 sequence (greengenes accession no. prokMSA_id:470367).] The reverse PCR primer is barcoded with a 12-base error-correcting Golay code to facilitate multiplexing of up to 1,500 samples per lane, and both PCR primers contain sequencer adapter regions. American Gut Project Stool sample None Daily 5/19/43 no None ENVO:feces None Psoriasis None no no V4 American Gut Project 70 None no human None None None male None Outdoors 11/12/13 0.0 None 100 Less than 25% 23 no None 10297 no Wife None .1,g yes Never yes None Occasionally (1-2 times/week) None CCME UBERON:feces right None no no ENVO:human-associated habitat Psyllium Fiber 1 tbs daily 11:30 AM yes City None 8 or more hours Omnivore CCME None CCME no 178.0 None I do not have IBD no 0 9606 MiSeq 408170 11 to 20 None 152 None None no AGP6_rerun_L001 no Illumina I use deodorant Contact..., Housing... no apples 244 None no 60 MiSeq1 2191 None Fecal, oral and skin samples from round 3 MiSeq None Remained stable bread I do not have diabetes pocasset no Occasionally (1-2 times/week) no MA None 41.6862173 None yes no American_Gut_round 6
000004288.1213027 CGAAACTACGTA GTGTGCCAGCMGCCGCGGTAA 45 Within the past year yes n 12/18/13 None 33.0 70.0 None UBERON:feces None None no None 298.0795593 Housing... Rarely (few times/month) 35 no Caucasian Switzerland 100 Rarely (few times/month) 2191:2502097471 no 91104 -118.1181199 None None None None no None UBERON:feces None None None 30 4288 None Stool Within the past year GAZ:United States of America Not in the last year None human gut metagenome None None 16S rRNA sequencing by synthesis Not in the last year FWD:GTGCCAGCMGCCGCGGTAA; REV:GGACTACHVGGGTWTCTAAT no 21.47629439 ENVO:urban biome None Daily no None None CCME no years None This analysis was done as in Caporaso et al 2011 Genome research. The PCR primers (F515/R806) were developed against the V4 region of the 16S rRNA (both bacteria and archaea), which we determined would yield optimal community clustering with reads of this length using a procedure similar to that of ref. 15. [For reference, this primer pair amplifies the region 533_786 in the Escherichia coli strain 83972 sequence (greengenes accession no. prokMSA_id:470367).] The reverse PCR primer is barcoded with a 12-base error-correcting Golay code to facilitate multiplexing of up to 1,500 samples per lane, and both PCR primers contain sequencer adapter regions. American Gut Project Stool sample None Occasionally (1-2 times/week) 5/27/81 no None ENVO:feces None I do not have a skin condition None no no V4 American Gut Project 71 None no human None None None male None None 10/2/13 0.0 None no 25 to 50% 20 no None 4288 no None None .1,g no Rarely (few times/month) yes None Occasionally (1-2 times/week) None CCME UBERON:feces right None no no ENVO:human-associated habitat None 10:00 PM no Filtered None 8 or more hours Omnivore CCME None CCME no 183.0 None I do not have IBD None 0 9606 MiSeq 408170 11 to 20 None 220 None None no AGP6_rerun_L001 no Illumina Not sure, but I use some form of deodorant/antiperspirant None, Housing... no tomatoes 154 None no 70 MiSeq1 2191 None Fecal, oral and skin samples from round 3 MiSeq None Remained stable bread I do not have diabetes pasadena no Rarely (few times/month) no CA None 34.1657707 None no yes American_Gut_round 6
000007172.1213042 TCGCCGTGTACA GTGTGCCAGCMGCCGCGGTAA None Within the past month None n 12/18/13 None 1.0 10.0 None UBERON:feces None None no None 3.074560881 Housing... Never None no Caucasian Finland 0 Never 2191:1342447359 no 101 24.9410248 Contact... None None None no None UBERON:feces None None None None 7172 None Stool Within the past year GAZ:Finland In the past week None human gut metagenome None None 16S rRNA sequencing by synthesis Not in the last year FWD:GTGCCAGCMGCCGCGGTAA; REV:GGACTACHVGGGTWTCTAAT no 16.09365245 ENVO:urban biome None Daily no None No CCME yes years None This analysis was done as in Caporaso et al 2011 Genome research. The PCR primers (F515/R806) were developed against the V4 region of the 16S rRNA (both bacteria and archaea), which we determined would yield optimal community clustering with reads of this length using a procedure similar to that of ref. 15. [For reference, this primer pair amplifies the region 533_786 in the Escherichia coli strain 83972 sequence (greengenes accession no. prokMSA_id:470367).] The reverse PCR primer is barcoded with a 12-base error-correcting Golay code to facilitate multiplexing of up to 1,500 samples per lane, and both PCR primers contain sequencer adapter regions. American Gut Project Stool sample None None 10/20/12 no None ENVO:feces None Eczema None no no V4 American Gut Project 31 UTI prevention no human None None None female None None 9/26/13 0.0 None no None None no None 7172 no grandchild None .1,g yes Never None None Never None CCME UBERON:feces left None no no ENVO:human-associated habitat D vitamine 1:00 PM no City None 8 or more hours Omnivore CCME None CCME no 80.0 Nitrofurantoin I do not have IBD no 0 9606 MiSeq 408170 None None None None None no AGP6_rerun_L001 no Illumina I do not use deodorant or antiperspirant Contact..., Housing... no None 22 None no None MiSeq1 2191 milk Fecal, oral and skin samples from round 3 MiSeq yes None None I do not have diabetes helsinki no Never no None None 60.1733244 None no no American_Gut_round 6
