Stool became FDA-approved medicine for one infection, and other uses are still experiments

Key takeaways

• In 2019, the FDA reported that a patient died after a fecal transplant passed along a drug-resistant strain of E. coli that the donor stool had never been tested for.
• The FDA approved Rebyota in November 2022 and Vowst in April 2023, both to keep C. diff from coming back in adults after antibiotic treatment.
• In Vowst’s main trial, C. diff returned within eight weeks in 12.4% of patients, compared with 39.8% of those given a placebo.
• The American Gastroenterological Association advises against fecal transplants for IBS and inflammatory bowel disease except inside clinical trials.
• Studies in autism, obesity and cancer are small, and most had no placebo group, so treat exciting headlines as early leads.

In June 2019, the FDA issued a safety alert that read like a medical mystery. Two adults with weakened immune systems had received fecal transplants from the same donor. Both developed invasive infections with a drug-resistant strain of E. coli, and one of them died⁴.

No one had tested the donor’s stool for that kind of germ. Stored samples from the donor later turned up bacteria that matched the patients’ infections⁴.

Three and a half years later, the FDA approved the first medicine made from donated human stool³. A second one, taken as capsules, followed in April 2023¹.

That arc, from risky procedure to regulated product, sums up where microbiome therapy stands. For one problem, C. difficile infections that keep coming back, the evidence is strong. For nearly everything else, the research is early, and the risks of going it alone are real.

Here is what has been proven, what looks promising, and what to avoid.

A stool transplant earned its place against one stubborn infection

C. difficile, often shortened to C. diff, is a bacterium that causes severe diarrhea and colon inflammation. The CDC estimates almost half a million infections a year in the United States¹⁵. The FDA links it to 15,000 to 30,000 deaths a year¹.

Most cases strike during or soon after a course of antibiotics, when the risk can be up to ten times higher than normal¹⁵. Age 65 and older, a hospital or nursing home stay, a weak immune system and a past infection also raise the odds¹⁵. Each time C. diff returns, the chance of another bout goes up¹.

The thinking behind a fecal microbiota transplant, or FMT, is simple. Antibiotics clear out many of the gut’s resident bacteria, not just the harmful ones. Stool from a screened, healthy donor carries a full community of microbes that may help rebuild the gut’s natural defenses.

Medical groups now recommend FMT for some repeat infections. A 2021 guideline from the Infectious Diseases Society of America and the Society for Healthcare Epidemiology of America recommends it for people with multiple recurrences who have already tried the right antibiotics⁶. The panel’s view is that at least two recurrences should get antibiotic treatment first⁶.

The American Gastroenterological Association (AGA) agreed in its 2024 guideline. It suggests stool-based therapies after standard antibiotics to prevent another recurrence in selected adults⁵. It also suggests conventional FMT as an add-on for hospitalized adults with severe C. diff that isn’t responding to antibiotics⁵.

Conventional FMT, prepared by hospitals or stool banks, still isn’t an FDA-approved product. The FDA treats it as investigational. Under a policy it first announced in 2013, the agency relaxed its usual research paperwork only for C. diff that hasn’t responded to standard treatment, and only if patients are told the use is investigational⁴.

Two approved products, side by side

The products the FDA approved in 2022 and 2023 both start with screened donor stool, but they differ in form and in how they’re given. Both are for adults 18 and older who have finished antibiotics for a repeat C. diff infection. Neither one treats an active infection²³.

	Rebyota	Vowst
FDA approval	November 30, 20223	April 26, 20231
Maker	Ferring Pharmaceuticals3	Seres Therapeutics1
What it is	A liquid suspension of donor stool microbes3	Capsules of bacterial spores; the stool is treated with alcohol to kill other organisms2
How it’s given	One 150 mL dose into the rectum, 24 to 72 hours after antibiotics3	Four capsules a day for three days, after a bowel-cleansing drink2
Main trial	262 adults3	182 adults2
Key result	Treatment success at 8 weeks: 70.6% vs. 57.5% with placebo3	C. diff returned in 12.4% vs. 39.8% at 8 weeks, and 21.3% vs. 47.3% at 24 weeks2
Most common side effects	Belly pain, diarrhea, bloating, gas, nausea3	Bloating, fatigue, constipation, chills, diarrhea2

Two details deserve attention. Rebyota’s 8-week figure came from a statistical model that also drew on an earlier placebo-controlled study. At six months, its edge over placebo, 65.5% versus 56.5%, was not statistically significant³.

