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Fecal microbiota transplant


Fecal microbiota transplantation (FMT) helps to replace some of the "bad" bacteria of your colon with "good" bacteria. The procedure helps to restore the good bacteria that have been killed off or limited by the use of antibiotics. Restoring this balance in the colon makes it easier to fight infection.

Alternative Names

Fecal bacteriotherapy; Stool transplant; Fecal transplant; C. difficile colitis - fecal transplant; Clostridium difficile - fecal transplant; Clostridioides difficile - fecal transplant; Pseudomembranous colitis - fecal transplant


FMT involves collecting stool from a healthy donor. Your health care provider will ask you to identify a donor. Most people choose a family member or close friend. The donor must not have used antibiotics for the previous 2 to 3 days. They will be screened for any infections in the blood or stool.

Once collected, the donor's stool is mixed with saline water and filtered. The stool mixture is then transferred into your digestive tract (colon) through a tube that goes through a colonoscope (a thin, flexible tube with a small camera). The good bacteria can also be introduced into the body by way of a tube that goes into the stomach through the mouth. Another method is to swallow a capsule that contains freeze-dried donor stool.

Why the Procedure Is Performed

The large intestine has a large number of bacteria. These bacteria that live in your intestines are important for your health, and grow in a balanced manner.

One of these bacteria is called Clostridioides difficile (C difficile). In small amounts, it does not cause problems.

  • However, if a person receives repeated or high doses of antibiotics for an infection elsewhere in the body, most of the normal bacteria in the intestine may be wiped out. Bacteria grow and release a toxin.
  • The result may be that there is too much of the C difficile.
  • This toxin causes the lining of large intestine to become swollen and inflamed, causing fever, diarrhea, and bleeding.

Certain other antibiotics can sometimes bring the C difficile bacteria under control. If these do not succeed, FMT is used to replace some of the C difficile with "good" bacteria and restore the balance.

FMT also may be used to treat conditions such as:

Treatment of conditions other than recurrent C difficile colitis are considered experimental at present and are not widely used or known to be effective.


Risks for FMT may include the following:

  • Reactions to the medicine you are given during the procedure
  • Heavy or ongoing bleeding during the procedure
  • Breathing problems
  • Spread of disease from the donor (if the donor is not screened properly, which is rare)
  • Infection during colonoscopy (very rare)
  • Blood clots (very rare)

Before the Procedure

The donor will likely take a laxative the night before the procedure so they can have a bowel movement the next morning. They will collect a stool sample in a clean cup and bring it with them the day of the procedure.

Talk to your provider about any allergies and all medicines you are taking. DO NOT stop taking any medicine without talking to your provider. You will need to stop taking any antibiotics for 2 to 3 days before the procedure.

You may need to follow a liquid diet. You may be asked to take laxatives the night before the procedure. You will need to prepare for a colonoscopy the night before FMT. Your doctor will give you instructions.

Before the procedure, you'll be given medicines to make you sleepy so that you won't feel any discomfort or have any memory of the procedure.

After the Procedure

You will lie on your side for about 2 hours after the procedure with the solution in your bowels. You may be given loperamide (Imodium) to help slow down your bowels so the solution remains in place during this time.

You will go home the same day of the procedure once you pass the stool mixture. You will need a ride home, so be sure to arrange it ahead of time. You should avoid driving, drinking alcohol, or any heavy lifting.

You may have a low-grade fever the night after the procedure. You may have bloating, gas, flatulence, and constipation for a few days after the procedure.

Your provider will instruct you about the type of diet and medicines you need to take after the procedure.

Outlook (Prognosis)

This life-saving treatment is highly safe, effective and, low cost. FMT helps by bringing back normal flora through donor stool. This in turn helps in the recovery of your normal bowel function and health.


Galandiuk S, Netz U, Morpurgo E, Tosato SM, Abu-Freha N, Tyler Ellis C. Colon and rectum. In: Townsend CM Jr, Beauchamp RD, Evers BM, Mattox KL, eds. Sabiston Textbook of Surgery. 21st ed. St Louis, MO: Elsevier; 2022:chap 52.

Gerding DN, Young VB, Donskey CJ. Clostridiodes difficile (formerly Clostridium difficile) infection. In: Bennett JE, Dolin R, Blaser MJ, eds. Mandell, Douglas, and Bennett's Principles and Practice of Infectious Diseases. 9th ed. Philadelphia, PA: Elsevier; 2020:chap 243.

Rao K, Safdar N. Fecal microbiota transplantation for the treatment of Clostridium difficile infection. J Hosp Med. 2016;11(1):56-61. PMID: 26344412

Schneider A, Maric L. Fecal microbiota transplantation as a therapy for inflammatory bowel disease. In: Shen B, ed. Interventional Inflammatory Bowel Disease. Cambridge MA: Elsevier Academic Press; 2018:chap 28.

Last reviewed October 31, 2022 by Michael M. Phillips, MD, Emeritus Professor of Medicine, The George Washington University School of Medicine, Washington, DC. Also reviewed by David C. Dugdale, MD, Medical Director, Brenda Conaway, Editorial Director, and the A.D.A.M. Editorial team..

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