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MaximilianKohler edited this page Aug 17, 2019 · 66 revisions

Fecal Microbiota Transplants (FMT)

/r/FMTDatabase is trying to find people healthy enough to be FMT donors.

/r/FMTClinics and /r/fecaltransplant are related subs.

You can use the sidebar flair here to browse FMT studies, and more: https://old.reddit.com/r/humanmicrobiome/search?q=flair%3A%27FMT%27&sort=new&restrict_sr=on


Table of Contents:


Screening:

FMT screening questionnaire: http://HumanMicrobiome.info/FMTquestionnaire - FMT is only as safe as your donor is healthy. This is what healthy poop looks like.

European consensus guidelines tests: http://gut.bmj.com/content/66/4/569#boxed-text-3

OpenBiome donor screening/testing info: http://www.openbiome.org/s/The-OpenBiome-Quality-Safety-Program.pdf - http://www.openbiome.org/s/Quality-Metrics.pdf

Do not solely rely on testing (conventional or 16s) as it is very limited in value: http://HumanMicrobiome.info#Testing

If you cannot find a participating doctor, the tests can be ordered directly (have to pay cash yourself though, probably a few hundred dollars) from http://requestatest.com/ or https://www.ultalabtests.com/Patient. In the UK you can use https://www.medichecks.com.

For the stool testing portion you can use https://www.mymedlab.com to get the Diagnostic Solutions GI Map test. In the EU you can try https://ifu-wolfhagen.de/ or https://smartnutrition.co.uk/ to get the GI Map.

If you look at their Sample Report, it has most of the stool tests which are recommended for FMT donor screening. The donor will need to create an account on mymedlab and share the login info with you so you can order/pay for the test. If you get this test through a provider you need to specifically ask them to check off on the order the "beta-lactamase resistance" section, or "Antibiotic Resistance Genes, genotypes". Mymedlab said "when you receive your kit, you can make the change on the requisition form".

Blood testing can typically be done at a free STD clinic. https://gettested.cdc.gov/

Thepowerofpoop.com recommends Direct Labs - the "Labs for Fecal Diversity Tests Only" aren't that useful in my opinion (see the "testing" section of this wiki). The "Comprehensive Digestive Stool Analysis 2.0™ (CDSA 2.0)-Genova Kit" is probably the most useful directlabs test.

A few things to keep in mind when looking for a donor:

  • The gut microbiome is heritable and gets passed down generationally. Including dysbiosis, pathogens, and extinctions from poor diet and antimicrobials. A child with no lifetime antimicrobial use may not actually have an eubiotic, disease resistant gut microbiome, but rather they may have just not yet been exposed to an infectious pathogen that necessitated an antimicrobial.
  • Relatives can often have "pre disease" states of dysbiosis [1][2]. Meaning they have dysbiosis themselves but not yet enough to trigger the disease of the family member that needs the transplant. So contrary to common misinformation, relatives are often not ideal.
  • Both genetic and gut microbiome diversity are beneficial.
  • There is a large amount of evidence (in this wiki) that donor quality (rather than compatibility) is the #1 factor. But of course each donor is very unique and thus some donors would have certain microbes needed to treat certain conditions, while others do not.
  • Nearly anything wrong with a donor can be transferred via FMT.
  • Donors often misjudge their stool quality. So you probably want to get a daily sample for a few days in a row before using any of it, just to judge the quality and consistency yourself. If a person is having unstable stools it's probably not safe.

Soft stools seem to be from one or more of:

  1. A low quality gut microbiome that lacks certain microbes needed in the digestion of certain foods. Or lacks certain microbes that control/limit others.
  2. A pathogen that feeds off certain food items (iron for example), and thus causes soft stools & other problems when eating those foods.
  3. Temporary stomach upset from either mild food poisoning or poor hygiene/sanitary practices.

I had no idea how important stool type & consistency was coming into this, but it seems high quality donors have identical stools, while low quality donor's stools are heterogeneous, thus it's one of the major ways to judge stool quality. This Anna Karenina hypothesis supports this. As do the majority of case reports I've seen.

This 2017 study saying otherwise is only for c.diff (which requires much less strict donor criteria). And it's quite likely (looking at the donor criteria) that studies like that lacked high quality donors, so they may have only been comparing average/low quality donors with each other. Also I believe it is a matter of "the highest quality donors all have type 3 stools, but not every type 3 stool donor is high quality".

The discussion section of this 2014 review paper "Rural and urban microbiota - To be or not to be?" provides excellent info on gut microbiome, FMT, and donor selection: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4153773/

See the "impact factors" section under "scientific info" heading for more on donors, including supporting evidence for athletes.

2018 detailed experiences & lessons from 8 different donors


Procedure:

Check out the video on this page for a good overview of ASU's recent FMT study, which was one of the best I've seen: https://autism.asu.edu/ - they used both oral and rectal routes.

The most common/major flaws with FMT studies/procedures are:

  1. Donor criteria not strict enough [1][2][3][4]. Donors should be under 30 [1][2][3], have very limited life time antibiotic exposure (ideally none) [1], athletic & low body fat, and good mental health. Firm stool consistency seems important too. Typical donor criteria you see is a complete joke. Stuff like "no abx in past 3 months, 18-50 yrs old, no pathogens in stool & blood test".
  2. Insufficient treatment length. Many studies only do a single infusion, but for many people/conditions you might need to do it daily for 2+ months.
  3. Too much oxygen exposure. Blending is quite common and this oxygenates the stool sample.
  4. Colon-only procedures. The small intestine is very important [1], so completely ignoring it is a likely flaw for some conditions [1].

Keep in mind that c.diff is a lot easier to cure than other conditions. So even though a study shows 'x' is effective for c.diff, other harder to cure conditions will likely need stricter criteria.

It's common for the recipient to feel feverish & chills, and possibly some initial diarrhea & other temporary side effects after the first 1-2 FMTs. It seems to be a sign of a high quality donor. Symptoms of a "changing of the guard".

