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FMT Patient Resources

There are often many questions about fecal microbiota transplantation before and after the procedure. We want to help provide answers, and the most up-to-date science and information.

Thank you for being a part of the Fecal Microbiota Transplantation (FMT) National Registry patient community! The information you provide will help us better understand the long-term safety and effectiveness of FMT. We will be sending you a check-in survey once a year, every year for the next ten years. Please visit this page often so you can continue to learn and stay informed about the FMT National Registry and the latest science on FMT. This material will be updated regularly to make sure you have the most up-to-date information. If you have any questions about your participation in the FMT National Registry, please contact your FMT provider.This content was written with the support from Colleen Kelly, MD, co-chair and principal investigator of AGA’s Fecal Microbiota Transplantation (FMT) National Registry; Brown University Women’s Medicine and Collaborative.

Antibiotic use after fecal microbiota transplant


Frequently asked questions about FMT


Antibiotic Use After FMT

Can I use antibiotics after a fecal microbiota transplant?

As a patient who has finally beaten C. difficile (C. diff), you might be worried about the infection coming back. You may be reluctant to ever take antibiotics, again. The good news is that most patients successfully treated with fecal microbiota transplant (FMT) don’t develop C. diff-related symptoms again.

You may need take antibiotics at some point in the future to treat other infections. Tell your health care providers about your history of C. diff and then respect the decision of the providers treating you if they decide you need to take an antibiotic.

What are things I can do to protect myself from become sick again with C.diff?

1. Don’t take antibiotics unless you need them.

2. Don’t use certain antibiotics, if possible.

3. For some patients, taking probiotics during future courses of antibiotics may be protective against C. diff coming back. Review AGA’s patient education on probiotics and talk to your health care provider about whether probiotics may help you.

Patient FAQs about FMT

What is fecal microbiota transplantion?

Fecal microbiota transplantation (FMT) is when stool containing micro-organisms from the GI tract of a healthy donor is transferred into the colon of a patient to try to reintroduce or boost helpful organisms. FMT is most commonly used to treat Clostridioides difficile (C. diff) infection that has continued to come back despite multiple courses of antibiotic treatment. FMT is also used at some centers to treat hospitalized patients with very severe C. diff that is not responding to treatment. FMT for other conditions (such as IBS or IBD) must be given as part of a clinical trial.

What is C. diff?

C. diff is an infection from an overgrowth of bad bacteria that produces a toxin (poison) that can attack the cells in the large intestine and cause symptoms like nausea, watery diarrhea, fevers, or stomach pain or cramps. C. diff infections range in severity from mild to moderate to severe or fulminant in which there is a high risk of death or requiring surgery to remove the colon.

How does FMT work?

Our GI tract has thousands of different bacteria and other microorganisms, or germs, that are vital for good health. Antibiotics can disturb these bacteria and allow disease-causing bacteria, such as C. diff, to grow. FMT involves transferring good bacteria from a healthy donor into a patient with C. diff infection. These bacteria then start growing in the patient’s colon, or large bowel, and help stop C. diff from overgrowing.

How is the transplant performed?

Your health care provider will use donor stool and saline to create a liquid mixture that may be transferred into your GI tract. This is most commonly done during a colonoscopy or sigmoidoscopy. Other methods that have been used with success, and which may be used in select cases, include oral capsules containing donor bacteria (swallowed by mouth), fecal enemas (given through the rectum) and using a tube inserted through the nose and into the upper part of your GI tract.

There are many clinical trials in progress that are testing various formulations of FMT including encapsulated and enema preparations. Many are sponsored by pharmaceutical companies who are developed products which are hoped to be safer or more widely available. These studies are helping researchers and the FDA determine if these products are safe and effective for treatment of C. diff. You can look up studies going on near you by going to the website

What is the success rate?

There are more than 500 case reports in the world’s medical literature and at least 5 randomized controlled clinical trials, which report cure rates as high as 90 to 95 percent for C. diff using FMT as a treatment.

If your health care provider suggests you have an FMT, ask them to learn more about the AGA Fecal Microbiota Transplantation (FMT) National Registry. If you have received an FMT, you are strongly encouraged to join this community of patients helping us to better understand the long-term safety and impact of FMT.

Is FMT safe?

We are still learning about the long-term safety of FMT. Patients are asked to sign a consent form acknowledging the potential risks with the FMT (infection, allergic or immune reaction, or other disease transmissions). There is not a lot of long-term safety data on FMT, so there may be risks we still don’t know about.

Feces are a “bodily fluid” and proper testing of donors and donor stool is vital. The Food and Drug Administration (FDA) has reported a small number of cases where bacterial infections are thought to have been passed to patients through the donor stool used in the FMT procedure. Since these cases were announced, the FDA has updated its requirements for screening and testing of donors and donor stool to include these bacteria.

How can I find a doctor in my area who performs FMT?

If you are a patient interested in having an FMT, visit to see sites participating in the AGA Fecal Microbiota Transplantation (FMT) National Registry. You or your provider can contact the participating sites to learn more about enrolling.

Am I a candidate for FMT?

FMT is performed on patients who are suffering from recurring or severe C. diff. FMT patients who have had at least two C. diff infections may be candidates for FMT. There is ongoing research to determine if FMT may work for other health issues.

Who should be my donor?

The best donor is somebody in good health who has not taken any antibiotics for at least 90 days. Some patients choose a close family member, although the donor does not necessarily have to be related to the recipient. Many hospitals use donor stool from stool banks, in which healthy volunteers are screening and tested before they donate stool (like a blood bank).

What kind of screening tests are needed for donors? Are these tests covered by the donor’s health insurance?

Donors fill out a screening questionnaire like those done at blood banks and for organ or tissue transplants.

People are not allowed to donate stool if:

Donors should be aware that their health insurance may not cover the costs of these screening tests, which may cost several hundred dollars.

How much does FMT cost? Is it covered by my health insurance?

The procedure is performed during a colonoscopy or sigmoidoscopy, which is usually allowed for patients who have recurring C. diff infection with chronic diarrhea. Most insurance plans cover the costs of the patient’s laboratory testing and colonoscopy. However, to be sure, patients are urged to check with their insurance company to get detailed information about co-pays, deductibles, and requirements for referrals, especially for out-of-network or out-of-state providers. Few insurers are covering the cost of the donor material itself; this may be something you are asked to pay out of pocket or it may be provided by the hospital. It is good to ask.

Is FMT approved by the U.S. Food and Drug Administration (FDA)?

Because the long-term results of FMT are not known, the FDA only allows FMT to treat C. diff that has failed to respond to antibiotics or recurred despite standard antibiotic treatment. For all other health conditions, the FDA requires FMT to be done as part of a clinical trial.

Learn More


FMT Patient Education Page

From AGA’s GI Patient Center

Clostridium Difficile Patient Education Page


Probiotics Patient Education Page

Additional resources

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AGA Center for Gut Microbiome Research & Education

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