Vowst’s placebo group shows how stubborn this infection is. Nearly half of those patients had C. diff come back within 24 weeks².

Both labels carry the same two warnings. Even with donor testing, the products may transmit infectious agents, and they may contain food allergens²³.

The 2019 death showed why screening can’t be skipped

After the 2019 death, the FDA required new safeguards for investigational fecal transplants. Donors must be asked about risk factors for carrying drug-resistant germs, and donor stool must be tested for them. Stool that tests positive is thrown out⁴.

That case happened in a medical setting, not a kitchen. We did not find a published report of an infection traced to a home transplant, sometimes called DIY FMT. But the logic is hard to escape. If one missing test let a deadly germ through a medical program⁴, stool from a friend or relative, blended at home with no lab tests at all, carries at least that risk.

Donor choice matters in other ways, too. In 2015, doctors described a woman treated for repeat C. diff with stool from her overweight teenage daughter¹³. Over the next 16 months, she gained 34 pounds without trying, and her weight kept climbing¹³.

The doctors couldn’t prove the transplant caused it, since curing C. diff and treating another stomach infection may have played a role. Even so, they changed their policy and now use only donors who are not obese¹³. They also noted that patients may prefer a relative as donor, while frozen stool from unrelated donors works well against repeat C. diff¹³.

Some people should not receive any stool-based therapy. The AGA advises against these treatments for adults with severely weakened immune systems⁵.

If you or a family member has a problem after a fecal transplant or an approved product, report it to the FDA’s MedWatch program at 1-800-FDA-1088⁴.

Beyond C. diff, the trials are small and the results are mixed

Headlines have linked gut transplants to almost everything. Here is what the studies showed, condition by condition.

Ulcerative colitis. In a 2019 Australian trial published in JAMA, 73 adults with mild to moderate colitis got either pooled donor stool or their own stool as a comparison¹⁰. After eight weeks, 32% of the donor group reached remission without steroids, compared with 9% of the comparison group¹⁰. The authors called the results preliminary, and only 5 of the 12 donor-group responders were still in remission a year later¹⁰.

Irritable bowel syndrome. The AGA’s 2024 guideline advises against FMT for IBS and for inflammatory bowel disease except within clinical trials⁵. The panel concluded that FMT can’t yet be recommended for digestive conditions other than C. diff⁵.

Obesity and blood sugar. In a 2020 U.S. trial, 24 adults with obesity took capsules from lean donors or placebo capsules weekly for six weeks¹¹. The donor microbes took hold in most people’s guts. Yet insulin sensitivity didn’t improve significantly, and weight stayed about the same in both groups¹¹.

Autism. A U.S. research team treated 18 children with autism in an open-label study, meaning everyone knew they were getting the treatment¹². Two years later, gut symptom scores were 58% lower than at the start, and a professional evaluator rated autism severity 47% lower¹².

Those numbers are striking, but the authors listed serious limits. There was no placebo group, so a placebo effect can’t be ruled out¹². The protocol also included two weeks of an antibiotic, a bowel cleanse and a stomach-acid reducer, and the authors said follow-up studies are needed to tell whether the gains came solely from the antibiotic¹². And 12 of the 18 children changed medicines, diets or supplements after treatment¹².

Cancer immunotherapy. In 2021, two teams reported in the journal Science that fecal transplants helped some people with advanced melanoma whose cancer hadn’t responded to immunotherapy drugs. In a National Cancer Institute and University of Pittsburgh study, 6 of 15 patients responded⁷. In an Israeli study, 3 of 10 did⁸.

A 2023 trial tried healthy-donor stool alongside immunotherapy as a first treatment. Thirteen of 20 patients responded, and five had severe immune-related side effects from the combined treatment⁹. None of these studies had a comparison group, so no one can yet say how much the transplant added.

The next generation moves from whole stool to chosen microbes

Whole stool is hard to standardize. Every donor is different, and every batch must be screened.

Vowst hints at where the field is heading. Its maker treats donor stool with alcohol so that mainly hardy bacterial spores survive, then packs them into capsules². That is a step away from raw stool toward a more controlled product.

