README.md

Sample #1

I ordered 2 kits from 2 companies (on 3/3/2021):

Psomagen: Gene & GutBiome Combo and GutBiome+

Viome: Health Intelligence Test and Gut Intelligence Test

I very much hope that I can get raw data, but this does provide something that can be compared (even if I can't).

The 2 Psomagen kits arrived on 3/8/2021, and the 2 Viome kits arrived on 3/5/2021.

All 4 samples were collected and mailed on 3/11/2021. Please note that you may need to use 2 different e-mail addresses in order to compare 2 samples at the same time from Viome.

I recieved my Psomagen Gene & GutBiome report on 3/31/2021.

I recieved my Psomagen GutBiome+ report on 4/9/2021. I think this is a different report than the GutBiome portion of the other report, including diversity scores that are on different scales? For the same sample, I had a diversity value of 77 for Gene & GutBiome and 52 for GutBiome+.

The details are also somewhat different:

Genus	Psomagen Gene & GutBiome	Psomagen GutBiome+	Viome Gut Intelligence (downgraded)	Viome Gut Intelligence (as purchased)
Agathobacter rectalis	7.6%	2.3%	Not Active?	Not Active?
Akkermansia muciniphila	3.0%	1.0% (Akkermansia sp)	Active	Active
Alistipes	4.5% (genus-level)	10.7% (7 species)	Active (9 species)	Active (9 species)
Bacteroides stercoris	19%	24.3%	Active (ATCC 43183) (ATCC CC31F) (ATCC CL09T03C01) (ATCC DSM)	Active (ATCC 43183) (ATCC CC31F) (ATCC CL09T03C01) (ATCC DSM)
Bacteroides uniformis	5.5%	8.2%	Active	Active
Bacteroides vulgatus	17%	13.8%	Active (ATCC 8482)	Active (ATCC 8482)
Lachnospira eligens	1.5%	?	Active? (Lachnospiraceae bacterium?)	Active? (Lachnospiraceae bacterium?)
Faecalibacterium prausnitzii	9.2%	1.9%	Active	Active
Parasutterella excrementihominis	2.0%	0.6%	Active (YIT 11859)	Active (YIT 11859)
Ruminococcus bicirculans	2.5%	0.8%	Active	Active
Ruminococcus bromii	2.1%	?	Not Active?	Not Active?

I think this seems like expected varation (where I would usually want replicates for metagenomics), but I hope that is made clear (and "high" and "low" are different enough to to be less likely for even biological replicates, if these had some from different stool samples - in this case, everything submitted was from the same stool sample).

This matches what I would expect for 16S biological replicates (even if these are from the same sample, rather than different samples). So, this doesn't surprise me, but I hope this is made clear to most customers. For example, I might check for for uncommon genera, and/or changes of greater than 5% (or maybe even greater than 10% or 15%) in absolute frequency. However, Psomagen explained that they are doing shotgun metagenomics, rather than 16S (and the raw data shows noticably more reads for my GutBiome+ sample). Nevertheless, I think the varialbity might match what I have seen with 16S data.

The Psomagen Gene&GutBiome and Viome (downgraded) Health Intelligence Test come from the same location in the 1 stool. The Psomagen GutBiome+ and Viome Gut Intelligence Test come from the same location in the stool sample, but it is different than the other 2 samples (even though all 4 came from the same stool sample).

After sending an e-mail request, Psomagen provided me with my raw data on 4/12/2021:

GutBiome+:

http://ngs2.macrogenlab.com/~customer/2104/2103DNHX-0611/C229-J888-E267_R1.fastq.gz http://ngs2.macrogenlab.com/~customer/2104/2103DNHX-0611/C229-J888-E267_R2.fastq.gz

Gene & GutBiome (GutBiome):

http://ngs2.macrogenlab.com/~customer/2104/2103DNMI-0598/B374-R052-T972_R1.fastq.gz http://ngs2.macrogenlab.com/~customer/2104/2103DNMI-0598/B374-R052-T972_R2.fastq.gz

Gene & GutBiome (Gene):

http://ngs2.macrogenlab.com/~customer/2104/2103DNSC-0599/A374-R052-T972.zip

Viome said that they do not currently provide raw data.

I don't believe that I recieved an e-mail, but I noticed my results were available for my downgraded Viome Health Intelligence Test on 4/15/2021 (and I believe the sample information says that this was available on 4/14/2021). My regular Gut Intelligence was not ready, as of 4/15/2021.

