Towards a Standard Protocol for Fecal Microbiota Transplantation in Irritable Bowel Syndrome [meta-analysis/summary, Apr 2026] FMT

[SFBayFMT5]

This was recently published. It's not a new study, rather it summarizes the current state of knowledge and experience. In a number of cases it addresses things that Michael, myself, or others posting online have noticed but that I haven't noticed being mentioned before.

https://pmc.ncbi.nlm.nih.gov/articles/PMC13071414/

Here are a number of quotes with my commentary:

The selection of the donor does not affect the clinical efficacy of FMT in patients with CDI, whereas the success of FMT in inflammatory bowel disease and other disorders is donor-dependent. A new definition of superdonor has been coined to describe a donor who is normobiotic and has a positive microbial signature. A previous attempt to use fecal-transplant pooling as a superdonor surrogate was not successful, and what constitutes a positive microbial signature in a superdonor remains unclear....

The bacterial diversity is reduced due to the negative effects on the gut microbiota of aging, smoking/smoking cessation, having been born by cesarean section, having been formula-fed, receiving frequent treatment with antibiotics or having a regular intake of non-antibiotic drugs. On the other hand, regular exercise and consuming a sport-specific diet are known to be associated with favorable gut microbiota.

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This seems very much in accordance with some things that Michael as well as Marco from Gezonde Darmflora have been saying.

Stability of the bacterial profile of the donor’s fecal transplant has been reported to be one of the factors associated with a favorable response to FMT. In an RCT of FMT in IBS with high response rates and durable effects, the bacterial profiles of the donors’ fecal transplants were stable during a 2-year follow-up

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This seems to back up the idea of Michael's that donors whose stool type remains constant are better than donors whose stool type is more variable.

Different anaerobic systems have been proposed for collecting the donor’s fecal transplant under anaerobic conditions to avoid damaging anaerobic bacteria. However, collecting the donor’s fecal transplant under anaerobic conditions could damage the aerobic bacteria and other microorganisms in the fecal transplant, resulting in the transplantation of only anaerobic bacteria. Processing the fecal transplant directly under strict anaerobic conditions results in non-viability of about 50% of the faecal-transplant bacterial contents.

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This is the first time I've seen someone suggest this possibility. However, just one paragraph earlier the authors suggest that exposure to air could also skew the microbial balance in a negative way. So I read what they're saying as just an admission that almost any method of stool collection and/or processing could change the bacterial balance, and we don't know enough about what bacteria do what in order to say anything conclusive about whether it's helpful or harmful.

Direct freezing of the donor’s fecal transplant appears to be the best alternative for preserving the microbiota viability since the freeze-thaw process does not significantly alter the composition of viable microbiota. The donor’s fecal transplant should not be exposed to room temperature for more than 4 hours or kept at 4°C for no more than 24 hours. However, fecal transplants can be stored at −20°C for up to a few months or at −80°C for up to 2 years.

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In other words, they encourage processing post-thawing, rather than pre-freezing. The donor freezes the raw sample immediately after passing, it's lowered to dry ice temperature ASAP if possible, and then it's blended with saline after being thawed at the hospital immediately prior to administration. I've never seen anyone else recommend this but this is a case where HM, by selling stool pieces for recipients to make treatments out of later, came closest to this recommendation of anything I've seen.

Using 10-20% (volume/volume) glycerol as a cryoprotectant to preserve the bacterial viability upon freeze-thawing has been recommended. However, glycerol changes the fecal transplant into an insufficiently dry and sticky product, could penetrate cell membranes and change certain characteristics of the fecal transplant, and upon thawing causes medium enrichment, which may increase the levels of certain bacteria and thereby alter the original microbiota composition. Rapid deep-freezing to −80°C without using glycerol or stabilizers such as RNAlater is strongly recommended....

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This is the only source written by doctors that I have ever seen that recommends NOT using glycerol. This would back up the people who have said that using glycerol vs. not didn't help with efficacy. On the other hand, they recommend this in the case that ultracold (dry-ice-level) storage is available.

It's also the first source I've seen that even considered the possibility that glycerol could play a role in boosting bacteria counts besides mere protection from freezing, however, they suggest that this could be a negative effect, whereas my own experience with both stool and saliva samples suggests a positive one.

It is noteworthy that in the studies with the best outcomes of FMT in IBS, the donors’ fecal transplants were frozen directly at −20°C, transported frozen to the hospital and stored at −80°C for a few months before transplantation. Furthermore, the fecal transplants were thawed at 4°C, mixed with physiological solution at 4°C and kept at 4°C before being administered to the patients at that temperature.

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So they did "slow" thawing on ice, like OpenBiome did at the time of my successful transplant, rather than thawing in 37C (body temperature) water like Marco in the Netherlands recommends, as well as some newer stool bank protocols. I noticed that Marco's pills seemed more effective if they weren't brought directly from dry ice to body temperature in one step.

Administering the donor’s fecal transplant to the small or large intestine in FMT to treat CDI does not appear to impact the outcome...

In FMT for IBS the administration route appears to be an important factor for the efficacy. Oral administration of the fecal transplant in the form of capsules had no effect at all, while administering into the large intestine resulted in short-lasting effects. On the other hand, delivering the donor’s fecal transplant to the small intestine resulted in positive and durable effects.

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So to probably nobody's surprise, IBS is "pickier" than C. diff in terms of what makes a difference in effectiveness. Also, it wasn't that bottom-up delivery didn't provide any benefits at all, but rather that they didn't last.

Abstract​

Randomized controlled trials (RCTs) of fecal microbiota transplantation (FMT) in patients with irritable bowel syndrome (IBS) have produced outcomes varying from no effect at all to high efficacy and durable effects over time.

This review analyzed differences in the protocols used in FMT RCTs for IBS in the recently published literature with the aim of identifying the factors responsible for the success or failure of these RCTs. The results of this analysis might be useful in formulating an effective standard protocol for FMT in IBS.

A systematic search was conducted in the PubMed database of the literature published in English from January 2015 to December 2023 using several search phrases comprising MeSH expressions. Those RCTs that carefully selected donors based on environmental factors that are known to affect the gut microbiota positively and ensured bacterial diversity before and during FMT produced successful outcomes.

Furthermore, direct freezing of the donor’s fecal transplant, storing it at −80°C until the FMT is performed, and then thawing it at 4°C and mixing it manually appear to be factors associated with the success of FMT in IBS. Administering the donor’s fecal transplant into the small intestine results in durable effects of FMT and long-term colonization of beneficial bacteria.

A standard protocol for FMT with large and durable effects should include (1) careful donor selection, (2) handling the donor’s fecal transplant in a way that preserves its microbiota contents, and (3) administering the transplant into the small intestine.

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