000010227.1213108 TTGGTAAAGTGC GTGTGCCAGCMGCCGCGGTAA 40 More than one year ago None n 12/18/13 None 45.0 135.0 None UBERON:feces Lack of sleep Depression yes Stress 141.5803528 Indoor Regularly (3-5 times/week) 40 no Caucasian USA 100 Never 2191:1364835663 no 17569 -76.1154669 Moderate None None None no None UBERON:feces None Weekly no 20 10227 yes Stool Within the past year GAZ:United States of America In the past 6 months None human gut metagenome None None 16S rRNA sequencing by synthesis In the past year FWD:GTGCCAGCMGCCGCGGTAA; REV:GGACTACHVGGGTWTCTAAT yes 43.04081633 ENVO:urban biome None Regularly (3-5 times/week) no None None CCME no years None This analysis was done as in Caporaso et al 2011 Genome research. The PCR primers (F515/R806) were developed against the V4 region of the 16S rRNA (both bacteria and archaea), which we determined would yield optimal community clustering with reads of this length using a procedure similar to that of ref. 15. [For reference, this primer pair amplifies the region 533_786 in the Escherichia coli strain 83972 sequence (greengenes accession no. prokMSA_id:470367).] The reverse PCR primer is barcoded with a 12-base error-correcting Golay code to facilitate multiplexing of up to 1,500 samples per lane, and both PCR primers contain sequencer adapter regions. American Gut Project Stool sample None Occasionally (1-2 times/week) 5/8/69 no yes ENVO:feces None I do not have a skin condition None no no V4 American Gut Project 70 sinus infection yes human yes None None male None Outdoors 10/12/13 0.0 None no 25 to 50% 20 no None 10227 no None yes .1,g no Never None None Rarely (few times/month) None CCME UBERON:feces right None no no ENVO:human-associated habitat None 11:15 AM no Well None 5-6 hours Omnivore CCME None CCME no 178.0 amoxicllin I do not have IBD no 0 9606 MiSeq 408170 6 to 10 no 140 None None yes AGP6_rerun_L001 no Illumina I use deodorant dog, Moderate, Indoor yes lettuce 300 None no 80 MiSeq1 2191 None Fecal, oral and skin samples from round 3 MiSeq None Increased more than 10 pounds oatmeal I do not have diabetes reinholds no Rarely (few times/month) no PA None 40.2670462 None yes no American_Gut_round 6
000010839.1213095 AACAAACTGCCA GTGTGCCAGCMGCCGCGGTAA 42 Within the past 6 months None n 12/18/13 None 49.0 70.0 None UBERON:feces None None no None 5.508056164 Indoor Daily 15 no Caucasian France 96 Never 2191:411205444 no 2143 -71.1002881 Moderate None None None no None UBERON:feces None None None 33 10839 None Stool More than one year ago GAZ:United States of America Not in the last year None human gut metagenome None None 16S rRNA sequencing by synthesis In the past month FWD:GTGCCAGCMGCCGCGGTAA; REV:GGACTACHVGGGTWTCTAAT no None ENVO:urban biome None Daily no None None CCME no years None This analysis was done as in Caporaso et al 2011 Genome research. The PCR primers (F515/R806) were developed against the V4 region of the 16S rRNA (both bacteria and archaea), which we determined would yield optimal community clustering with reads of this length using a procedure similar to that of ref. 15. [For reference, this primer pair amplifies the region 533_786 in the Escherichia coli strain 83972 sequence (greengenes accession no. prokMSA_id:470367).] The reverse PCR primer is barcoded with a 12-base error-correcting Golay code to facilitate multiplexing of up to 1,500 samples per lane, and both PCR primers contain sequencer adapter regions. American Gut Project Stool sample None Occasionally (1-2 times/week) 10/1/64 no None ENVO:feces None Psoriasis yes no no V4 American Gut Project None None no human None None None male None Outdoors 11/18/13 0.0 None no Less than 25% 39 no None 10839 yes None None .1,g no Never None None Regularly (3-5 times/week) None CCME UBERON:feces right None no no ENVO:human-associated habitat None 1:20 AM no Filtered None 6-7 hours Omnivore CCME None CCME no None None I do not have IBD yes 0 9606 MiSeq 408170 11 to 20 None 170 None None no AGP6_rerun_L001 no Illumina I use an antiperspirant cat, Moderate, Indoor no carrot 155 None no 67 MiSeq1 2191 None Fecal, oral and skin samples from round 3 MiSeq None Remained stable whole wheat bread I do not have diabetes somerville no Never no MA None 42.3808757 None no yes American_Gut_round 6
000009476.1213012 CGATGTGTGGTT GTGTGCCAGCMGCCGCGGTAA 45 More than one year ago None n 12/18/13 None 34.0 80.0 None UBERON:feces None None no None 399.9625244 Indoor Occasionally (1-2 times/week) 12 no Caucasian USA 100 Never 2191:509669328 no 92082 -117.0341967 Moderate None None None no None UBERON:feces None None None 80 9476 None Stool More than one year ago GAZ:United States of America Not in the last year None human gut metagenome None None 16S rRNA sequencing by synthesis Not in the last year FWD:GTGCCAGCMGCCGCGGTAA; REV:GGACTACHVGGGTWTCTAAT no 24.13850309 ENVO:urban biome None Daily no None None CCME yes years None This analysis was done as in Caporaso et al 2011 Genome research. The PCR primers (F515/R806) were developed against the V4 region of the 16S rRNA (both bacteria and archaea), which we determined would yield optimal community clustering with reads of this length using a procedure similar to that of ref. 15. [For reference, this primer pair amplifies the region 533_786 in the Escherichia coli strain 83972 sequence (greengenes accession no. prokMSA_id:470367).] The reverse PCR primer is barcoded with a 12-base error-correcting Golay code to facilitate multiplexing of up to 1,500 samples per lane, and both PCR primers contain sequencer adapter regions. American Gut Project Stool sample