Fecal Microbiota Transplant

Fecal Microbiota Transplant (FMT)

Why do we do this procedure?

FMT is a treatment for patients who suffer from recurrent infection with a bacteria called Clostridium difficile (C. diff). This bacteria can cause significant and debilitating diarrhea. Antibiotics are the first line treatment, but occasionally patients do not respond well, and then the infection comes back. In this case, we offer FMT, which is the transfer of a healthy population of colon bacteria from a donor to the patient with C. diff infection. This often has a cure rate of > 90% after 1 or 2 treatments.

What is the procedure?

Our practice performs FMT in the hospital using either endoscopy or colonoscopy. The majority of patients will have the FMT delivered via a colonoscopy. This will require a bowel preparation (please see the additional section on colonoscopy). The purified FMT material with the healthy bacteria is procured from a company in Massachusetts called Openbiome©. This non-profit organization carefully selects the healthiest donors and uses the most rigorous screening standards for quality control.  Please visit their website at www.openbiome.org for more information.

The purified FMT material is then delivered into your colon. You may be advised to take a dose of Imodium following the procedure and we will have you lie on your right side for 30 minutes to ensure that the FMT gets distributed equally in your colon.

Please discuss holding antibiotics with your provider. We will often have you stop all antibiotics 24 hours prior to the procedure and continue to hold them after the FMT.

Follow up

It is normal to experience some continued diarrhea and loose stool after the FMT. This should improve over several days. If the diarrhea persists or you develop pain, fever or blood in your stool, contact your provider for instructions. Some patients require a second treatment depending on how you respond to the first FMT.


FMT is quite safe and the material is screened for all known pertinent infections. There is a very small risk of infectious disease transmission, both known and unknown. Side effects also include, but are not limited to; abdominal pain, fever, diarrhea, rectal bleeding, colon perforation, pneumonia, and medication allergy.

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