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What is fecal microbiota transplantation?

Fecal microbiota transplantation (FMT) is a treatment in which stool is collected from a healthy donor and transplanted into the gastrointestinal tract of the recipient. There are several ways in which the fecal matter can be transferred to the recipient, including pills, enemas, colonoscopy, gastroscopy, nasojejunal or gastrointestinal tubes, or duodenal infusions.1,2

When antibiotics are not effective, the use of FMT as a drug is accepted by FDA as a treatment for recurrent Clostridium difficile infections (or RCDI), which comprise approximately 25% of C. difficile infections.3 Studies suggest that FMT is highly effective4 and cost-effective5 for treatment of RCDI.

While FMT significantly improved the gut microbiome health of patients with ulcerative colitis,6 there is still limited data about the impact of FMT in treating Crohn’s disease, chronic constipation, pouchitis, and irritable bowel syndrome.7 Other trials have even evaluated FMT as a treatment for autism spectrum disorders8, metabolic syndrome9, fibromyalgia10 and others. However, more and better designed trials are required for those conditions.

Pouchitis is the inflammation of the ileal pouch (an artificial rectum surgically created out of ileal gut tissue in patients who have undergone a colectomy), which is created while managing gastrointestinal conditions such as ulcerative colitis.

What are the common effects?

FMT can result in RCDI remission in patients for whom antibiotic treatment has been unsuccessful. FMT also seems to be effective in treating other conditions, but more evidence is required (see above), and the FDA has not approved FMT to treat them.

What are the mechanisms of action?

Studies in human patients have shown that:

  • FMT can help repair the gut microbiota by altering the recipient’s indigenous flora.11,12 One study showed that an appreciable percentage (~22%) of microorganisms present in the microbiota of the donor can be conserved in the recipient even 8 weeks post-FMT.13
  • FMT can restore gut barrier integrity and function by improving the stability of the microbiota.14
  • FMT can restore healthy secondary bile acid metabolism in the gut microbiota, a potential factor influencing C. difficile colonization.15
  • It is hypothesized that other components of fecal matter – such as colonocytes, bacteriophages, and fecal fungi – can have a positive influence on the gut microbiota.16

How does this relate to my microbiome?

FMT can modify and improve gut microbiota function and activity in patients with recurrent C. difficile infection.

How can people take action? (follow guidelines of, e.g. gastroenterology associations or standard of care)

FMT is only approved by the FDA as a “drug” for RCDI3 when the infection is not responding to standard therapies. To be accepted for use, the FMT product must be “qualified by screening and testing performed under the direction of the licensed health care provider.” 3

There is presently no non-experimental use of FMT in treating other health conditions.


1. Aroniadis, O. C., & Brandt, L. J. (2014). Intestinal microbiota and the efficacy of fecal microbiota transplantation in gastrointestinal disease. Gastroenterology & Hepatology, 10(4), 230–237.

2. Kao, D., et al. (2017). Effect of Oral Capsule– vs Colonoscopy-Delivered Fecal Microbiota Transplantation on Recurrent Clostridium difficile Infection. JAMA, 318(20), 1985–1993.

3. U.S. Department of Health and Human Services, Food and Drug Administration (2016). Enforcement Policy Regarding Investigational New Drug Requirements for Use of Fecal Microbiota for Transplantation to Treat Clostridium difficile Infection Not Responsive to Standard Therapies.

4. Quraishi, M. N., Widlak, M., Bhala, N., Moore, D., Price, M., Sharma, N., & Iqbal, T. H. (2017). Systematic review with meta-analysis: the efficacy of faecal microbiota transplantation for the treatment of recurrent and refractory Clostridium difficile infection. Alimentary Pharmacology & Therapeutics, 46(5), 479–493.

5. Arbel, L. T., Hsu, E., & McNally, K. (2017). Cost-Effectiveness of Fecal Microbiota Transplantation in the Treatment of Recurrent Clostridium Difficile Infection: A Literature Review. Cureus, 9(8), e1599.

6. Sun, D., et al. (2016). Fecal Microbiota Transplantation as a Novel Therapy for Ulcerative Colitis. Medicine, 95(23), e3765.

7. Rossen, N. G., MacDonald, J. K., de Vries, E. M., D’Haens, G. R., de Vos, W. M., Zoetendal, E. G., & Ponsioen, C. Y. (2015). Fecal microbiota transplantation as novel therapy in gastroenterology: A systematic review. World Journal of Gastroenterology, 21(17), 5359–5371.

8. Kang, D.-W., et al. (2017). Microbiota Transfer Therapy alters gut ecosystem and improves gastrointestinal and autism symptoms: an open-label study. Microbiome, 5(1), 10.

9. Vrieze, A., et al. (2012). Transfer of Intestinal Microbiota From Lean Donors Increases Insulin Sensitivity in Individuals With Metabolic Syndrome. Gastroenterology, 143(4), 913–916.e7.

10. Thurm, T., Ablin, J. N., Buskila, D., & Maharshak, N. (2017). Fecal Microbiota Transplantation for Fibromyalgia: A Case Report and Review of the Literature. Open Journal of Gastroenterology, 07(04), 131–139.

11. Flannigan, K. L., et al. (2017). Changes in Composition of the Gut Bacterial Microbiome after Fecal Microbiota Transplantation for Recurrent Clostridium difficile Infection in a Pediatric Heart Transplant Patient. Frontiers in Cardiovascular Medicine, 4, 17.

12. Khanna, S., et al. (2017). Changes in microbial ecology after fecal microbiota transplantation for recurrent C. difficile infection affected by underlying inflammatory bowel disease. Microbiome, 5(1), 55.

13. Lee, S. T. M., et al. (2017). Tracking microbial colonization in fecal microbiota transplantation experiments via genome-resolved metagenomics. Microbiome, 5(1), 50.

14. Khoruts, A., & Sadowsky, M. J. (2016). Understanding the mechanisms of faecal microbiota transplantation. Nature Reviews Gastroenterology & Hepatology, 13(9), 508–516.

15. Weingarden, A. R., et al. (2016). Changes in Colonic Bile Acid Composition following Fecal Microbiota Transplantation Are Sufficient to Control Clostridium difficile Germination and Growth. PLOS ONE, 11(1), e0147210.

16. Bojanova, D. P., & Bordenstein, S. R. (2016). Fecal Transplants: What Is Being Transferred? PLOS Biology, 14(7), e1002503.