For feedback, edits, contributions, suggestions, etc. use the current meta sticky. can be used to bypass paywalls.


of what we currently know about the gut microbiome's influence on the entire body, and various disease states: /s/HumanMicrobiome/wiki/intro


Research in the area of the microbiome is growing rapidly in recent years due to advances in detection/sequencing techniques: - this means that many long standing positions are being debunked, and even much of what you read (here or elsewhere) can become quickly outdated.

Blog: Understanding Microbiome Research:

Researcher Elisabeth Bik's list of other sources of microbiome info:

Some of 2016's most discussed research papers: | Same for 2017: -

Do NOT eat dirt [1].

Things which are detrimental:

Acid suppression medicines [1][2][2].

Advanced glycation end products (AGEs) [1].

Air Pollution [1][2][3][4][6].

Alcohol: Chronic vapour alcohol exposure [1]. Acute-on-chronic alcohol [1]. Detrimental to mouth microbiome [1]. Alcohol induced alterations of the microbiome may explain reward-seeking behaviors as well as anxiety, depression, and craving in withdrawal and increase the risk of developing psychiatric disorders [1]. Increases susceptibility to pneumococcal pneumonia in a humanized murine HIV model mediated by intestinal dysbiosis [1].

Antibiotics (see abx section below).

Artificial sweeteners [1][2][3].

Cadmium [1].

Diet soda [1][2].

Food additives [1][2]. Emulsifiers [1][2][3][4][5]. Soy lecithin [1]. Sulfites [1]. Glycerol Monolaurate [1]. Trehalose (sugar additive) [1]. Carrageenan and carboxymethylcellulose (CMC) [1]. CMC and polysorbate 80 (P80) [1].

Insecticides: aldicarb [1].

Lead [1][2].

PCBs [1].

Pesticides: Organophosphates [1][2][3]. Glyphosate [1][2,3].

Plastic: Polystyrene microplastics [1][2]. BPA [1][2][3].

Poor diet (which compounds over generations) [1][2][3].

Stress [1].

Tobacco: Smoking dokha [1].

Trans fats [1].

Tributyltin (TBT) [1].


IV vs oral, which is more harmful:

Many studies showing long-term damage:

Non-antibiotic drugs promote antibiotic resistance. These accidental bactericides included proton-pump inhibitors such as omeprazole, calcium-channel blockers, antihistamines, painkillers and antipsychotics. (2018): /r/HumanMicrobiome/comments/85qi1g

More via "antibiotics" flair in sidebar:

Why your doctor’s advice to take all your antibiotics may be wrong: /r/HumanMicrobiome/comments/6pz1n2

In a lab, researchers created three new antibiotics that kill C. difficile by preventing the expression of bacterial genes that are important for its survival. This approach — called antisense therapy — allows the drug to kill only C. difficile, unlike many antibiotics that kill multiple forms of bacteria. (2018):

Antimicrobial peptides:

Peptides are created by gut bacteria, as well as by eukaryotic hosts during symbiotic interactions with bacteria.

AMPs are involved in aging:

Antimicrobial Peptides Vs. Antibiotics:

Spider peptides battle superbugs and cancer - Gomesin, an antimicrobial peptide (AMP) from a spider, can function as an antibiotic, and it also has anticancer activity. Australian scientists synthesized new versions that were 10 times better at killing most bacteria than previously reported:

Review, 2018: Role of antimicrobial peptides in controlling symbiotic bacterial populations:!divAbstract


Bile is a major player in shaping the gut microbiome and its influence on various disease states. Bile acid metabolism & absorption is also a gut-microbe-mediated process.


"What we eat becomes who we are."