None Occasionally (1-2 times/week) 7/7/80 no yes ENVO:feces None I do not have a skin condition None no no V4 American Gut Project 72 None yes human None None None male None Outdoors 10/4/13 0.0 None no 51 to 75% 43 no None 9476 no Spouse None .1,g no Never None None Never None CCME UBERON:feces right None no no ENVO:human-associated habitat None 11:00 AM no Filtered None 6-7 hours Omnivore CCME None CCME no 183.0 None I do not have IBD no 0 9606 MiSeq 408170 6 to 10 None 168 None None no AGP6_rerun_L001 no Illumina I do not use deodorant or antiperspirant 3 dogs, Moderate, Indoor no Onion 178 None no 20 MiSeq1 2191 None Fecal, oral and skin samples from round 3 MiSeq None Remained stable Bread I do not have diabetes valley center no Rarely (few times/month) no CA None 33.2183701 None yes no American_Gut_round 6
000010832.1212946 AACTCCTGTGGA GTGTGCCAGCMGCCGCGGTAA 15 Within the past year None n 12/18/13 None 38.0 97.0 None UBERON:feces None None yes None 668.5264282 Housing... Regularly (3-5 times/week) 45 no Caucasian Canada 100 Never 2191:3623651863 yes 89123 -115.1533426 Contact... None no None no None UBERON:feces None None None 30 10832 None Stool More than one year ago GAZ:United States of America Not in the last year None human gut metagenome None None 16S rRNA sequencing by synthesis Not in the last year FWD:GTGCCAGCMGCCGCGGTAA; REV:GGACTACHVGGGTWTCTAAT no 27.60135135 ENVO:urban biome None Daily no None None CCME no years None This analysis was done as in Caporaso et al 2011 Genome research. The PCR primers (F515/R806) were developed against the V4 region of the 16S rRNA (both bacteria and archaea), which we determined would yield optimal community clustering with reads of this length using a procedure similar to that of ref. 15. [For reference, this primer pair amplifies the region 533_786 in the Escherichia coli strain 83972 sequence (greengenes accession no. prokMSA_id:470367).] The reverse PCR primer is barcoded with a 12-base error-correcting Golay code to facilitate multiplexing of up to 1,500 samples per lane, and both PCR primers contain sequencer adapter regions. American Gut Project Stool sample None Occasionally (1-2 times/week) 3/31/76 no None ENVO:feces None I do not have a skin condition None no no V4 American Gut Project 74 None no human None None None male None Both 11/3/13 0.0 yes no Less than 25% 40 no None 10832 yes None None .1,g yes Never None None Regularly (3-5 times/week) None CCME UBERON:feces left 11/16/11 yes no ENVO:human-associated habitat Alpha Brain, Omega 3 fish oil, piracetam 7:30 AM yes City None 5-6 hours Omnivore CCME Paleo CCME no 188.0 None I do not have IBD yes 0 9606 MiSeq 408170 6 to 10 None 30 None None no AGP6_rerun_L001 no Illumina I use an antiperspirant Contact..., Housing... yes lettuce 215 None no 70 MiSeq1 2191 None Fecal, oral and skin samples from round 3 MiSeq None Increased more than 10 pounds corn Type II las vegas no Rarely (few times/month) no NV None 36.0357492 None yes yes American_Gut_round 6
000004219.1213074 CTTCGCGGATGT GTGTGCCAGCMGCCGCGGTAA 50 Within the past 3 months None n 12/18/13 yes 30.0 74.0 None UBERON:feces None None no None 1619.837158 Outdoor, Outdoor Regularly (3-5 times/week) 10 no Caucasian USA 100 Never 2191:4095514450 no 80303 -105.2077798 Moderate, Moderate None None None no None UBERON:feces None None None 90 4219 None Stool More than one year ago GAZ:United States of America Not in the last year None human gut metagenome yes None 16S rRNA sequencing by synthesis Not in the last year FWD:GTGCCAGCMGCCGCGGTAA; REV:GGACTACHVGGGTWTCTAAT no 23.01031541 ENVO:urban biome None Daily no None None CCME yes years None This analysis was done as in Caporaso et al 2011 Genome research. The PCR primers (F515/R806) were developed against the V4 region of the 16S rRNA (both bacteria and archaea), which we determined would yield optimal community clustering with reads of this length using a procedure similar to that of ref. 15. [For reference, this primer pair amplifies the region 533_786 in the Escherichia coli strain 83972 sequence (greengenes accession no. prokMSA_id:470367).] The reverse PCR primer is barcoded with a 12-base error-correcting Golay code to facilitate multiplexing of up to 1,500 samples per lane, and both PCR primers contain sequencer adapter regions. American Gut Project Stool sample None Regularly (3-5 times/week) 5/4/84 no None ENVO:feces None Eczema None no no V4 American Gut Project 71 None yes human None Three None unknown None Outdoors 10/17/13 0.0 None no Less than 25% 40 yes None 4219 no roommate None .1,g no Rarely (few times/month) None None Daily None CCME UBERON:feces right None no no ENVO:human-associated habitat None 10:15 AM no City no 6-7 hours Omnivore CCME None CCME no 180.0 None I do not have IBD no 0 9606 MiSeq 408170 11 to 20 None 267 None None yes AGP6_rerun_L001 no Illumina I use deodorant dog, dog, Moderate, Moderate, Outdoor, Outdoor no tomato 165 None no 10 MiSeq1 2191 None Fecal, oral and skin samples from round 3 MiSeq None Remained stable beer I do not have diabetes boulder no Rarely (few times/month) no CO no 40.0005378 None yes yes American_Gut_round 6
