Is There a Role for Fecal Microbiota Transplantation (FMT) in Inflammatory Bowel Disease (IBD)?

Health Professional

The gut contains 1,000-1,200 different bacterial species, or up to 1014 bacteria. Most bacteria are found in the colon and play many beneficial roles, including synthesizing vitamins, digesting carbohydrates, metabolizing bile, and influencing the maturation of the gut immune system by interacting with the factors in the gut lining.

The microbiota is affected by the use of antibiotics, which could lead to removal, or decrease of, the beneficial bacteria. Many patients with Crohn’s disease are treated with antibiotics for peri-anal disease. This places them at risk for negative changes to their microbiota. In addition, it has been suggested that some bacteria in the microbiota may actually have a role in causing IBD by negative interactions with the immune response of the gut lining. These observations resulted in the rationale for studying the effect of FMT in IBD.


FMT involves implanting stool from a healthy donor into a colon of an individual with a gut microbiome that may have negative health effects, such as in patients with IBD. There are several methods of administration of fecal intestinal microbiota. Enemas can be used to directly insert donor feces into the recipient; however, the extent of microbiota distribution is limited to the left colon. Administration directly to the colon through colonoscopy or passage of stool through tubes inserted in the nose and passed to the stomach or small intestines allow for administration throughout the entire colon. Frozen capsules of fecal microbiota have been developed, as well, which  are taken by mouth and also allow for administration of donor microbiota throughout the entire colon.

Studies in IBD

Very few studies have been completed studying the effect of FMT in IBD.  The studies that have been conducted are weak in that they are underpowered. In a review of all the studies available, it was found that clinical remission of IBD was achieved in only 36 percent of patients who were treated solely with FMT, or with FMT in addition to other therapies. Studies which showed that FMT has a positive effect on disease activity in IBD were largely driven by the pediatric population.   At this time, FMT has not been shown to be an effective therapy, either alone, or in combination with other medical therapies, in IBD.


FMT is generally tolerable and safe. Some potential adverse events include infection, pain, vomiting, fevers, and possibly severe IBD flares refractory to biologics, although rare. It is recommended that family members, spouses, or close friends act as donors. However, IBD and the gut microbiota are inherited, and therefore, a rigorous screening protocol of the donor and donor stool is imperative. The role of donor selection remains under investigation.

In Conclusion

The cause for IBD is complex, and it remains unclear as to whether alterations to the microbiota have a direct causal effect on disease or are associated with disease flares.  The use of FMT in IBD is in the very early stages of investigation, and much work needs to be done in this arena in order to clarify its utility, if one exists. Studies need to be conducted looking at the different modalities of delivery, the actual microbiome in recipients and donors, and the effect of FMT in active disease. In addition, timing of FMT in IBD patients may also play a role in the clinical utility of FMT in IBD needs to be tested.