The less delay between the donor having the BM and the recipient using it, the better. 15 minutes or less might be ideal, but it can be hard to always be there when your donor has a BM, so it's possible to use a insulated lunch bag like this:

Insulated lunch bag

with ice packs & ziplock bags in it that the donor keeps with them during the day. Then just make sure to flatten the air out before zipping it shut and putting it back in the ice bag.

Freezing the stool for either shipping or storage is common. Glycerol is the commonly used antifreeze additive, but it's also a laxative, and therefore problematic for many people. If glycerol is used it should make up 10-15% of the total volume of added liquid. About 1 tablespoon of glycerol for every 9 tablespoons of saline. Glycerol and glycerin are the same thing.

Many department/grocery stores should carry it. Read the label and make sure the only ingredient is glycerol. It is also available online:

When adding liquid, saline should be used instead of pure water. Saline provides osmotic protection for microbial cells, helping to maintain cell integrity and viability.

To create saline: Add 1 teaspoon of non-iodized salt to 2 cups of filtered or distilled water. Or 1/4th teaspoon of salt for 1 cup of water.


Treatment length:

Length is unknown and depends on the condition being treated, procedure quality, and donor quality. For some conditions like IBS, as little as one enema has been reported to be effective. For the recent ASU autism study [1,2] daily oral FMTs were done over a period of 10 weeks, and gradual improvements were seen throughout, which suggests that 10 weeks or longer might be necessary in some cases. However, there were many procedure & donor deficiencies in their study, so treatment length should decrease if one is able to rectify those deficiencies.


Upper vs lower routes:

Upper, also known as "top down" or oral, can be done directly, or via capsules, or via naso tube.

Lower/rectal route, can be done via retention enema, or colonoscopy.

Lower-only is possibly inferior to capsules because it only gets the colon, which is a small part of the entire digestive system.

With the oral route, some people have concerns about stomach acids & bile killing off sensitive microbes before they make it to the colon. But this study showed that for c.diff, capsules are equally effective as colonoscopy procedures. The 2017 ASU Autism study also tested both routes and found no difference. Personally I found that with certain donors it seemed that rectal was more effective. And others have reported that oral seemed more effective for them. So I would recommend trying both routes if possible. I later experimented with upper vs lower and discovered that lower-only was incomplete.

March 2019 review of FMT for c.diff in Germany shows that lower route alone has a higher cure rate than upper alone, both together have the highest cure rate, but the results were confounded by age so the authors think there's no difference. Chart image.

For worries about SIBO see the SIBO section below.

OpenBiome, the main US stool bank (c.diff only) offers all 3 methods (enema, naso tube, capsules): http://www.openbiome.org/fmtcapsules/ - http://www.openbiome.org/clinical-guidance

Regarding safety:

https://archive.is/JRWmc - https://archive.is/0fNsW

Adverse events in faecal microbiota transplant: a review of the literature (2015): https://doi.org/10.1016/j.jhin.2015.10.024

The long-term effects of faecal microbiota transplantation for gastrointestinal symptoms and general health in patients with recurrent Clostridium difficile infection (2017): http://onlinelibrary.wiley.com/doi/10.1111/apt.14443/abstract

Two documented cases of aspiration pneumonia occurred during upper gastrointestinal tract endoscopy. Similar cases have been identified by other authors (Mar 2019): https://journals.sagepub.com/doi/10.1177/2050640619839918

For IBD: "My colleagues and I have now followed a small number of IBD patients undergoing FMT over 4 years, and no safety concerns have been found" http://www.gastroenterologyandhepatology.net/archives/may-2018/update-on-fecal-microbiota-transplantation-in-patients-with-inflammatory-bowel-disease/


Before the procedure:

Depending on the condition, it might be helpful to take an antibiotic (for at least a few days, but they're typically prescribed for 1-2 weeks I believe) in order to clear out the current microbes so the new ones have an easier time to establish themselves [1][2][3][4][5]. But the evidence for most conditions isn't here yet, and antibiotics can have a wide range of severe, long term detriments.

This 2010 rat study showed antibiotic intake prior to transplantation did not increase establishment of the donor phylotypes. It also showed that broad-spectrum antibiotics do not "wipe everything out, letting you start from a clean slate", but rather antibiotics only temporarily suppress certain types and allow others to increase, but after antibiotic cessation, bacterial load generally returns to the previous state, but diversity seems reduced for the long-term, including after FMT. [1]. - "Clearly, host factors also play a role in shaping the intestinal microbial ecosystem, and those factors might be also altered by antibiotic intake". "Although this finding makes ecological sense, that antibiotics might be almost as deleterious to the input community as to the endogenous community, is a highly counterintuitive result that should be taken into account in designing future bacteriotherapy protocols".

A conflicting result using human-to-mouse FMT with and without abx [1], and some discussion on possible reasons for the difference.

Another 2019 mouse study (STAMP) showed 3 out of 4 antibiotics (vancomycin, cefotaxime, metronidazole) used for pre-treatment "resulted in impaired transplantation efficacies". The 4th antibiotic (polymyxin) seemed to help colonization: https://www.nature.com/articles/s41467-019-09267-x

"A recent multicenter study of ulcerative colitis patients who received SER-287 (Seres Therapeutics), a microbiome-based therapy composed of a consortium of bacterial spores. Initially, the trial used vancomycin pretreatment, but the researchers found that it did not improve the results" (Jan 2019): https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6423689/

"specific preparation of the patient using an antibiotic induction regimen, proton pump inhibitors, or antimotility agents did not impact treatment success" (Mar 2019) https://journals.sagepub.com/doi/10.1177/2050640619839918

"Pre-treatment with antibiotics before FMT did not have any significant impact on clinical outcomes in IBS-D patients" (June 2019) https://www.healio.com/gastroenterology/irritable-bowel-syndrome/news/online/%7Bb7ea1e6f-d12c-4b81-9978-2f0d64528018%7D/oral-fmt-with-antibiotics-does-not-improve-symptoms-of-ibs-d

If you take antibiotics prior you are making a bet that the donor will restore everything the antibiotic kills off/damages. Two mouse studies showed FMT may not completely restore immune function damaged by antibiotics: (2017), (2018).

