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Using fecal microbiota transplants to treat digestive disease

An FDA scientist and clinicians weigh in on using fecal microbiota transplants as effective treatment interventions.

Using fecal bacteria to treat disease? Yes, it does exist. Two articles, both published in Cell Host and Microbiome, indicate the possibility of using fecal microbiota transplants (FMT) to treat inflammatory bowel disease—like ulcerative colitis and Crohn’s disease—and C. difficile.

Why FMT?

The idea behind FMT is simple: transfer good gut bacteria into those with gastrointestinal problems with the hope that the good bacteria restores the digestive tract. In C. difficile patients who did not respond to standard therapies, treatment with FMT has shown successful results. This has sparked further research into the area of FMT, particularly for those suffering from ulcerative colitis and Crohn’s disease.

Why isn’t FMT widely used?

The Food and Drug Administration (FDA) is exercising caution when it comes to making it more mainstream. More research needs to be done, especially in human clinical trials.

What are the risks with FMT?

The gut is full of live bacteria: transplanting new bacteria without knowing how it will react may result in adverse reactions. In 2019, two immunocompromised patients died as a result of FMT, both developing E.coli infections. Investigating gut-bacteria interactions may help minimize fatal reactions. It is also important to make sure that the transplanted material is pure, devoid of possible contaminants.  

Where do fecal microbiota transplants come from?

They can come from a number of sources. Some examples are the following:

  1. Oneself: FMT from an individual can be screened for deleterious bacteria, banked, and then used when the individual’s microbiome changes for the worse. The issue with this approach is that it could be stored for a long time, so it could become costly to keep it banked for so long.
  2. Family donor: This can come from a close relative sharing similar intestinal features. However, it does not mean that the FMT will harbour the same bacteria to treat the patient. It may differ and have no effect.
  3. Stool banks: This would be a repository of FMT that has been screened and ready for immediate transplantation. The only issue is variability. Each one can be different and it may take time to find the optimal sample for the patient.

What are some setbacks?

The biggest setback is finding a way to collect and screen the material to ensure there are no pathogens. The process for this is in its early stages, and the FDA is pushing for a more rigorous approach. Another problem is storage. Some bacteria only function in anaerobic (no oxygen) environments. Finding ways to preserve the bacteria is a challenge that researchers have to solve moving forward.   

What is the significance of using FMT to treat disease?

Overall, if FMT can be put to clinical use, it holds the potential to revolutionize treatment outcomes for hard-to-treat gastrointestinal diseases.  

Written by Shayna Goldenberg


  1. EurekAlert!. (2020). What would it take to make FMT mainstream? Two publications consider the opportunities. [online] Available at: [Accessed 20 Feb. 2020].
  2. Markey, K., van den Brink, M. and Peled, J. (2020). Therapeutics Targeting the Gut Microbiome: Rigorous Pipelines for Drug Development. Cell Host & Microbe, 27(2), pp.169-172.
  3. Carlson, P. (2020). Regulatory Considerations for Fecal Microbiota Transplantation Products. Cell Host & Microbe, 27(2), pp.173-175.

Image by Arek Socha from Pixabay 



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