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Possible reason why FMT doesn't work long term


Senior Member
I really like the idea of FMT as a treatment option (fecal transplant). I think if it were in drug form people would be scrambling to try it given the results.
As pointed out by @MaximilianKohler , choosing the right donor is very important. We may even require tailor picked donors to help create better balance.
The main downside I see is that patients often find excellent short term improvement followed by (about 2 weeks) decline to baseline. This might be overcome by simply repeating the transplant, which will be much easier when the pills become mass produced.

However, I came across this study on patients with IBS:

It shows that patients with constipation given a probiotic found relief from that probiotic, but that their stool did not show an increase in the amount of probiotic bacteria. In contrast, the control group stools showed an increase in the amount of probiotic bacteria.

What this suggests is that healthy bacteria were somehow prevented from forming colonies in the guts of the patients. This made me wonder if we suffer from essentially the same problem, and this is why FMT is often only effective in the short term.

Would like to hear people's thoughts on the idea and this study (@Lassesen ?).


Senior Member
I think @ChrisArmstrong gave us the answer in last August's Stanford presentation.

Pwcfs/me in his research group were using most available lipids and Amino's for energy and were therefore unable to make the enzymes and bile needed for normal digestion.

In his sample group this lead to undigested proteins peptides and triglycerides making their way to the colon where they fueled dysbiosis (by providing the right substrate for the wrong bacteria).

I suspect that if you gave a fecal transplant to these patients the undigested proteins and fats would soon replicate the old dysbiosis.
Persistence of bacteria is a bit complex, I have a summary of studies in this post
Probiotics that can take up residency.
There are several possible issues:
  • The helper bacterium (bacteria interacts with each other) are not there, so they are do not get the needed support
  • The pH or amino acids mixture are wrong to keep the bacteria alive (similar to above)
  • The bacteria do not have the appropriate DNA signature and attacked as a foreign infection. For example, there are over 50 strains of L.Reuteri -- only about 8 are found in humans. Taking a L. Reuteri found in a goat will likely be rejected (like organ transplants are)
  • The dosage is insufficient to allow a successful establishment. There was a Swedish study where they cultured some Lactobacillus in an oat soap that was fed to patients. These lactobacillus did establish themselves --- I suspect the dosage was likely > 500 BCFU per serving.
The two best ones to take up residency are Mutaflor and Symbioflor-2. Both were human sourced from people in Germany, and the residency studies appear to have also been done with Germans. This may not be an insignificant factor.