000004218.1213002 AACTGCGATATG GTGTGCCAGCMGCCGCGGTAA 50 Within the past 3 months None n 12/18/13 yes 30.0 74.0 None UBERON:feces None None no None 1619.837158 Outdoor, Outdoor Regularly (3-5 times/week) 10 no Caucasian USA 100 Never 2191:4095514450 no 80303 -105.2077798 Moderate, Moderate None None None no None UBERON:feces None None None 90 4218 None Stool More than one year ago GAZ:United States of America Not in the last year None human gut metagenome yes None 16S rRNA sequencing by synthesis Not in the last year FWD:GTGCCAGCMGCCGCGGTAA; REV:GGACTACHVGGGTWTCTAAT no 23.01031541 ENVO:urban biome None Daily no None None CCME yes years None This analysis was done as in Caporaso et al 2011 Genome research. The PCR primers (F515/R806) were developed against the V4 region of the 16S rRNA (both bacteria and archaea), which we determined would yield optimal community clustering with reads of this length using a procedure similar to that of ref. 15. [For reference, this primer pair amplifies the region 533_786 in the Escherichia coli strain 83972 sequence (greengenes accession no. prokMSA_id:470367).] The reverse PCR primer is barcoded with a 12-base error-correcting Golay code to facilitate multiplexing of up to 1,500 samples per lane, and both PCR primers contain sequencer adapter regions. American Gut Project Stool sample None Regularly (3-5 times/week) 5/4/84 no None ENVO:feces None Eczema None no no V4 American Gut Project 71 None yes human None Three None unknown None Outdoors 10/12/13 0.0 None no Less than 25% 40 yes None 4218 no roommate None .1,g no Rarely (few times/month) None None Daily None CCME UBERON:feces right None no no ENVO:human-associated habitat None 2:25 PM no City no 6-7 hours Omnivore CCME None CCME no 180.0 None I do not have IBD no 0 9606 MiSeq 408170 11 to 20 None 267 None None yes AGP6_rerun_L001 no Illumina I use deodorant dog, dog, Moderate, Moderate, Outdoor, Outdoor no tomato 165 None no 10 MiSeq1 2191 None Fecal, oral and skin samples from round 3 MiSeq None Remained stable beer I do not have diabetes boulder no Rarely (few times/month) no CO no 40.0005378 None yes yes American_Gut_round 6
000001540.1213103 ACCACCGTAACC GTGTGCCAGCMGCCGCGGTAA 50 More than one year ago None n 5/20/13 None 43.0 66.0 None UBERON:feces None None no None 1575.246948 None Occasionally (1-2 times/week) 30 no Caucasian USA 100 Daily 2191:3773137776 yes 80301 -105.2077798 None None None None no None UBERON:feces None None None 60 1540 None Stool More than one year ago GAZ:United States of America Not in the last year None human gut metagenome None None 16S rRNA sequencing by synthesis In the past 6 months FWD:GTGCCAGCMGCCGCGGTAA; REV:GGACTACHVGGGTWTCTAAT no 20.50009919 ENVO:urban biome None Daily no None None CCME no years None This analysis was done as in Caporaso et al 2011 Genome research. The PCR primers (F515/R806) were developed against the V4 region of the 16S rRNA (both bacteria and archaea), which we determined would yield optimal community clustering with reads of this length using a procedure similar to that of ref. 15. [For reference, this primer pair amplifies the region 533_786 in the Escherichia coli strain 83972 sequence (greengenes accession no. prokMSA_id:470367).] The reverse PCR primer is barcoded with a 12-base error-correcting Golay code to facilitate multiplexing of up to 1,500 samples per lane, and both PCR primers contain sequencer adapter regions. American Gut Project Stool sample None Regularly (3-5 times/week) 1/19/71 no None ENVO:feces None Rosacea None no no V4 American Gut Project 71 None None human None None None male None Indoors 2/15/13 0.0 None no Less than 25% 20 no None 1540 no None None .1,g no Never None None Rarely (few times/month) None CCME UBERON:feces right None no no ENVO:human-associated habitat None 12:00 PM no Filtered None 7-8 hours Omnivore CCME None CCME no 180.0 None I do not have IBD no 0 9606 MiSeq 408170 Less than 5 None 23 None None no Knight_AFG_16s_w_phiX_NoIndex_L001 no Illumina I use deoderant dog yes bean 147 None yes 40 MiSeq1 2191 None Fecal, oral and skin samples from round 3 MiSeq None Remained stable bread I do not have diabetes boulder no Never no CO None 40.0406506 None yes yes American_Gut_round 6
000001025.1213131 AGGCTAGCAGAG GTGTGCCAGCMGCCGCGGTAA 50 More than one year ago None n 12/18/13 None 47.0 79.0 None UBERON:feces None None no None 36.93350601 Housing... Occasionally (1-2 times/week) 20 no Caucasian USA 100 Never 2191:3052610923 no 2445 -71.1389101 Contact... None None None no None UBERON:feces None None None 60 1025 None Stool More than one year ago GAZ:United States of America In the past year None human gut metagenome None None 16S rRNA sequencing by synthesis Not in the last year FWD:GTGCCAGCMGCCGCGGTAA; REV:GGACTACHVGGGTWTCTAAT no 22.59459459 ENVO:urban biome None Daily no None None CCME no years None This analysis was done as in Caporaso et al 2011 Genome research. The PCR primers (F515/R806) were developed against the V4 region of the 16S rRNA (both bacteria and archaea), which we determined would yield optimal community clustering with reads of this length using a procedure similar to that of ref. 15. [For reference, this primer pair amplifies the region 533_786 in the Escherichia coli strain 83972 sequence (greengenes accession no. prokMSA_id:470367).] The reverse PCR primer is barcoded with a 12-base error-correcting Golay code to facilitate multiplexing of up to 1,500 samples per lane, and both PCR primers contain sequencer adapter regions. American Gut Project Stool sample None Regularly (3-5 times/week) 4/11/67 no None ENVO:feces None I do not have a skin condition None yes no V4 American Gut Project 74 chlamydia no human None Two None male None Both 11/18/13 0.0 None no 25 to 50% 30 yes None 1025 no None None .1,g yes Never None None Regularly (3-5 times/week) None CCME UBERON:feces right None no no ENVO:human-associated habitat tumeric, vit d, bowsellia, fish oil, fenugreek, resveratrol 9:00 AM no City no 6-7 hours Omnivore CCME None CCME no 188.0 azithroymcin I do not have IBD no 0 9606 MiSeq 408170 21 to 30 None 280 None None no AGP6_rerun_L001 no Illumina I use deodorant Contact..., Housing... yes romaine lettuce 176 None no 40 MiSeq1 2191 None Fecal, oral and skin samples from round 3 MiSeq None Remained stable pasta I do not have diabetes brookline yes Rarely (few times/month) no MA no 42.3328027 None yes yes American_Gut_round 6
