Overview

Fecal Microbiota Transplantation (FMT) is a medical procedure that involves the transfer of fecal material from a healthy donor into the gastrointestinal tract of a recipient. This procedure aims to restore a healthy balance of gut microbiota in individuals with gastrointestinal disorders, such as recurrent Clostridioides difficile infection (CDI), inflammatory bowel disease (IBD), and irritable bowel syndrome (IBS). FMT has been shown to be effective in treating these conditions by introducing beneficial bacteria and reducing the presence of harmful pathogens. The procedure can be performed through various routes, including enema, colonoscopy, nasojejunal tube, and oral capsules. FMT is considered a promising treatment option for various gastrointestinal and non-gastrointestinal diseases, with ongoing research exploring its potential applications. ^[1][2]

Process of FMT

Fecal Microbiota Transplantation (FMT) begins with selecting a healthy donor whose microbiome is carefully analyzed to ensure suitability for the recipient. The donor’s fecal sample is then processed and prepared for transplantation, which may be administered via colonoscopy, enema, or oral capsules. After the transfer, the transplanted microbiota colonizes the recipient’s gut, replacing or augmenting the existing microbiome. Ultimately, the success of FMT is influenced by various factors, including the donor’s microbiome composition, the recipient’s overall health status, and the chosen transplantation method. ^[3][4][5][6]

Conditions

FMT is being investigated for various conditions, including cardiometabolic disorders, neurological disorders, psychiatric disorders, neoplastic disorders, autoimmune/inflammatory disorders, and gastrointestinal disorders. Research has shown promise in using FMT to treat conditions such as obesity, type 2 diabetes, Parkinson’s disease, and certain types of cancer. FMT has also been investigated as a potential treatment for psychiatric disorders, including mood disorders, substance use disorder, and eating disorders. Additionally, FMT has been explored as a treatment for autoimmune/inflammatory disorders, such as multiple sclerosis and inflammatory bowel disease. While more research is needed to confirm the effectiveness of FMT for these conditions, the current evidence suggests that it may be a promising treatment option. ^{[8][9][10][11][12]}

Success Rate of FMT 

The success rate of FMT varies depending on the condition being treated and the method of administration. For recurrent Clostridium difficile infection (CDI), FMT has been shown to be effective in up to 90% of cases. In a study of 137 patients who received FMT for CDI, 82% had no recurrence of CDI at follow-up. For other conditions, such as irritable bowel syndrome (IBS), the success rate of FMT is less clear, with a meta-analysis of five studies showing a pooled odds ratio of improvement in IBS symptoms of 3.7 compared to placebo. However, the long-term durability and safety of FMT are still being studied and more research is needed to fully understand its effectiveness. ^[13][14]

Future Directions

Fecal Microbiota Transplantation (FMT)—recognized as a microbiome-based therapeutic intervention (MBTI)—holds a promising future, with ongoing research and clinical trials examining its potential to address diseases such as inflammatory bowel disease, autism spectrum disorder, and type 2 diabetes. However, several challenges remain, including the standardization of donor screening, sample preparation, and transplantation methods, as well as the development of effective storage and transportation protocols for frozen FMT products. Advances in microbiome analysis and sequencing technologies will help clarify the mechanisms that drive FMT’s therapeutic benefits and pave the way for more effective treatment strategies. Equally important is the establishment of a unified FMT registration system and clear, evidence-based guidelines to ensure safe and effective application of this therapy. Ultimately, these developments could lead to the advent of truly personalized medicine, where FMT-based interventions are tailored to an individual’s unique microbiome profile. ^[15][16]

FAQs

What conditions is FMT used for, and why is it performed?

FMT is primarily used to treat recurrent Clostridioides difficile infections (rCDI) that do not respond to standard therapies. Researchers are also exploring its potential in a range of other conditions—such as inflammatory bowel disease (IBD), irritable bowel syndrome (IBS), and certain neurological and metabolic disorders like Parkinson’s disease and Multiple Sclerosis (MS)—due to its ability to restore a balanced gut microbiome. ^{[17][18][19][20]}

How safe is FMT, and what are the potential risks?

When conducted under medical supervision and with proper donor screening, FMT is generally considered safe. However, risks include infections from insufficiently screened donors, immune reactions, and, in very rare cases, unintended long-term microbiome shifts that may affect metabolism or other physiological functions. Common minor side effects can include diarrhea, abdominal discomfort, and transient bloating. ^[21]

How effective is FMT, and does it provide long-term benefits?