I can tell that I am not going to avoid a lot of the Viome recommendations to "Avoid" (such as Almonds) or take any of the recommended supplements.

I also added some notes in the table with the Psomagen samples above.

I was able to download my reports for my 2nd Viome sample on 4/26/2021.

I am not currently planning on ordering 2 of each kit for each subsequent sample.

However, for the 1st sample, this also provides the opporunity to compare the scores for the 2 Viome samples for the same sample:

Genus	Viome Gut Intelligence (downgraded)	Viome Gut Intelligence (as purchased)
Gut Microbiome Health	41 Not Optimal	49 Average
Inflammatory Activity	41 Average	36 Average
Metabolic Fitness	28 Average	29 Average
Digestive Efficiency	56 Average	71 Good
Gut Lining Health	67 Average	68 Average
Protein Fermentation	42 Average	28 Good
Gas Production	46 Average	30 Good
Active Microbial Diversity	1st Percentile Not Optimal	12th Percentile Average
Vegetables to Avoid	Bell Pepper Broccoli Brussels Sprouts Cabbage Mustard Greens Tomato	Bell Pepper Tomato
Proteins and Fats to Avoid	Almonds Chicken Egg Yolk Pistachios	Almonds Pistachios
Fruits and Grains to Avoid	None	None
Other Food Items to Avoid	None	None

So, I think it is fair to say that you should probably hesitate to take any action based upon these results. I expected this for most values with thresholds that I would guess were within a normal distribution. However, I was a bit surprised by the 1st to 12th percentile difference, even though the absolute difference is perhaps comparible to other categories (where I would guess I should probably be "average" for most or all of them).

Sample #2

I ordered 3 kits from 3 companies on 4/26/2021 (1 for each program):

Psomagen: GutBiome+

Viome: Gut Intelligence Test

thryve: Gut Health Test

The Viome and thryve kits arrived on 4/29/2021.

My Psomagen kit arrived on 4/30/2021.

All 3 samples collected on 5/3/2021.

I did not make any changes to my diet, based upon the previous set of results.

I recieved my thryve results on 5/19/2021. This includes CSV assignments for classifications, as well as FASTQ files.

I received a notification that my Viome sample would need to be reprocessed (same sample, new sequencing run) on 5/27/2021.

I recieved by Psomagen report on 5/29/2021.

Similar to before, here is a comparison of classification for this same sample:

Genus	Psomagen GutBiome+	Viome Gut Intelligence (as purchased)	thryve
Agathobacter rectalis	2.2%	Not Active?	Not Classified?
Akkermansia sp	1.4%	Active	0.916% (genus-level)
Alistipes	13.2% 7 species	Active 9 species	3.223% (genus-level)
Bacteroides stercoris	26.5%	Active 4 strains	54.456% (genus-level)
Bacteroides uniformis	5.1%	Active	see above
Bacteroides vulgatus	9.1%	Active	see above
Bifidobacterium	Not Detected	Active 5 subsp / strains	0.026% (genus-level)
Blautia	Not Reported?	Active 14 species / strains	3.949% (genus-level)
Eubacterium	Not Reported?	Active 7 species / strains	6.802% (genus-level)
Faecalibacterium prausnitzii	2.0%	Active	1.687% (genus-level)
Lactobacillus	Not Detected	Active 8 species / strains	0.006% (genus-level)
Parasutterella excrementihominis	0.9%	Active	0.011%
Pseudomonas	Not Reported?	Active 2 species	0.002% (genus-level) (bad bacteria, healthy level)
Roseburia	Not Reported?	Active 6 species / strains	0.717% (genus-level)
Ruminococcus bicirculans	0.3%	Active 6 species	6.734% (genus-level)

I sent an e-mail to Psomagen to obtain my FASTQ files on 5/29/2021, and I recieved links to download the FASTQ files on 6/8/2021:

http://ngs2.macrogenlab.com/~customer/2106/2105DNHX-0230/C058-S779-Y072_R1.fastq.gz

http://ngs2.macrogenlab.com/~customer/2106/2105DNHX-0230/C058-S779-Y072_R2.fastq.gz

I recieved my Viome results on 6/16/2021 (and I recieved e-mails about sample reprocessing on 5/27/2021 and 6/10/2021).