000009572.1212991 GCATTACTGGAC GTGTGCCAGCMGCCGCGGTAA 51 Within the past 3 months None n 12/18/13 None 53.0 50.0 None UBERON:feces None None yes None 148.5522461 Housing... Occasionally (1-2 times/week) 19 no Caucasian USA 100 Regularly (3-5 times/week) 2191:1011229057 yes 27516 -79.0558445 Contact... None None None no None UBERON:feces None None None 60 9572 None Stool More than one year ago GAZ:United States of America Not in the last year None human gut metagenome None None 16S rRNA sequencing by synthesis In the past year FWD:GTGCCAGCMGCCGCGGTAA; REV:GGACTACHVGGGTWTCTAAT None 20.11706556 ENVO:urban biome None Daily no None No CCME no years None This analysis was done as in Caporaso et al 2011 Genome research. The PCR primers (F515/R806) were developed against the V4 region of the 16S rRNA (both bacteria and archaea), which we determined would yield optimal community clustering with reads of this length using a procedure similar to that of ref. 15. [For reference, this primer pair amplifies the region 533_786 in the Escherichia coli strain 83972 sequence (greengenes accession no. prokMSA_id:470367).] The reverse PCR primer is barcoded with a 12-base error-correcting Golay code to facilitate multiplexing of up to 1,500 samples per lane, and both PCR primers contain sequencer adapter regions. American Gut Project Stool sample None Occasionally (1-2 times/week) 5/30/61 no None ENVO:feces None I do not have a skin condition None no no V4 American Gut Project 62 None no human None None None female None Depends on the season 9/26/13 0.0 None no 25 to 50% 30 no None 9572 yes None None .1,g no Never yes None Daily None CCME UBERON:feces right None no no ENVO:human-associated habitat None 6:35 PM None Well None 7-8 hours Omnivore CCME None CCME no 157.0 None I do not have IBD no 0 9606 MiSeq 408170 11 to 20 None 153 None None no AGP6_rerun_L001 no Illumina Not sure, but I use some form of deodorant/antiperspirant Contact..., Housing... no salad greens 110 None no 40 MiSeq1 2191 None Fecal, oral and skin samples from round 3 MiSeq None Remained stable vegetables I do not have diabetes chapel hill no Never no NC None 35.9131996 None yes no American_Gut_round 6
Blank28.A4.1213055 GATCCTCATGCG GTGTGCCAGCMGCCGCGGTAA None None None n 12/18/13 None None None None None None None None None 1624.1 None None None None None None None None 2191:unknown None 80309 -105.79 None None None None None None None None None None None Blank28.A4 None Blank None GAZ:United States of America None None unclassified metagenome None None 16S rRNA sequencing by synthesis None FWD:GTGCCAGCMGCCGCGGTAA; REV:GGACTACHVGGGTWTCTAAT None None ENVO:aquatic biome None None None None None CCME None years None This analysis was done as in Caporaso et al 2011 Genome research. The PCR primers (F515/R806) were developed against the V4 region of the 16S rRNA (both bacteria and archaea), which we determined would yield optimal community clustering with reads of this length using a procedure similar to that of ref. 15. [For reference, this primer pair amplifies the region 533_786 in the Escherichia coli strain 83972 sequence (greengenes accession no. prokMSA_id:470367).] The reverse PCR primer is barcoded with a 12-base error-correcting Golay code to facilitate multiplexing of up to 1,500 samples per lane, and both PCR primers contain sequencer adapter regions. American Gut Project blank None None None None None ENVO:sterile water None None None None None V4 American Gut Project None None None None None None None unknown None None None 0.0 None None None None None None Blank28.A4 None None None .1,g None None None None None None CCME None unknown None None None ENVO:water None None None None None None None CCME None CCME None None None None None 0 None MiSeq 408169 None None None None None None AGP6_rerun_L001 None Illumina None None None None None None None None MiSeq1 2191 None Fecal, oral and skin samples from round 3 MiSeq None None None None boulder None None None CO None 40.02 None None None American_Gut_round 9