FMT demonstrates high success rates (often 85%–90%) in resolving recurrent C. difficile infections. Its effectiveness in other conditions varies based on disease type and individual patient factors. Research is ongoing.^[22]

Research Feed

Update History

References

1. Fecal Microbiota Transplant.. Kao D, Surawicz C.. (Elsevier eBooks. 2019.)
2. Fecal Transplant: The Benefits and Harms of Fecal Microbiota Transplantation.. Goldenberg, D., Melmed, G.Y.. (Clinical Understanding of the Human Gut Microbiome. Springer, Cham. 2023.)
3. Understanding the Scope of Do-It-Yourself Fecal Microbiota Transplant.. Ekekezie C, Perler BK, Wexler A, Duff C, Lillis CJ, Kelly CR.. (Am J Gastroenterol. 2020.)
4. Expanded Fecal Microbiota Transplantation use for the Treatment of Clostridioides difficile: A study of the Economic and Policy Implications.. Persing NM.. (Jhu.edu. 2021.)
5. Recipient independent high accuracy FMT prediction and optimization in mice and humans.. Oshrit Shtossel, Sondra Turjeman, Alona Riumin et al.. (PREPRINT. 2022)
6. Droplet-based high-throughput cultivation for accurate screening of antibiotic resistant gut microbes.. J. Watterson, M.Tanyeri, A.R. Watson, S. Tay et al.. (Microbiology and Infectious Disease. 2020.)
7. Droplet-based high-throughput cultivation for accurate screening of antibiotic resistant gut microbes.. J. Watterson, M.Tanyeri, A.R. Watson, S. Tay et al..
8. Abstract CT258: Phase II trial of fecal microbiota transplantation in combination with ipilimumab and nivolumab in patients with advanced cutaneous melanoma (FMT-LUMINate trial).. Sreya Duttagupta, Meriem Messaoudene, Jamal R, et al.. (Cancer Research. 2024.)
9. The Potential Role of Fecal Microbiota Transplant in the Reversal or Stabilization of Multiple Sclerosis Symptoms: A Literature Review on Efficacy and Safety.. Laeeq T, Vongsavath T, Tun KM, Hong AS.. (Microorganisms. 2023.)
10. Fecal Microbiota Transplantation to Prevent and Treat Chronic Disease: Implications for Dietetics Practice.. Opoku-Acheampong I, McLaud T, Anderson OS.. (J Acad Nutr Diet. 2022)
11. Recipient-independent, high-accuracy FMT-response prediction and optimization in mice and humans.. Shtossel O, Turjeman S, Riumin A, Goldberg MR, Elizur A, Bekor Y, Mor H, Koren O, Louzoun Y.. (Microbiome. 2023.)
12. Recipient-independent, high-accuracy FMT-response prediction and optimization in mice and humans.. Shtossel O, Turjeman S, Riumin A, Goldberg MR, Elizur A, Bekor Y, Mor H, Koren O, Louzoun Y.. (Microbiome. 2023.)
13. Durability and Long-term Clinical Outcomes of Fecal Microbiota Transplant Treatment in Patients With Recurrent Clostridium difficile Infection. Mamo Y, Woodworth MH, Wang T, Dhere T, Kraft CS.. (Clin Infect Dis. 2018.)
14. German Clinical Microbiome Study Group (GCMSG). Fecal Microbiota Transplant in Patients With Recurrent Clostridium Difficile Infection.. Hagel S, Fischer A, Ehlermann P, Vehreschild M. et al.. (Dtsch Arztebl Int. 2016)
15. Understanding the Scope of Do-It-Yourself Fecal Microbiota Transplant.. Ekekezie C, Perler BK, Wexler A, Duff C, Lillis CJ, Kelly CR.. (Am J Gastroenterol. 2020)
16. Fecal microbiota transplantation: Current status and challenges in China.. Shi YC, Yang YS.. (JGH Open. 2018.)
17. The Potential Role of Fecal Microbiota Transplant in the Reversal or Stabilization of Multiple Sclerosis Symptoms: A Literature Review on Efficacy and Safety.. Laeeq T, Vongsavath T, Tun KM, Hong AS.. (Microorganisms. 2023.)
18. Fecal Microbiota Transplantation to Prevent and Treat Chronic Disease: Implications for Dietetics Practice.. Opoku-Acheampong I, McLaud T, Anderson OS.. (J Acad Nutr Diet. 2022)
19. Recipient-independent, high-accuracy FMT-response prediction and optimization in mice and humans.. Shtossel O, Turjeman S, Riumin A, Goldberg MR, Elizur A, Bekor Y, Mor H, Koren O, Louzoun Y.. (Microbiome. 2023.)
20. Recipient-independent, high-accuracy FMT-response prediction and optimization in mice and humans.. Shtossel O, Turjeman S, Riumin A, Goldberg MR, Elizur A, Bekor Y, Mor H, Koren O, Louzoun Y.. (Microbiome. 2023.)
21. Durability and Long-term Clinical Outcomes of Fecal Microbiota Transplant Treatment in Patients With Recurrent Clostridium difficile Infection. Mamo Y, Woodworth MH, Wang T, Dhere T, Kraft CS.. (Clin Infect Dis. 2018.)
22. Durability and Long-term Clinical Outcomes of Fecal Microbiota Transplant Treatment in Patients With Recurrent Clostridium difficile Infection. Mamo Y, Woodworth MH, Wang T, Dhere T, Kraft CS.. (Clin Infect Dis. 2018.)