Fecal Bacterial (Microbial) Transplantation (FMT)



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



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Published: July 12, 2013