000009177.1212957 CGCACTACGCAT GTGTGCCAGCMGCCGCGGTAA None More than one year ago None n 12/18/13 None None None None UBERON:feces None None no None 6.554501057 Housing... None None yes Caucasian USA 0 None 2191:2251397584 yes 97211 -122.6386722 Contact... None None None no None UBERON:feces None None None None 9177 None Stool More than one year ago GAZ:United States of America Not in the last year None human gut metagenome None None 16S rRNA sequencing by synthesis Not in the last year FWD:GTGCCAGCMGCCGCGGTAA; REV:GGACTACHVGGGTWTCTAAT no None ENVO:urban biome None Daily no None None CCME no years None This analysis was done as in Caporaso et al 2011 Genome research. The PCR primers (F515/R806) were developed against the V4 region of the 16S rRNA (both bacteria and archaea), which we determined would yield optimal community clustering with reads of this length using a procedure similar to that of ref. 15. [For reference, this primer pair amplifies the region 533_786 in the Escherichia coli strain 83972 sequence (greengenes accession no. prokMSA_id:470367).] The reverse PCR primer is barcoded with a 12-base error-correcting Golay code to facilitate multiplexing of up to 1,500 samples per lane, and both PCR primers contain sequencer adapter regions. American Gut Project Stool sample None Daily None no None ENVO:feces None None yes None no V4 American Gut Project None None no human None None None unknown None Outdoors 9/26/13 0.0 None no None None None None 9177 no None None .1,g yes Never None None Never None CCME UBERON:feces right None yes no ENVO:human-associated habitat fish oil, vitamin B12, vitamin D 12:50 PM no City None 7-8 hours Omnivore CCME no refined sugar, no corn sweetener, no alcohol, no coffee, no caffiene CCME no None None None yes 0 9606 MiSeq 408170 None None None None None yes AGP6_rerun_L001 no Illumina I use deodorant Contact..., Housing... no None None None no None MiSeq1 2191 rice Fecal, oral and skin samples from round 3 MiSeq yes Remained stable None I do not have diabetes portland None Never None OR None 45.5767359 None yes None American_Gut_round 6
000009398.1213034 AGCTCTAGAAAC GTGTGCCAGCMGCCGCGGTAA 50 More than one year ago None n 12/18/13 None 60.0 60.0 None UBERON:feces Other Lack of sleep yes Foods; red wine 37.53943634 Indoor Occasionally (1-2 times/week) 14 no Caucasian USA 100 Regularly (3-5 times/week) 2191:3176867499 no 10706 -73.8787461 None yes None None no None UBERON:feces None A few times a year yes 40 9398 None Stool More than one year ago GAZ:United States of America Not in the last year yes human gut metagenome None None 16S rRNA sequencing by synthesis In the past year FWD:GTGCCAGCMGCCGCGGTAA; REV:GGACTACHVGGGTWTCTAAT yes 24.32336108 ENVO:urban biome None Daily no maxalt No CCME no years None This analysis was done as in Caporaso et al 2011 Genome research. The PCR primers (F515/R806) were developed against the V4 region of the 16S rRNA (both bacteria and archaea), which we determined would yield optimal community clustering with reads of this length using a procedure similar to that of ref. 15. [For reference, this primer pair amplifies the region 533_786 in the Escherichia coli strain 83972 sequence (greengenes accession no. prokMSA_id:470367).] The reverse PCR primer is barcoded with a 12-base error-correcting Golay code to facilitate multiplexing of up to 1,500 samples per lane, and both PCR primers contain sequencer adapter regions. American Gut Project Stool sample None Occasionally (1-2 times/week) 11/19/53 no yes ENVO:feces None I do not have a skin condition None yes no V4 American Gut Project 62 None no human None None None female None Depends on the season 9/28/13 0.0 None no 51 to 75% 36 no None 9398 yes None None .1,g yes Never None None Rarely (few times/month) None CCME UBERON:feces right None no no ENVO:human-associated habitat vitamin d 11:50 AM no Filtered None 7-8 hours Omnivore CCME None CCME no 157.0 None I do not have IBD yes 0 9606 MiSeq 408170 6 to 10 yes 65 deh None no AGP6_rerun_L001 no Illumina I use an antiperspirant fish, None, Indoor no tomato 133 dehydration no 60 MiSeq1 2191 None Fecal, oral and skin samples from round 3 MiSeq None Remained stable bread I do not have diabetes hastings-on-hudson no Never no NY None 40.994542 None yes no American_Gut_round 6
000009549.1213129 TGTATCTTCACC GTGTGCCAGCMGCCGCGGTAA 10 Within the past month None n 12/18/13 None 71.0 71.0 None UBERON:feces None None yes None 1629.725708 Housing... Daily 12 no Caucasian USA 100 Never 2191:3496488243 no 80306 -105.2757789 Contact... None None None no None UBERON:feces None None None 25 9549 None Stool More than one year ago GAZ:United States of America In the past year None human gut metagenome None None 16S rRNA sequencing by synthesis In the past year FWD:GTGCCAGCMGCCGCGGTAA; REV:GGACTACHVGGGTWTCTAAT no 24.02119377 ENVO:urban biome None Daily no None None CCME no years None This analysis was done as in Caporaso et al 2011 Genome research. The PCR primers (F515/R806) were developed against the V4 region of the 16S rRNA (both bacteria and archaea), which we determined would yield optimal community clustering with reads of this length using a procedure similar to that of ref. 15. [For reference, this primer pair amplifies the region 533_786 in the Escherichia coli strain 83972 sequence (greengenes accession no. prokMSA_id:470367).] The reverse PCR primer is barcoded with a 12-base error-correcting Golay code to facilitate multiplexing of up to 1,500 samples per lane, and both PCR primers contain sequencer adapter regions. American Gut Project Stool sample None Daily 11/8/42 no yes ENVO:feces None I do not have a skin condition None no no V4 American Gut Project 68 None no human None None None male None Outdoors 8/22/13 0.0 None no Less than 25% 78 no None 9549 no None None .1,g no Never None None Occasionally (1-2 times/week) None CCME UBERON:feces right None yes no ENVO:human-associated habitat None 8:00 AM no Bottled None 6-7 hours Omnivore CCME no grains, no freash dairy, no high glycemic foods CCME no 173.0 None I do not have IBD no 0 9606 MiSeq 408170 More than 30 None 80 None None yes AGP6_rerun_L001 no Illumina I do not use deodorant or antiperspirant Contact..., Housing... no low carb veg, leafy greens, tomatoes, avocado, etc 158 None no 75 MiSeq1 2191 None Fecal, oral and skin samples from round 3 MiSeq None Remained stable low carb veg I do not have diabetes boulder no Never no CO None 40.0177245 None yes no American_Gut_round 6
