The Microbiome Brief
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What is a fecal transplant?

A fecal transplant — doctors call it fecal microbiota transplantation, or FMT — is a treatment that transfers stool from a healthy, carefully screened donor into a patient's gut. The goal is not the stool itself, but the trillions of microbes living in it.

The simple explanation

Your gut is home to an enormous community of bacteria, viruses, and fungi — your gut microbiome. When that community is damaged (most often by repeated courses of antibiotics), harmful bacteria such as Clostridioides difficile can take over and cause severe, recurring illness.

A fecal transplant replaces that damaged microbial community with a healthy one from a donor. Think of it less like a drug and more like a re-seeding: the donated microbes settle in the colon, crowd out the harmful bacteria, and restore the chemical balance the gut needs to stay healthy.

It is the most effective treatment known for repeated C. difficile infection — curing roughly 85–95% of cases where antibiotics keep failing — and it is being studied for a range of other conditions.

How the treatment actually happens

Despite the name, the procedure is clinical and routine. It works like this:

  1. A donor is screened. Blood and stool tests rule out infections — HIV, hepatitis, parasites, and drug-resistant bacteria. Most volunteer donors are turned away.
  2. The sample is processed. The stool is filtered and suspended in salt water, then used fresh, frozen, or dried into capsules.
  3. It is delivered to the gut. The main routes are a single rectal dose in clinic (Rebyota), a short course of swallowed capsules (Vowst), a colonoscopy, or a retention enema.
  4. The microbes take hold. Within days, the donor's bacterial community begins to establish itself in the colon.

What it treats — and what is still experimental

Only one use is fully established. Two FDA-approved products, Rebyota and Vowst, are licensed to prevent recurrent C. difficile infection in adults. Everything else — ulcerative colitis, IBS, autism, depression, metabolic disease — is investigational, studied in clinical trials with encouraging but not yet conclusive results.

FMT is not a probiotic (probiotics contain a few strains; FMT delivers an entire ecosystem), and it is not something to attempt at home — unprocessed stool has caused serious infections.

What it costs

In the US, the FDA-approved products carry high list prices — Rebyota is roughly $9,200 per dose — but insurance and Medicare generally cover treatment for recurrent C. difficile when medical criteria are met. In the UK, it is provided through the NHS. Investigational uses are usually not covered outside trials.