CCFA's Position on Fecal Bacterial (Microbial) Transplantation

April 29, 2013

Fecal Bacterial (Microbial) Transplantation

Position: Clostridium difficile infection can occasionally be very difficult to eliminate and usually requires
the administration of more antibiotics. In cases where antibiotics treatment fails, use of fecal microbial
transplantation (FMT) has been implemented.

The gastrointestinal tract, especially the colon, normally contains over ten trillion microscopic organisms
(bacteria or “bugs”) known scientifically as the microbiota, which outnumber the living human cells in the
body by a factor of 10. There are at least several hundred bacterial species living in the human gut which
exists in a mutually beneficial relationship with the human host (symbiosis). The number of species of
bacteria is also known as bacterial or microbial diversity. Gut bacteria contributes to good health by
producing vitamins, processing carbohydrates, providing nutrients to the cells lining the colon,
suppressing harmful bacteria and helping the immune system develop normally.

The usually finely balanced microbiota can be disrupted; this can particularly occur after using antibiotics
which may destroy part of the normal gut bacteria. There has likely been a decrease in the different types
of bacteria over time particularly in the Western world, possibly related to sanitation, increased public
hygiene and antibiotic use. This change in the composition of human gut bacteria is thought to be a
possible contributor to the increasing frequency of inflammatory bowel disease (Crohn’s disease and
ulcerative colitis) worldwide and especially in the developed and developing countries.

One common and most obvious consequence of microbial disturbance for an individual is infection with
the Clostridium difficile bacteria. This infection can cause severe illness, including diarrhea and abdominal
pain. Often, but not always, Clostridium difficile infection occurs after antibiotics have suppressed the
normal bacteria residing in the gastrointestinal tract. This infection has become a major problem for
inflammatory bowel disease patients, posing challenges for both diagnosis and therapy. Clostridium
difficile infection can occasionally be very difficult to eliminate and usually requires the administration of
more antibiotics. In cases where antibiotic treatment fails, use of fecal microbial transplantation (FMT),
has been implemented. This process involves transferring bacteria from the stool of a healthy donor to a
patient with recurrent Clostridium difficile infection. The donor is screened for a variety of infections
including C. difficile, HIV and other infectious organisms. The donor’s fecal bacteria are then transferred
to the patient’s gastrointestinal tract by colonoscopy, enema, or a tube inserted through the nose into the
upper gastrointestinal tract. Several studies from different health care centers indicate that this can be a
safe and effective treatment for refractory, unmanageable and recurrent Clostridium difficile infection.
This treatment is not FDA approved. It is considered experimental and long term safety has not been
clearly established. However, there is increasing consensus that fecal microbial transplantation is an
acceptable treatment for recurrent, difficult cases of Clostridium difficile infection – only if performed at a
healthcare center with established expertise.

A more challenging question is whether fecal microbial transplantation can be a treatment for
inflammatory bowel disease, in the absence of Clostridium difficile infection. It is known that the
gastrointestinal microbiota of inflammatory bowel disease patients contains different bacteria from that of
people without IBD or those with IBD in remission. These observations suggest that FMT may be a
possible treatment for IBD. There have been, however, no definitive, good quality research studies.
Only small case series have been reported suggesting that FMT may be beneficial for treatment of active
IBD but there is concern that the results may have been biased by the low quality of the study methods
utilized. It should also be noted that unlike for C. difficile where a single treatment may be effective, in
IBD patients, maintenance treatment with multiple coursed of FMT may need to be considered.
Therefore, treatment of Crohn’s disease or ulcerative colitis with FMT should be considered experimental
and only performed as part of a properly designed and supervised research trial.

CCFA Patient Education Committee
April, 2013

Crohn's & Colitis Foundation

The Crohn's & Colitis Foundation's mission is to cure Crohn's disease and ulcerative colitis, and to improve the quality of life of children and adults affected by these diseases. The Foundation ranks third among leading health non-profits in the percentage of expense devoted to research toward a cure, with more than 80 cents of every dollar the Foundation spends going to mission-critical programs. The Foundation consistently meets the standards of organizations that monitor charities, including the Better Business Bureau's Wise Giving Alliance ( and the American Institute of Philanthropy (

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