Fecal Transplant (FMT): What It Is and What It Treats

What is fecal microbiota transplantation?

The gut contains trillions of bacteria and other microorganisms — a community called the microbiome. In some diseases, this community becomes severely disrupted, allowing harmful bacteria to overgrow. FMT works by introducing stool from a carefully screened healthy donor into a patient's intestinal tract. The donor's diverse microbial community crowds out the harmful bacteria and helps restore balance.

Donors undergo extensive screening for infections, parasites, and other conditions. FMT is now also available in standardized, FDA-approved forms: Rebyota (RBX2660), approved in November 2022, is an enema-delivered live biotherapeutic product, and Vowst (SER-109), approved in April 2023, is the first orally administered capsule formulation for recurrent C. diff — reducing the complexity compared to traditional colonoscopy-delivered transplants 1Ref 1DuPont HL, DuPont AW, Tillotson GS (2024).Microbiota restoration therapies for recurrent Clostridioides difficile infection reach an important new milestone.Review of FDA-approved live biotherapeutic products for C. diff (RBX2660/Rebyota and SER-109/Vowst), their delivery routes, efficacy, and milestone significance.

What is FMT most clearly used for?

Recurrent Clostridioides difficile (C. diff) infection is the condition where FMT has the strongest evidence and is currently most clinically established.

C. diff is a bacterium that can cause severe, watery diarrhea, abdominal cramping, and fever — most often after antibiotic use has disrupted the normal gut flora. Standard antibiotic treatment (vancomycin, fidaxomicin) works for a first or second episode, but C. diff can recur repeatedly. For patients with two or more recurrences, the ACG Clinical Guidelines recommend FMT to prevent further recurrences — with colonoscopy-delivered FMT achieving prevention of recurrence in over 90% of appropriately selected patients 2Ref 2Kelly CR, Fischer M, Allegretti JR, LaPlante K, Stewart DB, Limketkai BN, Stollman NH (2021).ACG Clinical Guidelines: Prevention, Diagnosis, and Treatment of Clostridioides difficile Infections.ACG recommendation for FMT after two or more C. diff recurrences; preferred delivery routes; repeat FMT for recurrence within 8 weeks.

FMT is typically delivered through one of several routes: - Colonoscopy (most thorough delivery to the colon) - Enema (Rebyota) - Capsules taken orally (Vowst) - Upper endoscopy or a nasoenteric tube

Is FMT used for IBS or IBD?

This is an area of active research, and the answer is more nuanced than for C. diff:

Irritable Bowel Syndrome (IBS): Studies have examined FMT in IBS with mixed results. Some trials showed improvement in symptoms, while others showed no significant benefit over placebo. The 2021 ACG Clinical Guideline for IBS does not recommend FMT as a standard treatment 3Ref 3Lacy BE, Pimentel M, Brenner DM, Chey WD, Keefer LA, Long MD, Moshiree B (2021).ACG Clinical Guideline: Management of Irritable Bowel Syndrome.FMT is not recommended as a standard treatment for IBS per the current ACG guideline, reflecting the lack of consistent evidence. It remains investigational for IBS.

Inflammatory Bowel Disease (IBD — Crohn's disease and ulcerative colitis): Clinical trials in ulcerative colitis have shown some evidence of benefit in achieving or maintaining remission, but results have not been consistent enough to support routine clinical use outside of research settings. Major gastroenterology societies do not currently recommend FMT as a standard IBD treatment.

If you have IBS or IBD and have read about FMT, your gastroenterologist is the right person to explain whether any clinical trials are available and whether the evidence applies to your specific situation.

What does the procedure involve?

For colonoscopy-delivered FMT:

1. Bowel preparation — similar to a standard colonoscopy prep, to clean the colon 2. Colonoscopy — the gastroenterologist passes the scope to the end of the colon and instills the prepared donor material as the scope is withdrawn 3. Recovery — brief, similar to a routine colonoscopy

For capsule-based FMT (Vowst):

1. The patient takes a set number of capsules over one or two days 2. No bowel prep or sedation is required 3. The experience is much simpler, and uptake of this format is growing 1Ref 1DuPont HL, DuPont AW, Tillotson GS (2024).Microbiota restoration therapies for recurrent Clostridioides difficile infection reach an important new milestone.Review of FDA-approved live biotherapeutic products for C. diff (RBX2660/Rebyota and SER-109/Vowst), their delivery routes, efficacy, and milestone significance

Risks include the small possibility of transmitting an infection from a donor, though extensive donor screening minimizes this. FDA-approved standardized FMT products have additional safety oversight.

Finding the right specialist

FMT for C. diff is performed by gastroenterologists, often at academic medical centers or specialty GI practices. If you have had two or more C. diff infections and your antibiotic courses are not resolving the problem, a gastroenterology referral is appropriate. Gale's care team can help coordinate that referral and help you prepare questions for the visit.