Researchers want to go further, identifying the exact microbes that help and growing them in labs. After the Pittsburgh melanoma study, a National Cancer Institute scientist said it may become possible to give patients those organisms directly, with no fecal transplant at all⁷.

That future isn’t here yet. For now, the approved products still begin with a human donor, and their labels still warn about infection risk²³.

Probiotics are a different tool with a narrower record

A probiotic delivers one or a handful of microbe strains. A fecal transplant moves an entire community of microbes. The two aren’t interchangeable.

In 2020, the AGA reviewed probiotics for digestive conditions. According to the NIH Office of Dietary Supplements, the AGA recommended probiotics for ulcerative colitis and Crohn’s disease only within clinical trials¹⁴. It advised against them for U.S. and Canadian children with acute infectious gastroenteritis, a stomach bug that causes diarrhea¹⁴.

The AGA did recommend certain bacterial combinations for premature, low-birth-weight babies to help prevent a dangerous bowel disease¹⁴. Yet in 2023, the FDA warned that probiotics given to premature infants can cause serious, possibly fatal infections. It linked them to one infant death and more than two dozen other adverse events¹⁴.

For IBS, the NIH fact sheet says some probiotics might ease some symptoms, but more trials are needed to pin down which strain, dose and length of use helps¹⁴. If you try one, pick a product studied for your problem, agree on a trial period with your clinician, and stop if it doesn’t help.

Respecting the gut’s ecosystem means respecting its risks

The success of fecal transplants for C. diff supports an idea many natural-health traditions have long held. Health depends on balance, and the living community inside you matters. Restoring that community worked where repeated rounds of drugs had failed.

But a stool transplant is not gentle simply because it’s natural. Stool is a living biological material that can carry dangerous germs, as the 2019 case showed⁴. The approved products start with screened donors and tested stool²³.

Respect for the body’s ecosystem cuts both ways. It means taking the gut seriously enough to protect it from untested material.

A decision guide before you try a microbiome therapy

Use this table to match your situation with the evidence and a sensible next step. Bring it to your appointment.

Your situation	What the evidence says	A sensible next step
C. diff came back after antibiotics	Strong evidence that stool-based therapy cuts repeat infections126	Ask a gastroenterologist or infectious disease specialist about FMT, Rebyota or Vowst
First C. diff infection	Guidelines start with antibiotics6	Treat the infection first; ask what happens if it returns
Severely weakened immune system	AGA advises against stool-based therapy5	Ask about other options
Ulcerative colitis or Crohn’s disease	Promising but early; AGA says trials only510	Ask about clinical trials; keep your current treatment
IBS	Not enough evidence; trials only5	Work on diet, stress and proven IBS care with your clinician
Weight or blood sugar	Microbes took hold, but weight didn’t change11	Skip it for weight loss
A child with autism	Open-label studies only12	Talk with the child’s care team; look for placebo-controlled trials
Cancer on immunotherapy	Promising but early, no comparison groups789	Ask your oncologist about trials
Home transplant or untested donor	Untested stool can carry dangerous germs, and donor traits may matter413	Don’t do it

Questions worth asking your clinician:

1. Am I a candidate for FMT, Rebyota or Vowst, and why that option over the others?
2. How is the donor material screened, and who made it?
3. Do I need to stop any medicines first, and how long after antibiotics should I wait?
4. What symptoms after treatment should make me call you?
5. If I’m asking about a use other than C. diff, is there a clinical trial I could join?

What the evidence supports

Claim	Evidence level	What the research shows
Stool-based therapy prevents repeat C. diff	Strong evidence	Placebo-controlled trials and two guidelines support it12356
FMT as an add-on for severe C. diff in the hospital	Promising but early	AGA suggests select use when antibiotics fail5
FMT induces remission in ulcerative colitis	Promising but early	One small trial showed more remission; trials only510
FMT improves response to cancer immunotherapy	Promising but early	Small studies with no comparison groups789
FMT treats IBS	Not enough evidence	AGA advises use only in trials5
FMT causes weight loss or better insulin use	Not enough evidence	No significant change in a placebo-controlled pilot11
FMT improves autism symptoms	Not enough evidence	Open-label studies with no placebo12
Stool that skips germ testing is safe to transplant	Evidence says no, or unsafe	Stool not tested for a drug-resistant germ caused a fatal infection; home transplants skip all testing4
Probiotics treat ulcerative colitis or Crohn’s	Not enough evidence	AGA recommends them only in trials14

Questions readers ask

The bottom line

Fecal microbiota therapy has earned a real place in medicine for one job: keeping C. diff from coming back after antibiotics. Two FDA-approved products and professional guidelines now support it, backed by placebo-controlled trials.

