Fecal Microbiota Transplantation (FMT)

Fecal microbiota transplantation (FMT) is a procedure that delivers healthy human donor stool to a person via colonoscopy, enema, nasogastric (NG) tube or in capsule form (popularly called “poop pills”). It may be prescribed for debilitating gasterointestinal infections, such as Clostridium difficile (C. diff), that keep recurring despite antibiotic therapy.

C. diff is a serious infection — one that causes debilitating diarrhea. Treating C. diff begins with administering antibiotics; however, recurrence is common. By the third episode of severe C. diff, it is unlikely antibiotics will cure the infection; so, your child’s doctor may consider FMT as an option.

Based on successful treatment of C. diff infections, FMT is now being looked at for a wide range of conditions. However, it’s still considered an experimental treatment, and shouldn’t be attempted without medical supervision.

The GI tract has an “ecosystem” of thousands of bacteria and other organisms that help keep the body healthy. When your child is given an antibiotic, this ecosystem is disrupted, allowing the growth of disease-causing bacteria, such as C. diff.

With a fecal transplant, “good” microorganisms from the donor stool are infused into the patient. Healthy bacteria begin to grow and prevent C. diff from recurring.

Stool donors are rigorously screened and stool samples are extensively tested before being used for FMT.

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.


There has been increasing interest in understanding the role of the human gut microbiome to elucidate the therapeutic potential of its manipulation. Fecal microbiota transplantation (FMT) is the administration of a solution of fecal matter from a donor into the intestinal tract of a recipient in order to directly change the recipient’s gut microbial composition and confer a health benefit. FMT has been used to successfully treat recurrent Clostridium difficile infection.

There are preliminary indications to suggest that it may also carry therapeutic potential for other conditions such as inflammatory bowel disease, obesity, metabolic syndrome, and functional gastrointestinal disorders.