FMT is a procedure that introduces a community of microorganisms from carefully screened donor stool—or a standardized microbiota-based product—into a patient’s gastrointestinal tract. The material is processed before use and delivered under clinical supervision.

The intestinal microbiome is the collection of bacteria and other microorganisms living in the digestive tract. Antibiotics, illness, and other factors can disrupt that community. FMT is intended to change the microbial environment. What happens afterward varies by the patient, product, delivery route, and condition being treated.

FMT is not the same as a probiotic supplement, and it should not be attempted at home. Clinical programs use screening and handling procedures designed to reduce the chance of transmitting an infection or other harmful material.

The clearest established clinical use of FMT is for people with recurrent C. difficile infection, especially after appropriate antibiotic treatment has not prevented recurrence. Whether FMT is suitable depends on medical history, current illness, previous treatments, and local clinical practice.

FDA-authorized microbiota products exist, including REBYOTA, which is administered rectally, and VOWST, an orally administered fecal microbiota product in capsule form, approved by the FDA on April 26, 2023 for the prevention of recurrence of Clostridioides difficile infection in individuals 18 years of age and older, following antibacterial treatment for recurrent CDI. These products have specific indications, labeling, preparation requirements, and routes of administration. A clinician can explain whether an authorized product, conventionally prepared FMT under applicable policy, another treatment, or a research study is relevant.

The route depends on the clinical program, product, patient needs, and medical judgment.

• Colonoscopy: Prepared material is placed in the colon during an endoscopic procedure. This usually involves bowel preparation and sedation, with the usual considerations and risks of colonoscopy.
• Enema: Material is introduced through the rectum. A patient may be asked to retain it for a period of time. Some FDA-authorized microbiota products use rectal administration.
• Oral capsules: Specially prepared capsules are swallowed according to a clinical protocol. These are not ordinary supplements and should come through a legitimate clinical or authorized-product pathway.

Availability varies. Ask exactly what material or product will be used, who prepared it, how it was screened, and why the proposed route fits your situation.

A clinician may review your diagnosis, the number and timing of recurrences, previous antibiotic courses, allergies, immune status, medications, pregnancy status, and other health conditions. They may request records or laboratory results.

• Ask whether you should change or stop any medicine. Do not stop antibiotics, blood thinners, or other medication without instructions.
• Follow the clinic’s bowel-preparation, fasting, and transportation instructions if the route requires them.
• Review the consent form, alternatives, expected follow-up, cost, and who to call with concerns.
• Tell the care team about fever, new infection symptoms, recent travel, or a change in your health before the appointment.

Your experience depends on the route. Colonoscopy generally takes place in a procedure unit and may involve sedation and monitoring. Rectal administration may occur while you are awake and may include instructions on position and retention time. Capsule protocols specify how and when capsules are swallowed.

The team should confirm your identity, explain the procedure, answer remaining questions, and review what will happen immediately afterward. Tell staff promptly if you feel unwell or do not understand an instruction.

Temporary digestive symptoms such as bloating, cramping, gas, constipation, or diarrhea may occur. The clinic should tell you which symptoms are expected, how long they may last, and what requires urgent attention.

Follow discharge instructions about diet, activity, medications, and driving after sedation. Keep scheduled follow-up and ask how the team will assess recurrence or complications. Do not self-treat new or worsening symptoms with leftover antibiotics or another unsupervised FMT.

Potential risks include transmission of infectious organisms, including drug-resistant organisms; reactions related to the procedure or product; and gastrointestinal symptoms. Colonoscopy and sedation carry their own risks. Long-term effects of changing the microbiome are still being studied.

Safety depends on more than the delivery step. Ask about donor eligibility, testing, manufacturing or preparation standards, traceability, infection-control practices, adverse-event reporting, and what happens if a later safety alert affects the material used.

Read the FDA safety communication on transmission of multidrug-resistant organisms.

• Start with a gastroenterologist, infectious-disease clinician, or your existing care team.
• Confirm that the professional is licensed and that the facility has a clear clinical protocol.
• Ask where the material or product comes from and how screening, storage, preparation, and administration are handled.
• Clarify whether the care is standard clinical treatment, use of an FDA-authorized product, or participation in research.
• Expect informed consent and a follow-up plan. Be cautious of guaranteed outcomes, broad claims across unrelated conditions, or at-home kits.

1. What diagnosis are we treating, and how was it confirmed?
2. Why are you considering FMT or a microbiota product for me now?
3. What alternatives are available, and what are their risks and uncertainties?
4. Is this an FDA-authorized product, conventional FMT, or an investigational treatment?
5. How is the donor or product screened, prepared, stored, and tracked?
6. Which delivery method do you recommend, and why?
7. What should I do with my current medicines before and after?
8. What side effects and serious complications should I watch for?
9. Who do I call after hours, and what symptoms require urgent care?
10. What follow-up is planned, and how will you judge whether further care is needed?
11. What costs may not be covered by insurance?
12. If this is a clinical trial, who is the sponsor and who oversees participant safety?