Neither Xifaxan nor Flagyl made low quality donors more effective for me. Certain conditions where a pathogen is a primary cause are more likely to benefit from antibiotics, but due to severe limitations in testing it can be hard to identify those individuals and the right antibiotic for them.

A clinic in Melbourne Australia gives Xifaxan 500mg 2x/day for 10 days, Flagyl 400mg 3x/day for 10 days, Nystatin 1 capsule 3x/day for 10 days prior to their FMTs: http://www.melbournefmt.com.au/fmt_procedure.html

Xifaxan only targets the small intestine [1][2] and thus may not be a good choice for cases of dysbiosis that are primarily in the colon. 2017 study showed little to no benefits from Rifaximin pre-treatment for UC [1].

I read somewhere that a Florida clinic (RDS Infusions) is giving Neomycin for 7 days prior to FMT.

You could also consider doing a colonoscopy prep[1], which includes inducing diarrhea to clear out the entire intestinal tract, but personal experience says it's not more effective than just doing the retention enema after a regular BM. Though inducing diarrhea itself may have some impacts/benefits [1][2].

Taking a bunch of multi-strain probiotics prior did not seem to have any benefits for me, and this 2018 study showed it can result in an increased rate of infection [1].

Diet:

Diet's role in FMT is not established.

A few studies showed that FMT success depends on changing bile acid metabolism [1], and this is very much inline with my own experiences. I did not notice a major impact from donor diet, except for when one donor ate nuts (which harm me), they were not fully digested and the undigested nuts in their stool also harmed me.

This 2017 article says OpenBiome said "their own data suggests that diet has no bearing on whether or not an otherwise healthy individual gives successful stool". The data was presented at this DDW conference.

Prebiotics and other whole foods that harmed me prior to FMT also harmed me during & after FMT. I do not think you should/can introduce these until you're pretty much in complete recovery. My experience with this says it is misguided to try and feed the new bacteria from the FMT. In my opinion you should continue to eat the foods which were the most beneficial to you prior to FMT. And also be aware that low quality donors may cause you to develop new food intolerances.

In cases of bile acid metabolism issues (which can cause a variety of things including diarrhea), a certain donor was able to correct/greatly improve that without doing anything special, when other donors had no impact. Donor quality seems to be the #1 factor for everything.


Upper route:

Using quick release capsules (Size 000 - largest possible: 1, 2) gets the entire digestive system. Using slow release (enteric coated) capsules still gets most of the small intestine and avoids stomach acids that may reduce some microbe counts.

For me it seems like with quick release methods, taking small amounts (maybe 10-15 capsules depending on their size, 1oz or less) on an empty stomach (2-3 hours after a meal and 1/2-1 hour before a meal) first thing in the morning with lots of water is more effective than taking it with a meal. Even when the meals contained prebiotics. This is likely due to various digestive system secretions triggered by meals (including large amounts of stool). Enteric coated capsules could be better but I haven't tried them.

Size 00 enteric coated: https://www.amazon.com/gp/product/B06XGM6HK9

How to:

Donor poops in ziplock bag:

ziplock bag

Then ASAP (within a few minutes) the stool is put in capsules, and capsules are swallowed. Using a 60ml Catheter Tip Disposable Syringe like this seems to be the best way:

syringe

You can shovel the whole stool into the syringe without any dilution. You may have to cut off the tip of the syringe and widen the opening by stretching the plastic with a drill bit or nail. And keep some toothpicks on hand to unstick the opening.

Without the syringe, a toothpick used as a shovel worked fine for me (about 20 capsules in ~10 minutes). A fast food straw split down the middle making a canoe shape might be a little better.

If you can stomach it you can skip the capsules and just straight up swallow the poop. As a plus side, unhealthy poop is going to be a lot more repugnant (some support: [1][2]). And if the stool is too soft it will melt the capsules anyway. You could also add water and use a straw to drink the liquid.


Lower route:

Donor poops in ziplock bag

ziplock bag

Distilled/filtered water or saline is added, mix gently (so as not to oxygenate the liquid) with hand from outside the bag, do enema (enema, not colonoscopy - IE: only needs to go in an inch or so) with wide-ended (so stool doesn't get stuck) turkey baster:

wide-ended turkey baster

Use lube.

Look at an image of the colon:

image of the colon

to understand which positions to lie in afterwards to get it to flow through the whole colon. Adding enough water to make it flow easy is important. The more you can elevate your hips at first, the better. An inversion table works great. You can also do yoga-type positions like this:

positions

And/or decline yourself off a couch/bed with your hips on the bed and your head on the floor.

Try to hold it in overnight. You can use Imodium if needed. Once you get the liquid to the right side of the colon you can stay in that position overnight or slowly revert to a standing position and from there gravity should keep the liquid at the cecum. If you keep it there it should reabsorb.

Regarding how long to stay in each position while trying to get it to flow through the whole colon depends on a variety of factors, including how much liquid you've added, whether your colon is cleared out, whether a person has structural defects in their colon, etc.. I generally do the retention enema after a BM (when colon is most empty) and use about 3-5 turkey basters worth (each baster is about 1.75 fl oz/52ml) and can feel the liquid flow into the top of my colon within ~10 seconds of being up side down on inversion table. In other cases you might have to lie on each side for ~15 minutes.