These studies explain the impacts and limitations of diet on shaping the gut microbiome:

Influence of early life exposure, host genetics and diet on the mouse gut microbiome and metabolome (2016):

Diabetes-Associated Alterations in the Cecal Microbiome and Metabolome are Independent of Diet or Environment in the UC Davis Type 2-Diabetes Mellitus Rat Model (2018):

Obesity-Linked Gut Microbiome Dysbiosis Associated with Derangements in Gut Permeability and Intestinal Cellular Homeostasis Independent of Diet (mice, 2018):

Diet matters less than evolutionary relationships in shaping gut microbiome. Study is the largest published comparative dataset of non-human primate gut microbiomes to date. | Evolutionary trends in host physiology outweigh dietary niche in structuring primate gut microbiomes (2018):

Diet-induced extinctions in the gut microbiota compound over generations (2016): - but reintroducing the food (fiber in this instance) does not return the microbes.

"So why can’t we supplement our diet with short-chain fatty acids? The ecosystem that produces the acids may be as important as the acids themselves. You can eat all the fiber you want (unless your food is contaminated with feces) and you’ll never re-acquire microbes like H. pylori. The only way to restore such microbes may be to deliberately reintroduce them."

Benefits of fasting and the ketogenic diet are dependent on the gut microbiome, and the benefits can be transferred via FMT [1][2].

"effects of individual differences outweighed the effect of experimental diets"

Diet can impact bacteria's phage production [1].

Review, 2017: Gut microbiota functions: metabolism of nutrients and other food components:

Review, 2018: Mechanisms by which gut microorganisms influence food sensitivities

Resistant starches can be a powerful tool.

The role of short-chain fatty acids, by Jun Kim Ph.D.

Fiber intake is associated with gut microbial diversity, and gut microbial diversity is generally good. So a variety of whole, fibrous foods from legumes, fruits, and vegetables (including root veg) is generally recommended[1][2][3][4][5][6]. However, since fiber feeds a broad range of microbes it can feed problematic ones as well. Thus "person to person variation" reigns supreme. One study showed that removing fiber from the diet improved all constipation symptoms and increased BM frequency[1]!

Iron may be feeding pathogens in some people. Experiment with removing it from your diet.

See also /s/HumanMicrobiome/wiki/prebiotics and "obesity & diet" section of the intro page: /s/HumanMicrobiome/wiki/intro.

Whole food > processed:

Purified/processed fibers are not adequate (in regards to protecting mucus barrier)[1,2,3]. And supplementing a low fiber/carb diet with prebiotics can actually have detrimental affects[1].

Whole grains > brans & refined grains [1][2].

Gut microbiota and systemic inflammation changes after bread consumption. Systemic inflammation was only detected after industrial bread consumption. Healthy bread properties seem to depend on its ingredients and manufacture process [1].

Variation from person to person:

There is a very significant variation from person to person (depending on their unique gut microbiota) regarding reactions to "generally healthy" foods. So you should definitely experiment for yourself and not force something that makes you feel worse but is very healthy for most other people [1][2][3][4][5].

One-size-fits-all is a size that fits no one. Excerpts from the foreword from the book "Primal Body, Primal Mind".

What you eat will protect you from flu — but only if you have the right gut bacteria.

BBC Two: firm links between a person’s individual response to food, and to the gut bacteria that they have.

Host Genetic Background and Gut Microbiota Contribute to Differential Metabolic Responses to High Fructose Consumption in Mice (2018):

Review, 2018: The Effect of Gluten-Free Diet on Health and the Gut Microbiota Cannot Be Extrapolated from One Population to Others "This argument is primarily based on the highly individualized pattern of gut microbial composition and metabolic activity in each person, the variability of the gut microbiota over time and the plethora of factors associated with this variation"

TMAO is a bacterial metabolite linked to heart disease. It is produced by gut bacteria after eating meat (dietary l-carnitine). But vegetarians can lack the bacteria that make TMAO, so their levels don't increase after eating meat. The same effect can be reproduced using antibiotics.