The Viome results are somewhat harder to compare. However, I can compare the scores between measurements. So, I have added the new sample in the table with earlier samples:

Genus	Viome Gut Intelligence (downgraded) 3/11/2021	Viome Gut Intelligence (as purchased) 3/11/2021	Viome Gut Intelligence (as purchased) 5/3/2021
Gut Microbiome Health	41 Not Optimal	49 Average	36 Not Optimal
Inflammatory Activity	41 Average	36 Average	44 Average
Metabolic Fitness	28 Average	29 Average	31 Good
Digestive Efficiency	56 Average	71 Good	41 Not Optimal
Gut Lining Health	67 Average	68 Average	67 Average
Protein Fermentation	42 Average	28 Good	75 Not Optimal
Gas Production	46 Average	30 Good	62 Average
Active Microbial Diversity	1st Percentile Not Optimal	12th Percentile Average	4th Percentile Not Optimal
Total Supplement Recommendation Count	28	30	37
Total Probiotic Recommendation Count	19	18	18
Vegetables to Avoid	Bell Pepper Broccoli Brussels Sprouts Cabbage Mustard Greens Tomato	Bell Pepper Tomato	Bell Pepper Sauerkraut Tomato
Proteins and Fats to Avoid	Almonds Chicken Egg Yolk Pistachios	Almonds Pistachios	Kefir (Cow Milk) Yogurt (Cow Milk, Plain)
Fruits and Grains to Avoid	None	None	Barley Blueberry
Other Food Items to Avoid	None	None	Coffee

I eat Activia with my lunch most days, and I think it helps some. So, I am not doing to stop taking that.

Again, please remember that I have not made any recommended changes from the previous collection. So, I drink almond milk, and I think that is helpful. However, I didn't do anything different for almonds to be removed from the foods to avoid.

Sample #3

I ordered 4 kits from 3 companies on 6/20/2021 (2 for thyrve, 1 for other companies):

Psomagen: GutBiome+ (1x)

Viome: Gut Intelligence Test (1x)

thryve: Gut Health Test (2x)

All 4 kits arrived on 6/23/2021.

I collected all 4 samples (from the same stool) on 6/27/2021. I dropped them off to mail that same day.

I recieved my thryve results on 7/14/2021. This includes CSV assignments for classifications, as well as FASTQ files.

I recieved my Psomagen results on 7/22/2021. I then sent an e-mail to recieve the raw FASTQ files. I recieved links to download the raw files on 7/26/2021.

http://ngs2.macrogenlab.com/~customer/2107/2107DNHX-0076/C882-L638-A372_R1.fastq.gz

http://ngs2.macrogenlab.com/~customer/2107/2107DNHX-0076/C882-L638-A372_R2.fastq.gzz

Also, similar to before, here is a comparison of classification for this same sample:

Genus	Psomagen GutBiome+	Viome Gut Intelligence (as purchased)	thryve (rep 1)	thryve (rep 2)
Agathobacter rectalis	2.0%	Not Active?	Not Classified?	Not Classified?
Akkermansia sp	2.9%	Active	4.692%	4.959%
Alistipes	20.7% (7 species)	Active (9 species)	4.226%	4.684%
Bacteroides stercoris	13.3%	Active (4 strains)	18.356%	16.176%
Bacteroides uniformis	7.2%	Active	4.669%	3.982%
Bacteroides vulgatus	4.1%	Active (ATCC 8482)	12.395%	11.154%
Bifidobacterium	Not Detected	Active (14 subspecies)	0.012%	0.027%
Blautia	Not Reported?	Active (12 species/strains)	5.408%	6.139%
Eubacterium	Not Reported?	Active (4 species)	4.296%	3.922%
Faecalibacterium prausnitzii	1.4%	Active	7.104%	5.226%
Lactobacillus	Not Detected	Active (delbrueckii species) (5 stains)	0.012%	0.011%
Parasutterella excrementihominis	0.6%	Active YIT 11859	0.685%	0.562%
Pseudomonas	Not Reported?	Active (aeruginosa species)	Not Classified?	Not Classified?
Roseburia	Not Reported?	Active (3 species)	0.986%	0.987%
Ruminococcus bicirculans	Not Reported?	Active (9 species)	Not Classified?	Not Classified?