Scientific info:

Wide benefit from fecal transplants (2015): http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4284325/

Fecal Microbiota Transplantation: Current Applications, Effectiveness, and Future Perspectives (2016): https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4895930/

Novel Indications for Fecal Microbial Transplantation: Update and Review of the Literature (2017): https://link.springer.com/article/10.1007%2Fs10620-017-4535-9

Guidelines: European consensus conference on faecal microbiota transplantation in clinical practice (2017): http://gut.bmj.com/content/66/4/569

Guidelines: The use of faecal microbiota transplant as treatment for recurrent or refractory Clostridium difficile infection and other potential indications: joint British Society of Gastroenterology (BSG) and Healthcare Infection Society (HIS) guidelines (2018): http://dx.doi.org/10.1136/gutjnl-2018-316818

Review, Feb 2019: Clinical Review on the Utility of Fecal Microbiota Transplantation in Immunocompromised Patients. Present literature weighs in favor of FMT in immunocompromised patients, with an acceptable adverse effect profile and minimal risk of infectious adverse events: https://link.springer.com/article/10.1007%2Fs11894-019-0677-6

Review, Mar 2019: Adjunctive fecal microbiota transplantation in supportive oncology: Emerging indications and considerations in immunocompromised patients: https://www.ebiomedicine.com/article/S2352-3964(19)30215-4/fulltext "Limited available evidence supports the notion that it is a safe therapy in immunocompetent individuals, however further studies are required"

Methodology/procedure:

FMT methodology has major impact. FMT with patient's own feces results in significant changes. Possibly due to exposure to aerobic conditions. High rate of adverse events in this group: http://www.gastrojournal.org/article/S0016-5085%2815%2901581-4/fulltext

Breakthrough study that took us from being able to culture only 1% of gut microbes to >70% did so by adhering to strict anaerobic conditions: http://www.the-scientist.com/?articles.view/articleNo/46019/title/Most-Gut-Microbes-Can-Be-Culturedhttp://www.nature.com/nature/journal/v533/n7604/full/nature17645.html

Oxygen tolerance of anaerobic bacteria isolated from human feces (1989): "Thirty O2-intolerant bacterial strains that reached 100% mortality after 120 min of air exposure were isolated. Ten of these strains were tested for their atmospheric O2 sensitivity as a function of air exposure time; all tested microorganisms showed a similar mortality trend on exposure to air. In fact, 50% of cells survive, on the average, after 4–5 min of atmospheric O2; this percentage decreases to 3–5% after only 20 min, and after 40 min only one cell in a thousand survives; all strains reached 100% mortality in a time range of 100–120 min." https://link.springer.com/article/10.1007/BF01568901

2017 OpenBiome/MIT study confirms that oxygen exposure is the most important factor to reduce during processing: http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0170922

Feb 2019: https://doi.org/10.1016/j.ebiom.2019.02.023 "The practice of preparing material for faecal transplantation in ambient air profoundly affects viable microbial content, disproportionately reducing the abundance of anaerobic commensals and the capacity for biosynthesis of important anti-inflammatory metabolites. In contrast, while reducing overall levels of viable bacteria, freeze-thaw did not significantly alter viable microbiota composition." Critique of this paper.

Impact of Different Fecal Processing Methods (homogenization & freezing) on Assessments of Bacterial Diversity in the Human Intestine (2016): http://journal.frontiersin.org/article/10.3389/fmicb.2016.01643/full

Freezing:

Effects of the long-term storage of human fecal microbiota samples collected in RNAlater (2019): https://www.nature.com/articles/s41598-018-36953-5 "Overall, long-term stool storage at -80?°C had only limited effects on the microbiota composition of human feces"

Interpersonal Variations in Gut Microbiota Profiles Supersedes the Effects of Differing Fecal Storage Conditions (2018) https://www.nature.com/articles/s41598-018-35843-0 "fecal samples can efficiently be stored in −20 °C freezers or in one of the presented storage buffers, without severe alterations in bacterial composition"

Freezing changes ratio of Firmicutes to Bacteroides: https://microbiomethod.blogspot.co.uk/2016/11/sampling-storing-and-extracting-dna.html and https://www.ijidonline.com/article/S1201-9712(18)33883-9/abstract Standardization of gut microbiota analysis: Variability in samples taken at different times from single case and the effect of the freezing the sample (2018)

Improved Preservation of Treponema pallidum and Other Bacteria by Freezing with Glycerol (1954): https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1056982 - Bacteria amounts are cut in almost half after just one freezing and thawing cycle if they are without glycerol, but the amount lost is negligible if stored in a 15% glycerol suspension. Least amount of damage when rapidly frozen and rapidly thawed

One study showed that for c.diff: Fresh > flash freeze > lyophilised (freeze dry) (2017): http://onlinelibrary.wiley.com/doi/10.1111/apt.13969/abstract

Another showed no difference from fresh vs frozen: Simple faecal preparation and efficacy of frozen inoculum in faecal microbiota transplantation for recurrent Clostridium difficile infection – an observational cohort study (2014): https://doi.org/10.1111/apt.13009

Is frozen fecal microbiota transplantation as effective as fresh fecal microbiota transplantation in patients with recurrent or refractory Clostridium difficile infection: A meta-analysis? (2017): https://doi.org/10.1016/j.diagmicrobio.2017.05.007 - no statistical difference.

For IBD: "my colleagues and I used both fresh and frozen stool in our study, and both types seemed to work" http://www.gastroenterologyandhepatology.net/archives/may-2018/update-on-fecal-microbiota-transplantation-in-patients-with-inflammatory-bowel-disease/

Dose:

This 2017 review comments on a C. diff study where a small dose (few capsules) was as effective as much larger doses: http://www.tandfonline.com/doi/full/10.1080/19490976.2017.1316447 - this is in line with my own experiences.