Many koalas could only eat certain species of eucalyptus. But after FMT from other koalas who were able to eat other species, it allowed them to also digest it (2018):

Anti-inflammatory effects of a dietary intervention were not related to changes in gut microbiota composition during the intervention, but were correlated with microbiota composition at baseline (2018): "Role of whole grains versus fruits and vegetables in reducing subclinical inflammation and promoting gastrointestinal health in individuals affected by overweight and obesity: a randomized controlled trial."

Bacterial community response to cruciferous vegetables was individual-specific (2009): Human Gut Bacterial Communities Are Altered by Addition of Cruciferous Vegetables to a Controlled Fruit- and Vegetable-Free Diet

"In the human study, two distinct and inverse responses to tart cherry consumption were associated with initial levels of Bacteroides" (2018):

Age is an important factor in this variation of responses to diet [1][2][3]. As is sex [1].

Elimination diets are extremely useful to figure out exactly what is good and bad for you. Establish a baseline by starting out with a liquid (milk, 100% raw fruit/vegetable juice, broth, etc.) you know you tolerate well, then add in one food at a time to see how it makes you feel. No not ignore the impact of spices when doing this! Many of them are officially prebiotics, and nearly all of them have phytochemicals like antioxidants, flavonoids, carotenoids, and polyphenols, which either feed bacteria or cause specific shifts in the gut microbiome that may be beneficial/detrimental to various people.

Be extremely skeptical of suggestions that detrimental affects are actually a good thing because they represent "die off/herx". This is probably one of the top most widespread & dangerous pieces of misinformation. If you are not seeing significant improvements from baseline after dipping below baseline from a hypothesized bad reaction from harmful microbes dying off, then you are likely simply harming yourself. Any genuine herx reaction should also be very temporary (1-2 days).

Protein & fat:

[Rat study] Nitrogen availability (protein intake) is a main factor in shaping the gut microbiome & health. Low protein, high carb diet associated with beneficial health markers: [1,2]

Low protein diet is recommended based on the evidence that excessive protein intake adversely affect health [1][2].

Worse inflammatory profile in omnivores than in vegetarians associates with the gut microbiota composition:

In general, fermentation metabolites from carbohydrates and associated phenolic compounds have beneficial effects; by the contrary protein derived fermentation products are detrimental for health [1].

There's a big difference between types/sources of fats & proteins [1][2]. The body processes them differently, thus they have very different impacts on weight and gut microbiome. Soy oil vs coconut oil.

Dietary protein sources differentially affect microbiota, mTOR activity and transcription of mTOR signaling pathways in the small intestine [mice]. 2018 review: "effects of high protein diet on the gut were dependent on the protein source (i.e. from plant or animal sources)"

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. 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 below). Haven't vetted their whole site.


FMT screening questionnaire: - FMT is only as safe as your donor is healthy. This is what healthy poop looks like.

European consensus guidelines tests:

OpenBiome donor screening/testing info: -

Do not solely rely on testing (conventional or 16s) as it is very limited in value: /r/HumanMicrobiome/comments/7gmq0k

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 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 intact, 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 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:

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:


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: - 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]. 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 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 bag like this 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 (10%) is the commonly used antifreeze additive, but it's also a laxative, and therefore problematic for many people.

  • "Top down", upper, oral vs lower, rectal routes:

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.

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): -

Regarding safety: -

The long-term effects of faecal microbiota transplantation for gastrointestinal symptoms and general health in patients with recurrent Clostridium difficile infection

  • Top down/oral procedure:

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:

How to:

Donor poops in 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. 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.

  • 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]. But the evidence for most conditions isn't here yet, and antibiotics can have various detrimental side effects.

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.

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

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:

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 of both the donor and recipient plays an important role[1], but the details are not 100% established yet. Some factors are nitrogen/protein content [1,2][3], bile production, age, and in general fiber intake is associated with diversity, and gut microbial diversity is generally good. So a variety of whole, fibrous foods from legumes, fruits, and vegetables (including root veg) is generally recommended [1][2][3][4][5], but as with everything, person-to-person variation reigns supreme. Purified/processed fibers are not adequate[1,2].