I recieved e-mails from Viome about sample reprocessing (such as on 8/12/2021 and 8/26/2021). The format was swappped relative to the 2nd sample. So, I might have also recieved earlier e-mail that I deleted (especially since I had recieved results from the other companies by 7/14-21/2021). Either way, the turn-around time for Viome has been noticably longer than the other options.

I later recieved my Viome results on 9/7/2021.

Again, for comparison, here are the differences in scores for the Viome samples:

Genus	Viome Gut Intelligence (downgraded) 3/11/2021	Viome Gut Intelligence (as purchased) 3/11/2021	Viome Gut Intelligence (as purchased) 5/3/2021	Viome Gut Intelligence (as purchased) 6/27/2021
Gut Microbiome Health	41 Not Optimal	49 Average	36 Not Optimal	46 Average
Inflammatory Activity	41 Average	36 Average	44 Average	35 Good
Metabolic Fitness	28 Average	29 Average	31 Good	27 Average
Digestive Efficiency	56 Average	71 Good	41 Not Optimal	61 Average
Gut Lining Health	67 Average	68 Average	67 Average	72 Average
Protein Fermentation	42 Average	28 Good	75 Not Optimal	51 Average
Gas Production	46 Average	30 Good	62 Average	29 Good
Active Microbial Diversity	1st Percentile Not Optimal	12th Percentile Average	4th Percentile Not Optimal	12th Percentile Average
Total Supplement Recommendation Count	28	30	37	34
Total Probiotic Recommendation Count	19	18	18	18
Vegetables to Avoid	Bell Pepper Broccoli Brussels Sprouts Cabbage Mustard Greens Tomato	Bell Pepper Tomato	Bell Pepper Sauerkraut Tomato	Bell Pepper Tomato
Proteins and Fats to Avoid	Almonds Chicken Egg Yolk Pistachios	Almonds Pistachios	Kefir (Cow Milk) Yogurt (Cow Milk, Plain)	Almonds Pistachios
Fruits and Grains to Avoid	None	None	Barley Blueberry	None
Other Food Items to Avoid	None	None	Coffee	Turmeric

Again, please remember that I have not made any recommended changes from the previous collection. I will also not make any changes based upon the current set of reports.

Also, on 9/9/2021, I recieved an e-mail that my Viome sample needed to be reprocessed. However, I have already recieved those results, so I think something may be technically wrong with the e-mail system. I believe there have also been inconsistencies in whether I recieved an e-mail about results, versus periodically checking and finding results. However, to be fair, I think I have noticed that for multiple genomics companies.

Sample #4

I ordered 4 kits from 4 companies on 9/6/2021:

Psomagen: GutBiome+

Viome: Gut Intelligence Test

thryve: Gut Health Test

BIOHM: Gut Test

I had still not recieved my previous Viome results at this time, but I used a different account (from when I had 2 submissions at the same time) in order to order another sample to have pairs for 3 thryve measurements.

My understanding is that the BIOHM Gut Test does not currently provide FASTQ files, but they would be willing to work with me to provide "raw" data individually (at least for Excel files with read classification counts).

The Psomagen, Viome, and BIOHM kits arrived within a normal period of time. However, for this sample, there was a substantial delay in the delivery of the thryve kit. I contacted customer support, and I recieved the following explanation on 9/17/2021: "Unfortunately, your order hasn't been shipped out yet. We recently transferred warehouse facilities and have begun shipping out orders. However, it may take 1-2 weeks to ship out." My thryve kit then arrived on 10/4/2021.

I collected all 4 samples on 10/6/2021. My sample looked more different than the other samples (it was harder and it was composed of more distinct smaller roughly spherical parts). However, as with all samples (except for the 1st one, with "a" and "b" sites), all collections were made from a similar location from the stool.

I recieved my thryve results on 10/19/2021. This includes CSV assignments for classifications, as well as FASTQ files.