000001585.1212947 AGTTGAGGCATT GTGTGCCAGCMGCCGCGGTAA 37 None None n 5/20/13 yes 68.0 81.0 None UBERON:feces None None None None 443.5621033 None Daily 16 no Caucasian USA 100 Occasionally (1-2 times/week) 2191:396855132 yes 85260 -111.8926303 None None None None yes None UBERON:feces None None None 20 1585 None Stool More than one year ago GAZ:United States of America In the past month None human gut metagenome None None 16S rRNA sequencing by synthesis Not in the last year FWD:GTGCCAGCMGCCGCGGTAA; REV:GGACTACHVGGGTWTCTAAT no 28.88820018 ENVO:urban biome None Daily no None No CCME no years None This analysis was done as in Caporaso et al 2011 Genome research. The PCR primers (F515/R806) were developed against the V4 region of the 16S rRNA (both bacteria and archaea), which we determined would yield optimal community clustering with reads of this length using a procedure similar to that of ref. 15. [For reference, this primer pair amplifies the region 533_786 in the Escherichia coli strain 83972 sequence (greengenes accession no. prokMSA_id:470367).] The reverse PCR primer is barcoded with a 12-base error-correcting Golay code to facilitate multiplexing of up to 1,500 samples per lane, and both PCR primers contain sequencer adapter regions. American Gut Project Stool sample None Daily 9/30/45 no None ENVO:feces None Psoriasis None yes no V4 American Gut Project 66 dental implant surgery yes human None None None female None Both 2/15/13 0.0 None no Less than 25% 47 no None 1585 no None None .1,g yes Never None None Rarely (few times/month) None CCME UBERON:feces right None yes no ENVO:human-associated habitat krill oil, vitamin D3, vitamin k2, magnesium citrate, ubiquinol, chlorella, aller-max w/quercetin & NAC, mercole joint formula w/HA & biovaflex 11:00 AM yes Filtered None 6-7 hours Omnivore CCME low carb, no legumes, no grains except occasional rice CCME yes 168.0 amoxicillin I do not have IBD no 0 9606 MiSeq 408170 11 to 20 None 309 None None None Knight_AFG_16s_w_phiX_NoIndex_L001 None Illumina I use deoderant None no greens 179 None no 80 MiSeq1 2191 None Fecal, oral and skin samples from round 3 MiSeq None Increased more than 10 pounds vegetable & fruit I do not have diabetes scottsdale yes Rarely (few times/month) no AZ None 33.6160293 None yes yes American_Gut_round 6
000002059.1213100 CACGCTATTGGA GTGTGCCAGCMGCCGCGGTAA 20 Never None n 12/18/13 None 18.0 59.0 None UBERON:feces None None no None 199.6077576 Housing... Never 30 no Caucasian USA 100 Never 2191:1528544799 no 14472 -77.5902759 Contact... None None None no None UBERON:feces None None None None 2059 None Stool More than one year ago GAZ:United States of America Not in the last year None human gut metagenome None None 16S rRNA sequencing by synthesis Not in the last year FWD:GTGCCAGCMGCCGCGGTAA; REV:GGACTACHVGGGTWTCTAAT no 20.35865449 ENVO:urban biome None Daily no None No CCME yes years None This analysis was done as in Caporaso et al 2011 Genome research. The PCR primers (F515/R806) were developed against the V4 region of the 16S rRNA (both bacteria and archaea), which we determined would yield optimal community clustering with reads of this length using a procedure similar to that of ref. 15. [For reference, this primer pair amplifies the region 533_786 in the Escherichia coli strain 83972 sequence (greengenes accession no. prokMSA_id:470367).] The reverse PCR primer is barcoded with a 12-base error-correcting Golay code to facilitate multiplexing of up to 1,500 samples per lane, and both PCR primers contain sequencer adapter regions. American Gut Project Stool sample None Rarely (few times/month) 12/30/95 no yes ENVO:feces None I do not have a skin condition None no no V4 American Gut Project 67 None no human None None None female None Outdoors 11/14/13 0.0 None no Less than 25% 50 no None 2059 no brother None .1,g yes Never None None Never None CCME UBERON:feces right None yes no ENVO:human-associated habitat vitamin D, zinc 4:30 PM no Filtered None 7-8 hours Omnivore CCME gaps diet - no processed foods, minimal dairy and fruit, minimal starches, lots of animal fats and vegetables CCME no 170.0 None I do not have IBD yes 0 9606 MiSeq 408170 6 to 10 None None None None yes AGP6_rerun_L001 no Illumina I use deodorant Contact..., Housing... no squash 130 None no None MiSeq1 2191 None Fecal, oral and skin samples from round 3 MiSeq None Remained stable None I do not have diabetes honeoye falls no Rarely (few times/month) no NY None 42.9522855 None no no American_Gut_round 6