A few studies showed that FMT success depends on changing bile acid metabolism [1, 2], 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.

  • The best enema-only procedure (possibly inferior to capsules because it only gets the colon, which is a small part of the entire digestive system) is:

Donor poops in 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 turkey baster (so stool doesn't get stuck). Look at an 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:, 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.

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 your right side for ~15 minutes.

  • 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.

Scientific info:

Wide benefit from fecal transplants (2015):

Fecal Microbiota Transplantation: Current Applications, Effectiveness, and Future Perspectives (2016):

Novel Indications for Fecal Microbial Transplantation: Update and Review of the Literature (2017):

Guidelines: European consensus conference on faecal microbiota transplantation in clinical practice (2017):

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):


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:

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:

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."

2017 OpenBiome/MIT study confirms that oxygen exposure is the most important factor to reduce during processing:

Impact of Different Fecal Processing Methods (homogenization & freezing) on Assessments of Bacterial Diversity in the Human Intestine (2016):


Effects of the long-term storage of human fecal microbiota samples collected in RNAlater (2019): "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) "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: and 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): - 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):

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):

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): - no statistical difference.

This 2017 review comments on a study where a small dose (few capsules) was as effective as much larger doses: - this is in line with my own experiences.

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.

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): The Safety of Fecal Microbiota Transplantation for Crohn’s Disease: Findings from A Long-Term Study

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. (2018):

Impact factors:

Donor species richness determines FMT success for IBD (2015): | 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):

Irritable Bowel Syndrome-Like Symptoms Following Fecal Microbiota Transplantation: A Possible Donor-Dependent Complication (2017):

FMT success may depend on changing bile acid metabolism: /s/HumanMicrobiome/wiki/bile

Gut fungal dysbiosis correlates with reduced efficacy of fecal microbiota transplantation in Clostridium difficile infection (2018): "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."

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

Different responses to FMT depending on age of donor (in chickens):

Vegetarians have fewer pathogens (Thai study):

Worse inflammatory profile in omnivores than in vegetarians associates with the gut microbiota composition:

Supporting evidence for young athletes being better donors: Athletes have higher diversity, and their gut microbiome differs at the functional metabolic level. Cardiorespiratory fitness is correlated with increased microbial diversity[1][2][3]. 2017 review, Exercise Modifies the Gut Microbiota with Positive Health Effects. Gut Microbiota Composition is Related to Cardiorespiratory Fitness in Healthy Young Adults [1]. Sports medicine review. Article referencing 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. Fecal microbiota transplantation confers beneficial metabolic effects of diet and exercise on diet-induced obese mice. Endurance exercise and gut microbiota: A review (2017) [1]. Grip strength, muscle mass, and reaction time as vital signs.

FUT2 genotype and secretory status are not associated with fecal microbial composition and inferred function in healthy subjects (2018):

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

Sterile fecal filtrate is effective for treating c.diff (implicating phages):

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.

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:


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

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 [1].

Guts of Fecal Transplant Patients Resemble their Donors' -

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"

FMT can transfer not only microbiota but also the donors’ intestinal innate immune status and improved intestinal integrity: | But may not completely restore immune function damaged by antibiotics (2017):

General FMT articles & videos:

Article covering OpenBiome stool bank, one of their donors, and the need for more donors:

Video covering one of OpenBiome's donors:

Video coverage of Florida FMT clinic & one of their donors:

VICE coverage of FMT and OpenBiome:

Fecal Transplants May Be a Miracle Cure for Some of Our Nastiest Illnesses:

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):

Doctors transfer the power of gut bacteria:

Guy does DIY FMT for IBS (does some extreme & unnecessary things):

Article's covering researcher Jeff Leach's microbiome experiments (including DIY FMT) with the Hadza tribe: - -

Article covering researcher Lauren Petersen, who cured herself of post-lyme illness with DIY FMT:

2017 study shows FMT helpful for Autism:

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:

Powerofpoop success stories:


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): -

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: - recipient develops SIBO from colon-only FMT.