Genus	Psomagen GutBiome+	Viome Gut Intelligence (as purchased)	thryve	BIOHM (Excel file, per 44255 Phylum-assigned reads)
Agathobacter rectalis	Not Classified?	Not Active?	Not Classified?	Not Classified
Akkermansia sp	7.7%	Active 2 species	21.463%	2.53%
Alistipes	26.3% 7 species	Active 9 species	7.396%	0.2%
Bacteroides stercoris	3.4%	Active 4 strains	2.959%	(5.29% genus total)
Bacteroides uniformis	4.9%	Active	2.140%	0.26%
Bacteroides vulgatus	2.5%	Active Strain ATCC 8482	2.094%	(5.29% genus total)
Bifidobacterium	0.1%	Active 8 strains/species	0.183%	0.1%
Blautia	0.4% 3 species	Active 9 strains/species	13.584%	2.85%
Eubacterium	0.2%	Active 6 species/strains	2.182%	1.4%
Faecalibacterium prausnitzii	Not Classified?	Active	0.102%	0.1%
Lactobacillus	Not Detected	Active 2 species	0.036%	0.038%
Parasutterella excrementihominis	0.4%	Active Strain YIT 11859	0.585%	Not Classified
Pseudomonas	Not Classified?	Not Active?	Not Classified?	0.2%
Roseburia	Not Classified?	Active 4 species	0.014%	0.032%
Ruminococcus bicirculans	0.1%	Active	Not Classified? (1.081% Ruminococcus)	18.1% (genus-level)

I recieved my Viome results on 10/20/2021.

Yet again, for comparison, here are the differences in scores for the Viome samples:

Genus	Viome Gut Intelligence (downgraded) 3/11/2021	Viome Gut Intelligence (as purchased) 3/11/2021	Viome Gut Intelligence (as purchased) 5/3/2021	Viome Gut Intelligence (as purchased) 6/27/2021	Viome Gut Intelligence (as purchased) 10/6/2021
Gut Microbiome Health	41 Not Optimal	49 Average	36 Not Optimal	46 Average	40 Not Optimal
Inflammatory Activity	41 Average	36 Average	44 Average	35 Good	41 Average
Metabolic Fitness	28 Average	29 Average	31 Good	27 Average	30 Average
Digestive Efficiency	56 Average	71 Good	41 Not Optimal	61 Average	47 Average
Gut Lining Health	67 Average	68 Average	67 Average	72 Average	70 Average
Protein Fermentation	42 Average	28 Good	75 Not Optimal	51 Average	71 Not Optimal
Gas Production	46 Average	30 Good	62 Average	29 Good	45 Average
Active Microbial Diversity	1st Percentile Not Optimal	12th Percentile Average	4th Percentile Not Optimal	12th Percentile Average	15th Percentile Average
Total Supplement Recommendation Count	28	30	37	34	30
Total Probiotic Recommendation Count	19	18	18	18	19
Vegetables to Avoid	Bell Pepper Broccoli Brussels Sprouts Cabbage Mustard Greens Tomato	Bell Pepper Tomato	Bell Pepper Sauerkraut Tomato	Bell Pepper Tomato	Bell Pepper Cucumber Tomato
Proteins and Fats to Avoid	Almonds Chicken Egg Yolk Pistachios	Almonds Pistachios	Kefir (Cow Milk) Yogurt (Cow Milk, Plain)	Almonds Pistachios	Shrimp (Domestic)
Fruits and Grains to Avoid	None	None	Barley Blueberry	None	Watermelon
Other Food Items to Avoid	None	None	Coffee	Turmeric	None

Again, please remember that I have not made any recommended changes from the previous collection. I will also not make any changes based upon the current set of reports.

For example, watermelon, cucumber and shrimp are some of my favorite foods, and I will not stop eating those. If anything, I think watermelon and cucumber can be helpful for my digestion.

I recieved an e-mail saying that my Psomagen were ready on 11/2/2021. However, I could not sign in to access my report. I think this was an issue with the set of links that were available, although I could briefly see information about "Kean Health" (although I did not sign up, based upon past experiences for Psomagen).

I recieved an e-mail that my BIOHM results were ready to download on 11/10/2021.

For Psomagen access to the typical report was still an issue on 11/13/2021. However, if I used Firefox instead of Google Chrome, I could view my report for my most recent sample. I also sent a separate e-mail to request the raw FASTQ files on that day.

I contacted BIOHM regarding getting additional information about my sample on 11/15/2021, and they kindly provided an Excel file with some additional information on 11/17/2021. They also provided some information on how to improve the quality of the PDF to download, which I then uploaded (after checking both boxes for "Headers and Footers" as well as "Background Graphics").

I recieved my FASTQ files for my Psomagen sample on 11/23/2021.

