What are the benefits of fecal microbiota transplantation (FMT) for chronic gastrointestinal (GI) issues?

Medical Advisory BoardAll articles are reviewed for accuracy by our Medical Advisory Board
Educational purpose only • Exercise caution as content is pending human review
Article Review Status
Submitted
Under Review
Approved

Last updated: April 16, 2025View editorial policy

Personalize

Help us tailor your experience

Which best describes you? Your choice helps us use language that's most understandable for you.

From the Guidelines

Fecal microbiota transplantation (FMT) is a highly effective treatment for chronic gut issues, particularly for recurrent Clostridioides difficile infection, with cure rates exceeding 90%. The procedure involves transferring stool from a healthy donor to the recipient's intestinal tract, typically via colonoscopy, enema, or capsules. FMT has been shown to be beneficial for other conditions like inflammatory bowel disease, irritable bowel syndrome, and functional constipation, although the results are less consistent 1. The benefits of FMT include reduced inflammation, improved gut barrier function, normalized bowel movements, decreased abdominal pain, and enhanced quality of life. The procedure works by introducing diverse beneficial bacteria that outcompete harmful microbes, restore metabolic functions, modulate the immune system, and repair the intestinal lining.

Key Considerations

  • FMT is most effective for recurrent Clostridioides difficile infection, with cure rates exceeding 90% 1.
  • For other conditions like inflammatory bowel disease, irritable bowel syndrome, and functional constipation, FMT shows promising but less consistent results 1.
  • FMT carries risks of infection transmission and temporary digestive discomfort, and patients should only receive FMT from medically screened donors in clinical settings 1.
  • Treatment protocols typically involve 1-3 sessions depending on the condition and response, and most patients experience improvement within days to weeks after treatment 1.

Recent Guidelines and Recommendations

  • The AGA clinical practice guideline on fecal microbiota-based therapies for select gastrointestinal diseases recommends FMT as a treatment option for multiply recurrent CDI and severe CDI not responding to standard treatment 1.
  • The international consensus conference on stool banking for faecal microbiota transplantation in clinical practice recommends that FMT be considered as a treatment option for fulminant CDI in patients unfit for surgery, and that FMT could induce remission in mild-to-moderate ulcerative colitis (UC) 1.

Conclusion Not Applicable - Answer Only

FMT is a valuable treatment option for chronic gut issues, and its use should be considered in clinical practice, particularly for recurrent Clostridioides difficile infection. However, further studies are required to fully understand the benefits and risks of FMT for other conditions, and to establish standardized treatment protocols.

From the Research

Benefits of Fecal Transplant for Chronic Gut Issues

  • Fecal transplantation has been shown to be effective in reducing the reoccurrence of refractory Clostridium difficile infection, with a cure rate of over 90% 2.
  • The treatment has also been found to be efficient in other gastrointestinal diseases, such as inflammatory bowel disease and irritable bowel syndrome 2, 3.
  • A study of 15,000 patients who underwent fecal microbiota transplantation (FMT) found that the overall rates of effectiveness of treatment were 71.8%, 64.4%, and 58.8% at 3,12, and 36 months after treatment, respectively 3.
  • FMT has been found to be effective in treating various intestinal disorders, including constipation, chronic diarrhea, and radiation enteritis, with clinical improvement rates ranging from 56.5% to 85.8% 3.
  • The treatment has also been found to be safe, with no serious adverse reactions reported in the majority of studies 2, 3, 4.
  • The use of FMT in combination with other therapies, such as probiotics and prebiotics, may also be beneficial in treating inflammatory bowel disease (IBD) 5, 6.
  • However, further studies are needed to determine the long-term outcomes of FMT and to establish personalized treatment protocols for different patients and conditions 4, 5.

Specific Benefits for Different Conditions

  • For Clostridium difficile infection, FMT has been found to be highly effective, with a cure rate of over 90% 2.
  • For inflammatory bowel disease, FMT has been found to be effective in inducing and maintaining remission, particularly in patients with ulcerative colitis 2, 5.
  • For irritable bowel syndrome, FMT has been found to be effective in reducing symptoms, with clinical improvement rates ranging from 60.4% to 70.6% 3.
  • For constipation, FMT has been found to be effective in improving bowel habits, with clinical improvement rates ranging from 56.5% to 70.3% 3.

Delivery Methods and Adverse Reactions

  • FMT can be delivered through various routes, including infusion of an enterobacterial solution through a nasoenteric tube, oral intake of enterobacterial capsules, and injection of a bacterial solution into the colon via colonoscopy 3.
  • The most common adverse reactions associated with FMT include respiratory discomfort, nausea and vomiting, and diarrhea, which are typically mild and resolve on their own 3.
  • Serious adverse reactions are rare, and FMT is generally considered to be a safe treatment option 2, 3, 4.

References

Guideline

Guideline Directed Topic Overview

Dr.Oracle Medical Advisory Board & Editors, 2025

Research

[Fecal microbiota transplantation for the treatment of intestinal disorders: An analysis of treatment of 15 000 patients].

Zhonghua wei chang wai ke za zhi = Chinese journal of gastrointestinal surgery, 2025

Research

Fecal microbiota transplantation: Review and update.

Journal of the Formosan Medical Association = Taiwan yi zhi, 2019

Professional Medical Disclaimer

This information is intended for healthcare professionals. Any medical decision-making should rely on clinical judgment and independently verified information. The content provided herein does not replace professional discretion and should be considered supplementary to established clinical guidelines. Healthcare providers should verify all information against primary literature and current practice standards before application in patient care. Dr.Oracle assumes no liability for clinical decisions based on this content.

Have a follow-up question?

Our Medical A.I. is used by practicing medical doctors at top research institutions around the world. Ask any follow up question and get world-class guideline-backed answers instantly.