Naso tube FMT study for IBS symptoms and predominant abdominal bloating see significant improvements 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):

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". /r/HumanMicrobiome/comments/8as82e

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):

List of doctors in the US who do FMT:

OpenBiome (stool bank - c.diff only):

Analysis of OpenBiome's safety and efficacy (2018):

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. They all charge thousands of dollars and there are multiple reports of people paying that money and getting little to no results. 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 firm 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:

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. DIY FMTs at home report high success rates, 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: /r/FMTClinics

Cost comparison of a few of the main clinics:

Discussion starting here on possible reasons for poor results from the clinics and OpenBiome:

The following list is an incomplete work in progress.

Taymount Clinic (multiple locations - UK, Bahamas):

Procedure details:

12/09/2018: Some very useful info about Taymount's donors: - pretty much confirms all my concerns about their donors. There's a 0 percent chance all those people are safe and effective donors. 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.

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": - 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're 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: -

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.

RDS infusions, Florida:

Giving Neomycin antibiotic for 7 days:

info (at)

Video coverage of the clinic, one of their donors, and some of their processing methods:

Michael Garcia, one of their donors, deals directly with people as well and has his own website: /r/FMTDatabase/comments/86we9f

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: - I found their stated donor criteria laughable.

12/18/2017: Horrible experience, and other info:

Melbourne FMT, Australia: - criteria seem weak. No mention of stool type. 11/25/2017

They give multiple antibiotics prior, for 10 days:

Thomas Borody's (leading FMT researcher) clinic in Sydney, Australia:

Here's a detailed 2011 paper titled "Treating Clostridium difficile Infection with Fecal Microbiota Transplantation" he published, but things might have changed since then:

Published papers:

Donor quality/requirements seem very poor:

Donor Recruitment for Fecal Microbiota Transplantation (2015):

Newbery Medicine, Argentina:

Newberry is closing down 4/18/2018.

"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: - 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:

Mediocre improvements from 5 implants:

FMT for IBS-D at Newbery Medicine (failure):

Dr Mark Davis's FMT Solution LLC, Mexico:

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.


See sidebar flair.







Probiotic guide.

Probiotic info archive: /s/HumanMicrobiome/wiki/probiotics


There are tons of microbes which are currently unknown and/or not tested for currently. 16s only tests for bacteria, and not down to the strain level, which is of vital importance.

This recent study for example, showing one bacterial strain inducing liver damage (2018): - That kind of thing is absolutely not tested for with either conventional or 16s commercial testing.

Till mid 2016 they were only able to culture an estimated 1% of gut microbes:

Only 35 to 65% of molecular species detected by sequencing have representative strains in culture (Apr 2017):

8/21/2017 Stanford study using shotgun sequencing says we still don't know 99% of human microbes:

9/16/2017 From an international database of more than 1,500 metagenomes, the UQ team reconstructed the individual genomes of 7,280 new bacteria and 623 new archaea. Of these microorganisms, roughly a third were unlike anything scientists had seen before, warranting the creation of 17 new bacterial phylums and three new achaeal phylums.

10/2/2017 NIH Microbiome Project Triples Number of Previously Identified Bacterial Genes:

3/19/2018 Researchers have used artificial intelligence (AI) to discover nearly 6,000 previously unknown species of virus

3/21/2018 Sanguibacter massiliensis sp. nov., Actinomyces minihominis sp. nov., Clostridium minihomine sp. nov., Neobittarella massiliensis gen. nov., and Miniphocibacter massiliensis gen. nov., new bacterial species isolated by culturomics from human stool samples

4/4/2018 Researchers have discovered more than 200 previously unknown viruses in a category whose members cause illnesses such as influenza and haemorrhagic fevers.

