What is Fecal Microbiota Transplantation? 

Video by MinuteEarth

The human body contains trillions of bacteria cells. This vast, largely unexplored bacterial community known as the microbiome has been linked to many aspects of human health, from gastrointestinal diseases to obesity. Importantly, disrupting the microbiome with antibiotics can cause disease by wiping out the helpful bacteria in our guts. 

Fecal Microbiota Transplantation (FMT) is an innovative investigational treatment that has – in randomized, controlled clinical trials – resolved 80-90% of infections caused by recurrent C. difficile that does not respond to antibiotics. During FMT, a fecal preparation from a carefully screened, healthy stool donor is transplanted into the colon of the patient. There are multiple routes of administration (e.g., via colonoscopy, naso-enteric tube, capsules), each of which has unique risks and benefits. 

How does FMT work?

Though the mechanism has yet to be determined, it is believed that FMT works by repopulating the patient’s microbiome with diverse microorganisms that competitively exclude C. difficile

In a healthy gut community, C. difficile is out-competed by many different bacterial species. However, receiving antibiotic treatment disrupts this ecosystem by killing those protective bacteria. C. difficile forms spores that are resistant to antibiotics. No longer outcompeted, this pathogen establishes itself in the gut and produces toxins that leave patients suffering from severe diarrhea, abdominal pain, and, often, fever. With an infusion of bacteria from a healthy donor's stool, the C. difficile is again out-competed.  

Researchers are also exploring FMT's potential role for treating other gastrointestinal diseases, such as IBS and Crohn's Disease. 

Although FMT is a compelling tool for treating C. difficile infection, there are also important risks. Stool is a complex living mixture of bacteria and other organisms. While stool donors can be carefully screened for known infectious agents, there is always a risk that the tests might fail to detect a pathogen. There are also procedural risks associated with receiving an FMT by colonoscopy or other methods of administration.


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About Clostridiodes difficile Infection

The following excerpts are drawn from the American Gastroenterological Association's FMT website, a helpful resource for patients, physicians, and the public to learn about FMT and its uses, especially regarding treatment of C. difficile infection. 

+ What is C. difficile?

Clostridioides difficile (formerly known as Clostridium difficile) – C. difficile for short – is a rod-shaped bacterium usually found in the soil, air, water, and human and animal feces. This aggressive intestinal bug infects about 500,000 Americans and causes up to 30,000 deaths each year, making it one of the most common hospital-acquired infections in the United States.

The bacteria produce toxins that destroy cells and cause inflammation, resulting in symptoms such as watery diarrhea three or more times a day, abdominal pain, and nausea. In more severe cases, the degree of inflammation in the colon may be more extensive and symptoms may include: watery diarrhea as often as 15 times per day, severe abdominal pain and cramping, fever and weight loss.

+ How does C. difficile spread?

Up to 10% of the population is thought to carry C. difficile. Though these individuals don't show symptoms, they still shed the bacterium through their feces and expose others if they don’t practice proper hygiene. For example, when people who carry C. difficile do not wash their hands after going to the bathroom, they can contaminate food and leave the bacteria on surfaces, exposing others who come into contact with them.

+ Where is it usually found?

C. difficile is commonly found in hospitals and long-term care facilities, such as nursing homes. Studies suggest that up to 20% of hospital patients and 50% of people in long-term care facilities carry C. difficile, even though many may not present symptoms. Unless a health facility follows special procedures for disinfection, C. difficile’s bacterial spores can remain on beds, toilets and medical equipment for months, and spread easily between health care providers and patients.

+ Who is at risk for developing C. difficile infection?

Healthy individuals are less likely to develop C. difficile infection thanks to the diversity of microorganisms in their gut. Though we often associate bacteria with illness, many bacteria are vital to maintaining health, and they help prevent C. difficile infection by occupying the sites on the intestinal wall where C. difficile could attach and multiply.

