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Gut BODY HANDBOOK
Gut · §61
Fecal Microbiota Transplant (FMT)
Recurrent C. difficile is a gut infection that comes back every time the antibiotics stop, and the standard answer is another antibiotic that sets up the next relapse. Here's what you didn't know you didn't know: a transplant of screened stool from a healthy donor restocks the bacteria the antibiotics killed, and cures 85–95% of these cases in one go Kelly 2016. That's a higher single-treatment cure rate than any antibiotic reached. For anything besides C. diff, the evidence is still too thin.
Do · As-needed Evidence Strong Chapter Gut

Broad-spectrum antibiotics take a wrecking ball to your gut. Most of the bacteria in a healthy colon are C. diff's police: they make bile-acid byproducts that keep its spores dormant and crowd it out for food and space. Kill that community and the spores, which survive antibiotics, walk right back in. Donor stool restocks the colon with the full community, and within days the infection has nowhere to grow 1.

For recurrent C. diff, this isn't fringe. The trial that broke it open was stopped early because withholding the transplant had become unethical: 81% cured with one infusion versus 31% and 23% for antibiotics alone 2. Replications held. Donor stool beat the patient's own, 91% to 63% 3. Swallowed capsules matched colonoscopy at 96% 4. It beat the best antibiotics head-to-head 5. Two standardised products are now FDA-approved: Rebyota, a single enema 6, and Vowst, a three-day capsule course 7.

For everything else, slow down. Ulcerative colitis, IBS, autism, obesity, depression: small trials, mixed results. The 2024 guideline says yes for recurrent C. diff, not yet for anything else 8.

If you're in the recurrence cycle, this is the conversation to have.

Days, not weeks. The diarrhoea usually stops within 48–72 hours. Cramping fades over the next few days; appetite returns within the first week. By three months the recurrence risk drops from almost certain to unlikely, and 85–95% of single-transplant recipients stay cured at eight weeks and symptom-free a year or two out 3. For the 10–15% whose infection returns, a second transplant salvages most of them 9. This isn't a better antibiotic. It's the difference between a chronic illness and a finished one.

The fine print — when to skip it, and what people get wrong

The real risk is donor pathogen transmission. In 2019 two immunocompromised adults got drug-resistant E. coli from an untested donor; one died 10. Screening became mandatory that year 11. The severely immunocompromised need case review first.

Probiotic capsules are not a small version of this. Pharmacy lactobacillus strains don't rebuild the anaerobic community that suppresses C. diff. And a DIY transplant with an unscreened donor can carry HIV, hepatitis, and resistant bacteria; the screen is what makes it safe.

References
  1. 1Ianiro G, Punčochář M, Karcher N et al. (2022). Variability of strain engraftment and predictability of microbiome composition after fecal microbiota transplantation across different diseases. Nature Medicine. link
  2. 2van Nood E, Vrieze A, Nieuwdorp M et al. (2013). Duodenal infusion of donor feces for recurrent Clostridium difficile. New England Journal of Medicine. link
  3. 3Kelly CR, Khoruts A, Staley C et al. (2016). Effect of fecal microbiota transplantation on recurrence in multiply recurrent Clostridium difficile infection: a randomized trial. Annals of Internal Medicine. link
  4. 4Kao D, Roach B, Silva M et al. (2017). Effect of oral capsule– vs colonoscopy-delivered fecal microbiota transplantation on recurrent Clostridium difficile infection: a randomized clinical trial. JAMA. link
  5. 5Hvas CL, Dahl Jørgensen SM, Jørgensen SP et al. (2019). Fecal microbiota transplantation is superior to fidaxomicin for treatment of recurrent Clostridium difficile infection. Gastroenterology. link
  6. 6Khanna S, Assi M, Lee C et al. (2022). Efficacy and safety of RBX2660 in PUNCH CD3, a phase III, randomized, double-blind, placebo-controlled trial with a Bayesian primary analysis for the prevention of recurrent Clostridioides difficile infection. Drugs. link
  7. 7Feuerstadt P, Louie TJ, Lashner B et al. (2022). SER-109, an oral microbiome therapy for recurrent Clostridioides difficile infection. New England Journal of Medicine. link
  8. 8Peery AF, Kelly CR, Kao D et al. (2024). AGA clinical practice guideline on fecal microbiota–based therapies for select gastrointestinal diseases. link
  9. 9Kelly CR, Fischer M, Allegretti JR et al. (2021). ACG clinical guidelines: prevention, diagnosis, and treatment of Clostridioides difficile infections. American Journal of Gastroenterology. link
  10. 10DeFilipp Z, Bloom PP, Torres Soto M et al. (2019). Drug-resistant E. coli bacteremia transmitted by fecal microbiota transplant. New England Journal of Medicine. link
  11. 11FDA (2019). Fecal microbiota for transplantation: safety alert — risk of serious adverse reactions due to transmission of multi-drug resistant organisms. link
Related in the handbook (4)
Alternatives
  • — These approved products do the same thing as a fecal transplant — re-seed the gut — just in a standardised pill or enema.
Related
  • — When antibiotics leave you stuck in a C. diff cycle, a stool transplant restores the gut they emptied.
  • — If recurrent C. diff is behind the diarrhea, a fecal transplant cures it in roughly 9 of 10 after antibiotics keep failing.
  • — When a capsule isn't enough, full microbiome reseeding is the heavy-duty end of the same idea.
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