Jan 2019 Q&A/overview of IBD studies mentions that low doses were as effective or more effective than larger ones: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6423689/

This 2014 review highlights one or more studies that found the opposite: efficacy was increased after increasing dose from 20 grams to 40 grams. And also says that it seemed at the time that rectal administration was more effective than oral. https://web.archive.org/web/20180802200322/https://webcache.googleusercontent.com/search?q=cache:92IjXZvAswIJ:https://www.omicsonline.org/open-access/upper-versus-lower-gastrointestinal-route-of-fecal-microbiota-transplantation-in-the-treatment-of-clostridium-difficile-infection-2161-069X-4-169.php

Purified fecal matter had lower rates of adverse events vs crude fecal matter. No significant difference in the rate of clinical response or clinical remission between the two groups of different methods. (2018): https://link.springer.com/article/10.1007%2Fs12325-018-0800-3 The Safety of Fecal Microbiota Transplantation for Crohn’s Disease: Findings from A Long-Term Study

Increasing the Dose and/or Repeating Faecal Microbiota Transplantation (FMT) Increases the Response in Patients with Irritable Bowel Syndrome (IBS) (June 2019) https://www.mdpi.com/2072-6643/11/6/1415/htm

Frequency:

We then compared four different strategies based on the frequency of FMT over four weeks: (1) twice a week; (2) once a week; (3) two FMTs; (4) one FMT. We were able to transfer human bacteria to mice, irrespective of the strategy used. We detected human bacteria after four weeks, even if only one FMT was performed, but there was a shift of the microbiota over time. FMT twice a week for four weeks was too frequent and perturbed the stability of the newly formed ecosystem. FMT once a week appears to be the best compromise as it allowed engraftment of Faecalibacterium, and a higher diversity of bacteria belonging to the Bacteroidales order. FMT was given orally. (2018): https://www.nature.com/articles/s41598-018-25300-3

For UC/IBD: "As for the frequency of FMT administration, once a week seemed to work in our study. The efficacy was similar in the Australian studies, in which FMT was performed 5 times a week for 8 weeks. Therefore, I think that FMT definitely needs to be given more than once, probably repeatedly over at least 6 weeks, unlike with C difficile infection" http://www.gastroenterologyandhepatology.net/archives/may-2018/update-on-fecal-microbiota-transplantation-in-patients-with-inflammatory-bowel-disease/


Impact factors:

Donor species richness determines FMT success for IBD (2015): https://doi.org/10.1093/ecco-jcc/jjv203 | The taxonomic composition of the donor intestinal microbiota is a major factor influencing the efficacy of faecal microbiota transplantation in therapy refractory ulcerative colitis (2017): http://onlinelibrary.wiley.com/doi/10.1111/apt.14387/abstract

Irritable Bowel Syndrome-Like Symptoms Following Fecal Microbiota Transplantation: A Possible Donor-Dependent Complication (2017): https://sci-hub.tw/10.1038/ajg.2016.472

One UC/IBD study showed "Stool from one donor appeared to do much better than from the others" http://www.gastroenterologyandhepatology.net/archives/may-2018/update-on-fecal-microbiota-transplantation-in-patients-with-inflammatory-bowel-disease/

Supporting evidence for young athletes being better donors:

Athletes have higher diversity, and their gut microbiome differs at the functional metabolic level. There is a direct connection with the mitochondria [1][2].

Cardiorespiratory fitness is correlated with increased microbial diversity[1][2][3]. Gut Microbiota Composition is Related to Cardiorespiratory Fitness [1][2].

2017 review, Exercise Modifies the Gut Microbiota with Positive Health Effects. Sports medicine review. Article referencing post-lyme FMT done with athlete & follow up study. Another by the same person (Peterson) discussing "poop doping".

There have been lots of articles, such as this one, on Jonathan Scheiman's Harvard lab which is studying athletes poop/gut microbiomes in regards to athletic performance. Their June 2019 study found a performance enhancing microbe (Veillonella atypica).

Fecal microbiota transplantation confers beneficial metabolic effects of diet and exercise on diet-induced obese mice. Endurance exercise and gut microbiota: A review (2017). Grip strength [1][2-4][5], muscle mass, strength, and reaction time as vital signs. Gut microbiome regulates skeletal muscle mass and function [1].


Vegetarians have fewer pathogens (Thai study): http://www.jmb.or.kr/journal/viewJournal.html?doi=10.4014/jmb.1603.03057

Worse inflammatory profile in omnivores than in vegetarians associates with the gut microbiota composition: https://dmsjournal.biomedcentral.com/articles/10.1186/s13098-017-0261-x

Pooled stools (multiple donors) can be more effective [1].

Different responses to FMT depending on age of donor (in chickens): http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0163932

FUT2 genotype and secretory status are not associated with fecal microbial composition and inferred function in healthy subjects (2018): https://doi.org/10.1080/19490976.2018.1445956

FMT success may depend on changing bile acid metabolism: http://HumanMicrobiome.info/bile

Gut fungal dysbiosis correlates with reduced efficacy of fecal microbiota transplantation in Clostridium difficile infection (2018): https://doi.org/10.1038/s41467-018-06103-6 "High abundance of C. albicans in donor stool correlates with reduced FMT efficacy. Furthermore, C. albicans reduces FMT efficacy in a mouse model of CDI, while antifungal treatment reestablishes its efficacy, supporting a potential causal relationship between gut fungal dysbiosis and FMT outcome."

Saliva may have beneficial impacts [1][2].

Sterile fecal filtrate is effective for treating c.diff (implicating phages): https://archive.is/gY07m

May 2017, OpenBiome presented data on donor efficacy factors and pediatric access at DDW. The nonprofit stool bank shared data from a 1,413 patient cohort of fecal transplant recipients and research from 14 abstracts at Digestive Disease Week. http://www.openbiome.org/press-releases/2017/5/23/openbiome-presented-data-on-donor-efficacy-factors-and-pediatric-access-at-ddw

According to their safety publications, OpenBiome has at least 1 donor with a 100% efficacy rate after more than 100 patients, while most of their other donors seem to be around 80%. This supports the notion that donor quality is the most important factor: https://archive.fo/py71w


Outcomes:

FMT changes to gut microbiome last long-term [1][2][3]

Not all donor microbes colonize the recipient. Two studies in March 2019 looked at which ones colonized [1][2].