However, patients and immunocompromised individuals are at an increased risk of developing infection. They often take antibiotics, which can wipe out these helpful organisms and leave room for C. difficile to lodge itself in the intestinal wall and multiply. In addition to antibiotic use, other risk factors include:

  • Being at least 65 years old
  • Having abdominal surgery
  • Having an existing health condition related to your intestines such as Irritable Bowel Disease; and
  • Previous infection with C. difficile

+ How can C. difficile infection be treated?

C. difficile infection is usually treated with antibiotics, but about 20% of patients continue to suffer from repeated infections. For this subgroup of patients, a promising new treatment called Fecal Microbiota Transplantation (FMT) brings hope. Physicians have discovered that transplanting screened and processed fecal material from a healthy donor into the colon of a sick patient can cure C. difficile infection in 90% of cases. For those who have spent months or even years restricted by their proximity to a bathroom, FMT can truly restore their quality of life.

OpenBiome has collaborated with Finch Therapeutics to develop CP101, a freeze-dried oral FMT capsule, to expand and ensure long-term access to FMT for recurrent C. difficile. Trial sites around the U.S. and Canada are now enrolling patients. Learn more about participating in the trial at prism3trial.com.

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Who is a candidate for FMT?

Current FDA guidance permits fecal microbiota transplantation only for the treatment of C. difficile infection that is not responsive to standard antibiotic therapy. According to the American Gastroenterological Association, FMT may be an option for people who have had one of the following:

  • At least three episodes of mild to moderate C. difficile infection that have not responded to six to eight weeks of treatment with antibiotics.
  • Have had at least two episodes of severe C. difficile infection that required them to be admitted to the hospital.
  • Moderate C. difficile infection that did not respond to antibiotics (namely vancomycin) for at least a week.
  • Severe C. difficile infection or severe colitis caused by C. difficile that did not respond to antibiotics within two days.

Physicians who wish to perform FMT for any other disease must file an Investigational New Drug (IND) application with the FDA or do so under a clinical research trial. You can read more about the federal regulations surrounding FMT here.

Moreover, patients who are immunocompromised may not be good candidates for FMT. The procedure is risky for people who are taking drugs that suppress their immune system, have had a recent bone marrow transplant, or have cirrhosis of the liver or advanced HIV or AIDS. If you fall into one of these categories, your doctor may advise against it, depending on how severe your C. difficile infection is and whether you have other complications. 


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Care after your fecal transplant

If you have recently undergone a fecal transplant for your C. difficile infection, your doctor may talk to you about possible temporary side-effects, such as nausea, bloating, and mild cramping. If you have any changes in your health or experience negative symptoms after your FMT, let your doctor know right away. 

OpenBiome’s Post-FMT Patient Guide offers guidance on how to care for yourself after a fecal transplant.  To minimize your risk of re-infection with C. difficile:

1. Disinfect your home with a tough cleaner, as C. difficile forms spores that are resistant to common household cleaners. We recommend you use an Environmental Protection Agency (EPA)-registered disinfectant with a C. difficile-sporicidal label claim, such as household bleach or a powerful chlorine agent. Make sure to scrub high-touch surfaces including toilets, faucets and showers, and scrub forcefully.

2. Protect yourself when cleaning. At a minimum wear disposable gloves, and wash your hands with soap and water immediately afterwards.

3. Communicate with your doctor. Make sure your PCP knows that you have undergone a fecal transplant to treat C. difficile so that he or she may factor this history into decisions about your care. Taking antibiotics after FMT increases the risk of C. difficile reinfection, but should you fall ill with an infection that requires antibiotics, talk to your doctor about options for lower-risk medicines.

Official Resources for Patients

Community Support & Getting Involved

If you would like to become more involved in efforts to make safe access to fecal transplants more widespread, there are several ways for you to become involved. Below is a list of patient advocacy groups and support groups working to bring fecal transplants to patients who need it. 


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