4/30/2018: About half of all oral bacteria are uncultivable

1-Mar-2018: How reliable is diagnostic testing for Zika? Almost two thirds of all laboratories showed false-positive or false-negative results.

1/17/2019: Thousands Of New Microbiome Species Found Living on the Human Body. The researchers estimate one of the new species is the seventh most prevalent intestinal microbe in the human microbiome

Current (2018) commercial testing (16s) has very limited value. Here's a great write up by a microbiologist about it. More: [1][2][3][4]. A real life example. Another researcher/professor in the field agreeing. Excellent podcast that supports and gets into the details.

A major factor is also that most testing is only for bacteria, but it's looking like phages might be more important. There's also fungi and archaea.

Commercial tests are currently using 16s sequencing, which is mostly only accurate to the genus level. Data at this level is not especially useful [1][2][3][4][5].

Here are a few articles questioning the accuracy of these tests: [1][2][3]

Here are examples of the same stool sample sequenced by two different companies, showing different results.

Nonsensical results like this are very common. And this paper explains why. Essentially, many people's stools are not uniform, thus depending on which part of the stool you sample, you'll get different results. Thus homogenizing the stool prior to sampling will give more consistent results, but also changes the proportions of the results. This is likely a major problem with uBiome for instance, who use a swab method rather than whole stool.

Various companies that do it: ubiome, genova, American Gut, uBiota, biocollective, doctor's data, bioscreen. Here's a comparison of the different microbes each test for.

Here's an example report from ubiome's $90 explorer kit. And an example (and discussion) of their SmartGut kit that goes through a doctor.

Here's an example report from BioScreen, which goes through a doctor and seems a little more useful.

Here's an example report from

Example report from Genova's GI Effects. has a variety of tests: - The "Comprehensive Digestive Stool Analysis 2.0™ (CDSA 2.0)-Genova Kit" is probably the most useful one.

This is essentially the best input you can expect to get from sharing your results.


The Intestinal Virome and Immunity (2018):

Bacteriophages (phages):

Review, 2018: Beyond Bacteria: Bacteriophage-Eukaryotic Host Interactions Reveal Emerging Paradigms of Health and Disease - "Phages may be naturally internalized into eukaryotic cells. As phages are significant reservoirs of genetic diversity and considering phages are capable of entering eukaryotic cells, this raises questions about the possibility of bidirectional trans-kingdom gene exchange between phages and their animal hosts."

Healthy human gut phageome identified (2016):

Review, 2017: Phages in the Human Body:

Review, 2017: Bacteriophages in the human gut: our fellow travelers throughout life and potential biomarkers of heath or disease. Phages are the largest part of the human microbiome:

Review, 2017: The human intestinal virome in health and disease:

Review, 2017: Bacteriophages in the gastrointestinal tract and their implications:

Source of phages doesn't seem to matter. Phages obtained from sewer have beneficial effects.

Phages vs antibiotics: "The upside and downside to using phage therapy is that the viruses are extremely specific. The upside is that phage will only kill a very specific type of bacterium, whereas antibiotics lay waste to many different bacteria, including friendly ones. The downside is that the phage are too specific."

Addressing superbug resistance with phage therapy. "The study is significant because it is the first time bacteriophage therapy has been used in the USA to treat a patient who had an antibiotic-resistant, blood stream infection."

Great article on the current (Nov 2017) status in the US of the use of phages for fighting an infectious disease: | Another from Nov 2017 about a separate occurrence: | Another from Dec 2017: (the video on the page has even more).

Phages are an important component of FMT success [1].

Transferring just the bacteriophage was sufficient to reduce resting metabolic rate and cause weight gain in control mice:

The Virus That Could Cure Alzheimer’s, Parkinson’s, and More:

Phage therapy via clinics ($1k-4k) or supplements ($30-200) - link.

Phages as prebiotic supplements in the US: /r/HumanMicrobiome/comments/6n76p9//dk7a2k4/

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