I am performing some additional analysis before creating a blog post. In some cases, I needed to go back and find additional screenshots. I am not sure how to get the optimal percent for the 2 replicates from the 3rd sample for thryve. However, on 11/28/2021, I in the interface for Ombre (which the previous result links redirect to) was almost identical to the interface from thryve.

Sample #5

I am not planning on purchasing additional Viome or BIOHM tests.

I ordered 2 kits from 2 companies on 11/29/2021:

Ombre (previously thyrve): Gut Health Test

Kean (previously Psomagen): Kean Gut

I think the Ombre results should be similar to the thyrve results, but I am ordering 1 more set of samples (in order to have something to share with others).

The options to order look a little different for Kean than Psomagen. Strictly speaking, I think the raw data may be more similar for Gut+, but the price-point is more similar for Gut (relative to thryve/Ombre). If there is still no collection liquid to stop bacterial growth after collection, I will not order any additional Kean kits in the future (although, to be fair, I will probably also not order additional Ombre/thryve results in the immediate future, and I will start a new collection of experiments if I do).

The Kean Gut kit arrived on 12/2/2021.

The Ombre Gut kit arrived on 12/6/2021.

I collected and mailed my sample on 12/11/2021.

Multiple collections for the same sample were more difficult when only using tissue paper, without the stool collector to attach to the tiolet (previously provided by Psomagen, but now not provided by Kean). However, my goal is to compare and contrast what is provided when the companies were under a different name. So, in that sense, this may be OK.

I believe my previous thryve samples were carried over to Ombre (and the interface is almost identical). However, I don't think that my Psomagen samples were carried over to Kean.

Also, I think only parts of the Terms of Service and Privacy Policy have currently been coverted to say "Kean" instead of "Psomagen." The mailing address at the bottom includes both, so this may be intentional (even if possibly somewhat confusing to me).

I recieved my Ombre results on 12/29/2021. This includes CSV assignments for classifications, as well as FASTQ files.

I recieved my Kean results on 1/13/2021. I was a little confused about the interface, where the hamburger button needed to be pressed to navigate (on a web browser). I had difficulties being able to download PDF files to share (using the print function). So, I downloaded complete webpages.

Psomagen provided FASTQ files upon e-mail, but the Kean report is very different. So, I sent a follow-up email about raw data access on 1/13/2021.

I recieved links to download the Kean FASTQ files on 1/19/2022:

http://ngs2.macrogenlab.com/~customer/2201/AN00001264/2DNYT6MDA4_R1.fastq.gz

http://ngs2.macrogenlab.com/~customer/2201/AN00001264/2DNYT6MDA4_R2.fastq.gz

Sample #6

I was not going to purchase additional Viome tests, but I have gained some better understanding of the 2 versions of Psomagen/Kean gut tests. So, I thought I should also have Viome results with the extra testing, and the stool collector should also be useful.

I ordered 4 kits from 2 companies on 4/28/2022:

Ombre (previously thyrve): Gut Health Test

Kean (previously Psomagen): Kean Gut as well as Kean Gut+

*Viome: Gut Intelligence

I collected my sample on 5/6/2022. Due to a problem with registring my Kean kits, I did not mail the samples back the same day. However, I mailed all 4 samples on Saturday 5/7/2022.

My understanding is that there was a bug in the system, and I successfully registered my Kean Gut and Kean Gut+ kits on Monday (5/9/2022).

I recieved my Ombre results on 5/24/2022. This includes CSV assignments for classifications, as well as FASTQ files.

I don't believe that I recieved an e-mail that my Kean results were ready. However, I did receive an e-mail asking me to rate the project on 6/10/2022. I then signed in, and I found that reports were available. I then contacted the company to receive the raw data. I then promptly recieved the raw fastq.gz files on 6/13/2022:

Kean (Gut, Sample 6a):

http://ngs2.macrogenlab.com/~customer/2206/AN00006955/2WP8H6PWY2_1.fastq.gz

http://ngs2.macrogenlab.com/~customer/2206/AN00006955/2WP8H6PWY2_2.fastq.gz

Kean (Gut+, Sample 6b):

http://ngs2.macrogenlab.com/~customer/2206/AN00006896/3AR4YF9DW3_1.fastq.gz

http://ngs2.macrogenlab.com/~customer/2206/AN00006896/3AR4YF9DW3_2.fastq.gz

I recieved my Viome results on 6/18/2022.