For colitis, IBS, weight, autism and cancer, the research is early, small and often uncontrolled. Those leads are worth following in clinical trials, not at home. Your gut’s ecosystem is worth protecting, and that starts with screened donors, careful clinicians and honest evidence.

Related reading

• Same stool, different verdicts: what home gut microbiome tests can tell you
• Most health products aren’t scams, but many just haven’t been proven
• How miracle-cure scams borrow the language you trust
• What a clinician must tell you before you agree
• What happens when you don’t tell your doctor about supplements

Sources

1. U.S. Food and Drug Administration. “FDA Approves First Orally Administered Fecal Microbiota Product for the Prevention of Recurrence of Clostridioides difficile Infection.” FDA news release, April 26, 2023. fda.gov
2. U.S. Food and Drug Administration. “VOWST (fecal microbiota spores, live-brpk) prescribing information.” FDA, 2023. fda.gov
3. U.S. Food and Drug Administration. “REBYOTA (fecal microbiota, live-jslm)” product page, with approval letter (November 30, 2022) and prescribing information. FDA. fda.gov
4. U.S. Food and Drug Administration. “Important Safety Alert Regarding Use of Fecal Microbiota for Transplantation and Risk of Serious Adverse Reactions Due to Transmission of Multi-Drug Resistant Organisms.” FDA, June 13, 2019.
5. Peery AF, Kelly CR, Kao D, et al. “AGA Clinical Practice Guideline on Fecal Microbiota–Based Therapies for Select Gastrointestinal Diseases.” Gastroenterology, 2024. profiles.wustl.edu
6. Johnson S, Lavergne V, Skinner AM, et al. “Clinical Practice Guideline by the Infectious Diseases Society of America and Society for Healthcare Epidemiology of America: 2021 Focused Update Guidelines on Management of Clostridioides difficile Infection in Adults.” Clinical Infectious Diseases, 2021. pubmed.ncbi.nlm.nih.gov
7. National Institutes of Health. “Fecal microbiota transplants help patients with advanced melanoma respond to immunotherapy.” NIH news release, February 4, 2021. nih.gov
8. Baruch EN, Youngster I, Ben-Betzalel G, et al. “Fecal microbiota transplant promotes response in immunotherapy-refractory melanoma patients.” Science, 2021. cris.tau.ac.il
9. Routy B, Lenehan JG, Miller WH Jr, et al. “Fecal microbiota transplantation plus anti-PD-1 immunotherapy in advanced melanoma: a phase I trial.” Nature Medicine, 2023. nature.com
10. Costello SP, Hughes PA, Waters O, et al. “Effect of Fecal Microbiota Transplantation on 8-Week Remission in Patients With Ulcerative Colitis: A Randomized Clinical Trial.” JAMA, 2019. pubmed.ncbi.nlm.nih.gov
11. Yu EW, Gao L, Stastka P, et al. “Fecal microbiota transplantation for the improvement of metabolism in obesity: The FMT-TRIM double-blind placebo-controlled pilot trial.” PLoS Medicine, 2020. journals.plos.org
12. Kang D-W, Adams JB, Coleman DM, et al. “Long-term benefit of Microbiota Transfer Therapy on autism symptoms and gut microbiota.” Scientific Reports, 2019. nature.com
13. Alang N, Kelly CR. “Weight Gain After Fecal Microbiota Transplantation.” Open Forum Infectious Diseases, 2015. pubmed.ncbi.nlm.nih.gov
14. NIH Office of Dietary Supplements. “Probiotics: Fact Sheet for Health Professionals.” NIH, updated March 25, 2025. ods.od.nih.gov
15. Centers for Disease Control and Prevention. “About C. diff.” CDC, updated May 13, 2026. cdc.gov