000004289.1213106 CCAATCGTGCAA GTGTGCCAGCMGCCGCGGTAA 52 Within the past year None n 12/18/13 None 26.0 74.0 None UBERON:feces None None no None 298.0795593 Housing... Never 20 not_sure Asian or Pacific Islander China 100 Never 2191:3918862628 no 91104 -118.1181199 Contact... None None None no None UBERON:feces None None None 45 4289 None Stool More than one year ago GAZ:United States of America Not in the last year None human gut metagenome None None 16S rRNA sequencing by synthesis Not in the last year FWD:GTGCCAGCMGCCGCGGTAA; REV:GGACTACHVGGGTWTCTAAT no 24.36357908 ENVO:urban biome None Daily no None None CCME no years None This analysis was done as in Caporaso et al 2011 Genome research. The PCR primers (F515/R806) were developed against the V4 region of the 16S rRNA (both bacteria and archaea), which we determined would yield optimal community clustering with reads of this length using a procedure similar to that of ref. 15. [For reference, this primer pair amplifies the region 533_786 in the Escherichia coli strain 83972 sequence (greengenes accession no. prokMSA_id:470367).] The reverse PCR primer is barcoded with a 12-base error-correcting Golay code to facilitate multiplexing of up to 1,500 samples per lane, and both PCR primers contain sequencer adapter regions. American Gut Project Stool sample None Regularly (3-5 times/week) 3/23/88 no None ENVO:feces None I do not have a skin condition None no no V4 American Gut Project 69 None no human None None None male None Both 10/3/13 0.0 None no 25 to 50% 28 no None 4289 no None None .1,g no Never None None Rarely (few times/month) None CCME UBERON:feces right None no no ENVO:human-associated habitat None 9:00 AM no Filtered None 7-8 hours Omnivore CCME None CCME no 178.0 None I do not have IBD no 0 9606 MiSeq 408170 11 to 20 None 26 None None no AGP6_rerun_L001 no Illumina I do not use deodorant or antiperspirant Contact..., Housing... no leafy greens 165 None no 55 MiSeq1 2191 None Fecal, oral and skin samples from round 3 MiSeq None Remained stable rice I do not have diabetes pasadena no Occasionally (1-2 times/week) no CA None 34.1657707 None no no American_Gut_round 6
000009534.1213088 CGTGCACAATTG GTGTGCCAGCMGCCGCGGTAA 35 More than one year ago None n 12/18/13 yes 58.0 63.0 None UBERON:feces None None no None 234.3610229 Indoor Occasionally (1-2 times/week) 19 yes Caucasian USA 100 Rarely (few times/month) 2191:410396684 no 61530 -89.2728627 Extensive None None None no None UBERON:feces None None None 20 9534 None Stool More than one year ago GAZ:United States of America Not in the last year None human gut metagenome None None 16S rRNA sequencing by synthesis Not in the last year FWD:GTGCCAGCMGCCGCGGTAA; REV:GGACTACHVGGGTWTCTAAT no 23.29467456 ENVO:urban biome None Daily no None No CCME no years None This analysis was done as in Caporaso et al 2011 Genome research. The PCR primers (F515/R806) were developed against the V4 region of the 16S rRNA (both bacteria and archaea), which we determined would yield optimal community clustering with reads of this length using a procedure similar to that of ref. 15. [For reference, this primer pair amplifies the region 533_786 in the Escherichia coli strain 83972 sequence (greengenes accession no. prokMSA_id:470367).] The reverse PCR primer is barcoded with a 12-base error-correcting Golay code to facilitate multiplexing of up to 1,500 samples per lane, and both PCR primers contain sequencer adapter regions. American Gut Project Stool sample None Regularly (3-5 times/week) 7/25/56 no None ENVO:feces None Rosacea None no no V4 American Gut Project 65 None no human None None None female None Both 9/3/13 0.0 None no Less than 25% 46 no None 9534 no None None .1,g no Never None None Rarely (few times/month) None CCME UBERON:feces right None yes no ENVO:human-associated habitat None 11:15 AM no City None 6-7 hours Omnivore CCME limit caffeine and grains CCME no 165.0 None I do not have IBD yes 0 9606 MiSeq 408170 11 to 20 None 192 None None yes AGP6_rerun_L001 no Illumina I use an antiperspirant Extensive, Indoor no leafy greens 140 None no 80 MiSeq1 2191 None Fecal, oral and skin samples from round 3 MiSeq None Decreased more than 10 pounds vegetable I do not have diabetes eureka no Occasionally (1-2 times/week) no IL None 40.7214251 None yes no American_Gut_round 6
Blank33.E12.1213000 TCGACCAAACAC GTGTGCCAGCMGCCGCGGTAA None None None n 12/18/13 None None None None None None None None None 1624.1 None None None None None None None None 2191:unknown None 80309 -105.79 None None None None None None None None None None None Blank33.E12 None Blank None GAZ:United States of America None None unclassified metagenome None None 16S rRNA sequencing by synthesis None FWD:GTGCCAGCMGCCGCGGTAA; REV:GGACTACHVGGGTWTCTAAT None None ENVO:aquatic biome None None None None None CCME None years None This analysis was done as in Caporaso et al 2011 Genome research. The PCR primers (F515/R806) were developed against the V4 region of the 16S rRNA (both bacteria and archaea), which we determined would yield optimal community clustering with reads of this length using a procedure similar to that of ref. 15. [For reference, this primer pair amplifies the region 533_786 in the Escherichia coli strain 83972 sequence (greengenes accession no. prokMSA_id:470367).] The reverse PCR primer is barcoded with a 12-base error-correcting Golay code to facilitate multiplexing of up to 1,500 samples per lane, and both PCR primers contain sequencer adapter regions. American Gut Project blank None None None None None ENVO:sterile water None None None None None V4 American Gut Project None None None None None None None unknown None None None 0.0 None None None None None None Blank33.E12 None None None .1,g None None None None None None CCME None unknown None None None ENVO:water None None None None None None None CCME None CCME None None None None None 0 None MiSeq 408169 None None None None None None AGP6_rerun_L001 None Illumina None None None None None None None None MiSeq1 2191 None Fecal, oral and skin samples from round 3 MiSeq None None None None boulder None None None CO None 40.02 None None None American_Gut_round 23