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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 must 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

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.

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

  • Many illnesses (such as upper respiratory infections, “sinus infections” and bronchitis) are caused by viruses, not bacteria, and should not be treated with antibiotics.
  • Other situations for which antibiotics may sometimes be given include:
    • Diarrheal illness.
    • Prophylaxis before procedures (to prevent potential health issues).
    • Before routine dental appointments in patients with artificial joints.
    • Treatment of urinary tract infections without symptoms.

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

  • Clindamycin is associated with C. diff and should never be used by patients who have previously had C. diff infection. (There is almost always another choice that is safer.)
  • Fluoroquinolones and broad spectrum cephalosporins are other antibiotics that put patients at higher risk of C. diff.
  • Safer choices include penicillin, trimethoprim-sulfamethoxazole, intravenous (IV) vancomycin, IV gentamycin or tetracycline.

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.

  • Probiotics are currently available in a variety of foods (such as yogurt or fermented foods like sauerkraut or kimchi) or as dietary supplements. For example, kefir is a probiotic yogurt drink that contains a number of probiotics. It can be found in the dairy aisle of most large grocery stores. The dose is 5 ounces twice daily (30 minutes before or 1 hour after meals). Begin within 48 hours of the antibiotic course and continue for one week after the antibiotics are finished.

Patient FAQs about FMT

Fecal microbiota transplantation (FMT) is when stool from a healthy donor is made into a liquid mixture and transferred into the colon of a different person to try to reintroduce or boost helpful organisms. FMT is only approved to treat Clostridioides difficile (C. diff) infection that has occurred three times despite adequate antibiotic treatment. FMT for other conditions must be given as part of a clinical trial.

Your body has a lot of good bacteria in its gastrointestinal (GI) tract, also called your digestive system. C. diff is an infection from an overgrowth of bad bacteria that can cause GI symptoms, like nausea, watery diarrhea, stomach pain and stomach cramps, that may be severe.

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 stop C. diff from overgrowing.

Your health care provider will use donor stool and saline to create a liquid mixture that may be transferred into your GI tract during a colonoscopy or sigmoidoscopy. Other methods that have been used with success, and which may be used in select cases, include fecal enemas (given through the rectum) and using a nasogastric (nasal) tube into the upper part of your GI tract.  

There are more than 500 case reports in the world’s medical literature so far and a recent randomized controlled clinical trial, reporting an overall cure rate of 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. 

There are currently no known cases of infection passed from a healthy donor to a receiving patient through FMT. However, feces are a “bodily fluid” and proper donor testing is vital. 

Patients are asked to sign a consent form acknowledging the risks of having colonoscopy, if appropriate, as well as potential risks with the FMT (infection, allergic or immune reaction, or other disease transmissions).  

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.

FMT is performed on patients who are suffering from recurring C. diff. FMT is an effective and approved procedure used to treat C. diff infection if it has occurred at least three times despite antibiotic treatment. Patients who have had two more severe C. diff infections (admitted to an intensive care unit) may also be candidates for FMT. There is ongoing research to determine if FMT may work for other health issues.

The best donor is somebody in good health who has not taken any antibiotics for at least 90 days. Most patients choose a close family member, although the donor does not necessarily have to be related to the recipient. 

Your health care provider’s office may have stool from a healthy volunteer available if you do not have a donor.  

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:

  • They are at risk for HIV or viral hepatitis.
  • They have major gastrointestinal or autoimmune disease.
  • They have a history of cancer.
  • Their blood tests positive for HIV, hepatitis A, hepatitis B, and hepatitis C, or syphilis.
  • Their stool tests positive for bad bacteria (such as salmonella), parasites or C. diff.

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

There is no “fee” for the FMT itself. 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. 

Because the long-term results of FMT are not known, the FDA only allows FMT to treat C. diff that has occurred at least three times despite antibiotic treatment. Health care providers must have FMT recipients sign an informed consent form, which confirms that the recipient understands the potential risks of FMT. For all other health conditions, the FDA requires FMT to be done as part of a clinical trial.

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