To provide a selected comparison of assignments (from the companies) for my 6th sample:

Genus	Kean Gut	Kean Gut+	Ombre	Viome Gut Intelligence (as purchased)
Akkermansia sp	?	8.3% (muciniphila)	0.288%	Active (muciniphila)
Alistipes	?	8.5% (shahii) 3.1% (communis) 2.1% (finegoldii) 1.9% (sp. dk3624) 1.8% (indistinctus)	3.096%	Active (4 species)
Bacteroides uniformis	?	2.1%	4.9%	Active
Bacteroides vulgatus Phocaeicola vulgatus	?	21.4%	10.9%?	Active (ATCC 8482)
Bacteroides [other]	?	7.9% (sp. CACC 737) 7.8% (sp. A1C1) 4.7% (sp. HF-162) 4.0% (thetaiotaomicron) 3.1% (ovatus) 2.8% (caccae) 2.8% (xylanisolvens) 1.5% (fragilis) 1.2% (sp. HF-5287)	38.131% (total)	Active (14 other species)
Phocaeicola dorei	?	1.6%	[Bacteroides]	[Bacteroides]
Bifidobacterium	Detected	Detected (<0.1%)	0.026%%	Active
Blautia	?	0.4% (sp. SC05B48) <0.1% (obeum) <0.1% (producta)	3.062%	Active (2 species)
Eubacterium	?	<0.1% (sp. NSJ-61)	6.040%	Not Detected?
Faecalibacterium prausnitzii	?	1.4%	0.791%	Active
Lactobacillus	Not Detected	Not Detected	0.037%	Detected (johnsonii)
Ruminococcus bicirculans	?	1.0%	21.105% (general)	Active (1 species)

Other Notes

1) There is no liquid in the Psomagen stool collection tubes, so I don't believe there is anything to stop or reduce bacterial growth post-collection.

Post-collection bacterial growth includes things like the "blooms" discussed in the American Gut project paper.

It looks like the blog post that caused me to design this experiement with newer metagenomics samples is now private. However, I believe that also tested technical replicates submitted to multiple companies.

2) I did not realize it at the time of ordering, but one of the Viome kits (including Viome Health Intelligence) requires a blood sample. To be fair, this is listed on the description for the product, if you scroll down or find the word "Collection Method"

To help me remember (and perhaps make more clear to others) here is the content related to the blood collection:

"Fasting: Viome requires fasting before collecting your Human Gene Expression™ (blood) sample. The simplest way to do this is to collect your sample right after you wake, before eating any food or drinking anything other than water (Note—your kit instructions may not contain this step, please disregard and follow the directions here).

Watch our step-by-step instruction video here for the best techniques for easy collection.

We recommend collecting both your blood and stool samples within the same day (if this is too difficult for you, a few days in between samples will not impact your results)."

My experiences with my nutrigenomics testing (which included some metabolite measurements) was that I don't think I prefer the at-home collection (if it can be avoided). In fact, if you watch that video, you will see that you need 4 Minivettes of blood (each of which appears to require multiple drops of blood, based upon 2:30 to 2:55 in the video). For this reason, I only submitted the stool sample for my Health Intelligence Test (converting my kit type, without requiring blood collection).

I am not concerned about the extra costs for the part that I do not want to collect (the blood samples). However, others might want to know that a partial refund is not possible (if they find themselves in a similar situation). For me, this was only an extra $100 with the sale price. However, I think the regular price difference is $300 (as of 3/10/2021).

3) It might also be worth noting that Psomagen provides other genomics services, but I believe the others are not Direct-To-Consumer.

4) I noticed that Nebula provides reviews for Psomagen, Viome, and Thryve. While I don't agree with everything, the Viome review includes other related companies at the end. Also, to be fair, the Viome ratings seem high, but the review also says "The validity of the Viome results provided are questionable" and repeats that the results should not be used for medical decisions (even though there are explicit supplement recommendations from the company). Likewise, the ratings for Thryve seem high to me, given the review says things like "Much of the microbiome analysis seems tailored to selling their own supplements" and "Some customers find supplements cause stomach discomfort" (where I think the later is arguably literally a description of some amount of harm being caused by the product's recommendation - or, if the individual was not already healthy, then they may benefit from seeing a health care professional).

I double-checked with the vendor and the Floré Gut Health Test Kit from Sun Genomics does not offer raw FASTQ files.