Recipient viromes resembled those of their donors for up to 12 months. Tracking individual bacteriophage colonisation revealed that engraftment of individual bacteriophages was dependent on specific donor-recipient pairings. Specifically, multiple recipients from a single donor displayed highly individualised virus colonisation patterns (2018) [1].

Guts of Fecal Transplant Patients Resemble their Donors' (2016) http://www.hcplive.com/medical-news/guts-of-fecal-transplant-patients-resemble-their-donors - http://bmcmedicine.biomedcentral.com/articles/10.1186/s12916-016-0698-z

For IBD: "We now have 4-year data. All 9 patients who went into remission have now relapsed. All but 1 patient chose to undergo FMT again and remission was induced in all but 1 of these patients. Most patients have elected to continue undergoing FMT anywhere between once every 2 weeks to once a month, and most are still in remission with this approach." http://www.gastroenterologyandhepatology.net/archives/may-2018/update-on-fecal-microbiota-transplantation-in-patients-with-inflammatory-bowel-disease/

Intestinal microbiota could transfer host Gut characteristics from pigs to mice [1], but not between mice & zebrafish [2]. "Failure of human-to-mouse FMT to recapitulate the precise microbial contents of the human donors" https://sci-hub.tw/https://www.nature.com/articles/s41435-018-0024-1

FMT can transfer not only microbiota but also the donors’ intestinal innate immune status and improved intestinal integrity: http://www.nature.com/articles/srep38599 | But may not completely restore immune function damaged by antibiotics (2017): https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5395657/

"By profiling bacteria coated with IgA, we identified IgA-coated bacteria associated with inflammation, and we found that microbial interactions with the host immune system can be transferred across people. This transfer of immune function is likely critical for gut microbiome therapeutics for immune-related diseases." (May 2019) https://www.biorxiv.org/content/10.1101/649384v1.full. Dynamic colonization of microbes and their functions after fecal microbiota transplantation for inflammatory bowel disease.

Fecal Calprotectin and Fecal Indole Predicts Outcome of Fecal Microbiota Transplantation in Subjects with Recurrent Clostridium difficile Infection (Mar 2019): https://www.sciencedirect.com/science/article/pii/S1075996419300459 "low calprotectin and high indole is associated with successful FMT in RCDI in both IBD positive and negative patients. We suggest that the ratio of calprotectin/indole should be evaluated for predicting outcome in FMT in RCDI"


General FMT articles & videos:

Article covering OpenBiome stool bank, one of their donors, and the need for more donors: http://news.wgbh.org/2017/04/13/science-and-technology/why-central-square-stool-bank-paying-40-poop-donation

Video covering one of OpenBiome's donors: http://www.cnn.com/videos/health/2015/08/25/fecal-transplant-poop-medicine.cnn

Video coverage of Florida FMT clinic & one of their donors: https://www.youtube.com/watch?v=BxtjWynqW7A

VICE coverage of FMT and OpenBiome: https://news.vice.com/story/your-poop-could-save-someones-life

Fecal Transplants May Be a Miracle Cure for Some of Our Nastiest Illnesses: https://www.wired.com/2016/11/microbiome-therapy-making-fecal-transplants-better/

There is growing evidence faecal transplants could be causing some patients to take on the physical and mental traits of their donors, including body shape and even symptoms of depression (2017): http://www.abc.net.au/news/2017-05-09/faecal-transplant-side-effects-explored-at-conference/8510270

Doctors transfer the power of gut bacteria: http://azdailysun.com/news/local/doctors-transfer-the-power-of-gut-bacteria/article_5956de37-7b12-52ab-9491-0853b067f39c.html

Guy does DIY FMT for IBS (does some extreme & unnecessary things): http://www.theverge.com/2016/5/4/11581994/fmt-fecal-matter-transplant-josiah-zayner-microbiome-ibs-c-diff

Article's covering researcher Jeff Leach's microbiome experiments (including DIY FMT) with the Hadza tribe: http://www.popsci.com/article/science/scientist-gives-himself-fecal-transplant-try-hunter-gatherers-microbiome - http://humanfoodproject.com/rebecoming-human-happened-day-replaced-99-genes-body-hunter-gatherer/ - http://www.rawstory.com/2017/07/heres-what-happened-to-a-professor-of-genetic-epidemiologys-gut-microbiome-when-he-lived-with-hunter-gatherers/

Article covering researcher Lauren Petersen, who cured herself of post-lyme illness with DIY FMT: http://mobile.the-scientist.com/article/49450/athletes-microbiomes-differ-from-nonathletes

2017 study shows FMT helpful for Autism: https://medicalxpress.com/news/2017-01-gut-microbe-potential-treatment-autism.html

Article covering a clinic in Tampa Florida that helps people do FMT for conditions other than c.diff. They also cover the ASU autism study, safety, and more: https://www.buzzfeed.com/nidhisubbaraman/inside-tampa-fecal-transplant-clinic

Powerofpoop success stories: http://thepowerofpoop.com/fecal-transplant-success-stories


SIBO:

Some claim using quick release capsules can cause SIBO [1][2]. But it's more likely due to inadequate donor screening/selection. Top-down methods that empty into the stomach or small intestine are common/standard in all types of official and experimental FMT practice, and there is no evidence that they cause or worsen "SIBO".

OpenBiome, the main US stool bank (c.diff only) offers all 3 methods (enema, naso tube, capsules): http://www.openbiome.org/fmtcapsules/ - http://www.openbiome.org/clinical-guidance

This 9 person FMT trial that used a nasal tube & tested for SIBO, reported no severe adverse events.

In ASU's 2017 FMT Autism study they used the oral route (filtered out most of the large particles so no taste, and then mixed it in with liquids that the patients drank) in some patients and rectal in others and found no differences.

This case seems to prove SIBO is a donor problem rather than a "quick release capsule" problem: https://archive.is/ixi6Y - recipient develops SIBO from colon-only FMT.

Naso tube FMT study for IBS symptoms and predominant abdominal bloating see significant improvements https://www.gastrojournal.org/article/S0016-5085(18)30860-6/abstract Fecal Microbiota Transplantation in Irritable Bowel Syndrome with Predominant Abdominal Bloating: Results from a Double Blind, Placebo-Controlled Clinical Trial

Review of 97 patients finds no difference between top and lower routes (2018): https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6305536/

Review of 150 patients finds "Small bowel exposure to donor stool was not related to symptoms" (2019): https://www.ncbi.nlm.nih.gov/pubmed/30882536

Myself and this person had no problems from DIY oral FMT. And I did it many times from multiple donors. I also experimented with lower vs upper route and lower route only does not seem to be complete.

SIBO - valid term or misnomer based on incorrect understanding of the gut microbiome? I argue the term should be replaced with simply "dysbiosis". https://medium.com/@MaximilianKohler/sibo-valid-term-or-misnomer-based-on-incorrect-understanding-of-the-gut-microbiome-f26c74be141b


FMT Clinics:

There are a large amount of clinics/doctors that provide stool and/or do the procedure themselves for c.diff:

Providers & trials (US & worldwide): http://thefecaltransplantfoundation.org/providers-trials/

List of doctors in the US who do FMT: https://mygijourney.org/c-diff-help/

http://thepowerofpoop.com/epatients/where-to-get-fecal-transplant/

OpenBiome (stool bank - c.diff only, you can use their site to find doctors): http://slice.mit.edu/2015/10/29/podcast-gross-science/http://www.openbiome.org/ | Analysis of OpenBiome's safety and efficacy (2018): https://archive.fo/qBk8g | 2019 follow up showing Openbiome donors are causing IBS in patients: https://archive.fo/eIm25


Below are the clinics who do FMT for things other than c.diff, and the info I have on them:

There are a variety around the world who do FMT themselves or refer you to tested donors. Most charge thousands of dollars and there are multiple reports of people paying that money and getting poor results or even being harmed. There is no relation between their cost and their quality. When I contact these clinics to try and get information to evaluate whether they're worth the money, they typically curtly decline. It seems they have more than enough desperate people coming with no questions asked that they don't bother with people who want answers first.

Most of these clinics do not have enough info on their sites for knowledgeable people to be able to vet their donors & procedures. For example, we need the kind of info in the screening questionnaire above for each clinic's donors. Do not spend thousands of dollars without them proving to you their donors & procedure are high quality!! In my experience, and from feedback from others, high quality donors are young (ideally under 25), athletic, 0 lifetime antibiotic usage, and have identical type 2/3 (NOT 4), dark, small, firm & dry stools.

When we do get to see more info like this video coverage of one of OpenBiome's donors we can see numerous problems, such as very low quality (type 5) stool, and a donor who in my opinion is not visibly in perfect health: http://www.cnn.com/videos/health/2015/08/25/fecal-transplant-poop-medicine.cnn

One of the most important things is actually seeing the whole stool, prior to processing. Otherwise you have no idea what the quality of the stool they are using is. Getting video/image coverage of the donors is also very helpful/important.

It seems that currently (Sept 2018) none of the major clinics in the US, AU, or UK have a good understanding of what makes a high quality donor, nor do they bother to collect enough data to determine the impact (safety & efficacy) of each donor.

Some of these clinics seem to be over-processing the stool. I have not seen any data suggesting this is needed/beneficial. And to the contrary there is data suggesting that there are a wide variety of beneficial organisms and compounds in whole stool [1][2], and processing can lead to detrimental exposures like oxygen. Many people have reported good results from DIY at home, and those are with zero processing. Thus my current opinion is that fresh, whole stool containing all microbes and microbial byproducts in their natural environment is the best.

I just created this sub for people to share their experiences: https://old.reddit.com/r/FMTClinics


Cost comparison of a few of the main clinics: http://www.ibsgroup.org/forums/topic/331018-taymount-clinic-vs-newbery-clinic-for-my-fmt/

Discussion starting here on possible reasons for poor results from the clinics and OpenBiome: http://www.ibsgroup.org/forums/topic/341042-fmt-at-taymount-clinic/page-2#entry1397794


The following list is an incomplete work in progress.

Taymount Clinic (multiple locations - UK, Bahamas):

Procedure details: https://www.youtube.com/watch?v=HxgME7hbnJc&t=57m30s

12/09/2018: Some very useful info about Taymount's donors: https://archive.fo/UtDaL - pretty much confirms all my concerns about their donors. There's a 0 percent chance all those people are safe and effective donors. That many donors coming and going certainly helps to explain some of the widely varying results people get from them. And Taymount's protocol of using a different donor each day for 10 days doesn't allow them to know which donors are safe or effective. It also gives us a peek at their questionnaire, which of course is also a joke - "no chemotherapy in last 3 months". My god.

This July 2019 publication gives additional info/confirmation about donor screening/criteria: https://www.sciencedirect.com/science/article/pii/S2452231719300077

They do FMT via enema only. Prep is colon cleansing via magnesium oxide salts, then colon hydrotherapy. They use the technique that replaces air with nitrogen when filtering the microbes during donor stool prep. They homogenize & filter out all the food almost down to microbe level size. They use a centrifuge to separate microbes. Then freeze.

In this video they refer to the process as "the full 10 days": https://www.youtube.com/watch?v=DTIPWFysINA - this is likely way too short a time period for many/most people/conditions.

Taymount's standard procedure is to do 1 transplant from a different donor each day for 10 days over 2 weeks. In theory getting 10 different donors has its benefits, but only if they're all high quality. And current reports are poor and suggest they are not. Using this method there is no way for them to determine which donors are having what impacts. It doesn't allow them to judge the safety and efficacy of each donor.

Sounds likely that it's over-processed: https://www.youtube.com/watch?v=lvz_P_TYdGA - https://www.youtube.com/watch?v=fOXoZGxvUzM

Adrienne Grierson, who is making a film on FMT says that both Taymount locations use the same donors, and the stool is shipped to the Bahamas from the UK, but there is no verification of this on their site. 11/25/2017

5/13/2018: Taymount announces (via facebook) that they're opening a new location in Canada, and they'll be using frozen stool shipped from the UK location (so same donors).

Taymount says lots of nice things about their donors that most lay people find very convincing, but I haven't seen any strong evidence that their donors are high quality. We need to see the stool types and the questionnaire info for the donors. Video coverage of donors is very helpful. 11/25/2017

01/15/2017 Taymount declined to allow patients to verify donor quality prior to committing to thousands of dollars for treatment.

Dove Clinic, UK

https://www.doveclinic.com/

Dove clinic uses stool/donors provided by Taymount.

This is a publication by them:

A Retrospective Outcome Study of 42 Patients with Chronic Fatigue Syndrome, 30 of Whom had Irritable Bowel Syndrome. Half were treated with oral approaches, and half were treated with Faecal Microbiome Transplantation (July 2019) https://www.sciencedirect.com/science/article/pii/S2452231719300077 "the FMT group improved to a greater extent"

RDS infusions, Florida:

Reportedly they've closed as of early-mid 2019. You can still order directly from their donors.

Giving Neomycin antibiotic for 7 days: http://www.ibsgroup.org/forums/topic/250274-ibs-d-started-rds-probiotic-infusion/

http://rdsinfusions.com/rds-probiotic-infusions

info (at) rdsinfusions.com

https://www.buzzfeed.com/nidhisubbaraman/inside-tampa-fecal-transplant-clinic?

Video coverage of the clinic, one of their donors, and some of their processing methods: https://www.youtube.com/watch?v=BxtjWynqW7A

Michael Garcia, one of their donors, deals directly with people as well and has his own website: https://archive.fo/qGpMx

Their other known donor is "AR" [1][2].

For anything other than c.diff they will not do the FMT, but will refer you to their tested donors. 11/25/2017

Probably the most affordable clinic: $80 per infusion and $10 per capsule. Dry ice shipping is the most expensive part - $160. The infusions seem more cost-effective for the amount you get.

I emailed them about their procedure & donor quality and they wouldn't provide info without paying for a consult ($300) 11/25/2017. And even after the consult I didn't feel that most of my questions were answered.

From the Buzzfeed article it seems like they have one or more low quality donors, and possibly one or more high quality donors.

This interview has some info: http://thepowerofpoop.com/interview-with-fecal-transplant-doctor/ - I found their stated donor criteria laughable.

12/18/2017: Horrible experience, and other info: https://archive.is/SSk2i

Melbourne FMT, Australia:

http://www.melbournefmt.com.au/donors_selection_screening.html - criteria seem weak. No mention of stool type. 11/25/2017

They give multiple antibiotics prior, for 10 days: http://www.melbournefmt.com.au/fmt_procedure.html

Queensland FMT, Australia:

https://www.qldfmt.com/patients/

Dr. Paul Froomes.

Mandatory antibiotics prior to the FMT.

Enema only, costing $400 per enema.

Donor criteria look poor.

Center for Digestive Diseases (CDD), Sydney, Australia:

Thomas Borody's (a leading FMT researcher) clinic.

http://centrefordigestivediseases.com/faecal-microbiota-transplantation/

Here's a detailed 2011 paper titled "Treating Clostridium difficile Infection with Fecal Microbiota Transplantation" he published, but things might have changed since then: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3223289

2015 one titled Fecal microbiota transplantation: A ‘How-To’ guide for nurses https://www.collegianjournal.com/article/S1322-7696(14)00081-X/fulltext

Published papers: https://orcid.org/0000-0002-0519-4698

Donor quality/requirements seem very poor:

Donor Recruitment for Fecal Microbiota Transplantation (2015): https://doi.org/10.1097/MIB.0000000000000405

https://centrefordigestivediseases.com/questionnaire-for-potential-donors

https://centrefordigestivediseases.com/cdd-fmt-protocol

Newbery Medicine, Argentina:

Newberry is closing down 4/18/2018.

http://newberymedicine.com/faqs/

"Healthy stool is mixed with saline solution and then ultra-filtered to extract everything except the microorganisms." Via rectal route only.

I emailed them about their procedure & donor quality and they wouldn't provide info. 11/25/2017

This interview has some info: http://thepowerofpoop.com/interview-dr-silvio-najt/ - looks like they have a preference for fresh stool, which is good, but they said they're building a frozen bank. And not enough info about donor selection.

This guy is doing FMT at Newbery for Ulcerative Colitis: https://medium.com/@scottsundvor

Mediocre improvements from 5 implants: https://robbwolf.com/2017/01/13/what-happened-when-i-got-a-fecal-transplant/

FMT for IBS-D at Newbery Medicine (failure): https://web.archive.org/web/20180203231309/http://www.ibsgroup.org/forums/topic/344097-my-fmt-for-ibs-d-at-newbery-medicine/

FMT Solution LLC, Mexico:

Jason Klop (naturopath) seems to be the main person running this project right now. Mark Davis (naturopath) is said to be involved at some level.

http://fmtsolution.com/

Mark Davis: https://archive.fo/JgB8W - https://web.archive.org/web/20190817083746/https://drruscio.com/fecal-transplant-therapy-with-dr-mark-davis-nd/

Very very expensive. $15,000 for 10 days of treatment. No info about donor quality.

12/10/2017: Not willing to help patients verify donor & procedure quality prior to the transplants. Not willing to help reduce costs in any way.


Thepowerofpoop.com has lots of good & useful info. But also some wrong/outdated info. The blending part of their instructions should be avoided. You don't want to do this since it will kill off a lot of anaerobic microbes (the gut is an anaerobic environment!). And their warning about capsules & SIBO is wrong (see the SIBO section on this page). Haven't vetted their whole site. Looks like the site went down early 2019. You might be able to use archive.org to see old pages.

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