Fecal Microbiota Transplantation in Inflammatory Bowel Disease Management

Fecal microbiota transplantation (FMT) has emerged as a promising therapeutic approach for inflammatory bowel disease (IBD), encompassing both ulcerative colitis (UC) and Crohn’s disease (CD). By transferring a diverse microbial community from a healthy donor to a dysbiotic gut, FMT aims to restore ecological balance, reinforce mucosal barrier integrity and recalibrate immune responses. Clinical protocols vary in terms of donor screening, stool preparation (fresh, frozen or washed), route of administration (colonoscopy, enema, nasoenteric tube or capsules) and dosing frequency. Across studies, FMT has achieved induction of remission in a substantial subset of patients, with particular success in UC, while maintenance of remission often requires repeated or adjunctive administrations. Mechanistic investigations implicate enhanced production of short-chain fatty acids (notably butyrate), modulation of tight junction proteins, suppression of pro-inflammatory cytokines and expansion of regulatory T-cell populations. Challenges remain in optimising donor selection, ensuring sustained engraftment, minimising adverse events and standardising long-term safety assessments. Emerging strategies include step-up or sequential FMT regimens, washed microbiota preparations and development of defined microbial consortia to replace crude stool preparations. FMT continues to advance towards personalised microbiome therapies for IBD.

Research from Nature Portfolio

Recent studies have illuminated host–microbe interactions following FMT in UC. Profiling the colonic mucosal transcriptome before and after transplantation revealed regulation of structural, metabolic and inflammatory pathways unique to responders. Downregulation of the inflammasome-related gene GBP5 correlated with clinical remission, and murine models lacking GBP5 exhibited reduced colitis severity, highlighting a novel molecular mediator of FMT efficacy. In Crohn’s disease complicated by intra-abdominal inflammatory masses, a one-hour fresh FMT protocol followed by repeated treatments every three months induced clinical response in over two-thirds of patients and sustained remission in nearly half at one year, accompanied by radiological improvement and no serious safety signals. These findings support both mechanistic insights into host regulation and practical protocols for sequential FMT in refractory CD.

Fecal Microbiota Transplantation in Inflammatory Bowel Disease Management publication trend

The graph below shows the total number of articles in fecal microbiota transplantation in inflammatory bowel disease management across all publications each year (not limited to Nature Index journals).

Technical terms

Fecal Microbiota Transplantation (FMT): Transfer of prepared faecal microbial communities from a healthy donor to a patient to restore gut microbial balance.

Dysbiosis: Disruption or imbalance in the composition and function of the gut microbiota associated with disease.

Engraftment: Successful establishment and persistence of donor microbes within the recipient’s intestinal ecosystem.

Metatranscriptomics: High-throughput sequencing approach that profiles active gene expression across microbial communities in a sample.

References

1. Profiling the colonic mucosal response to fecal microbiota transplantation identifies a role for GBP5 in colitis in humans and mice. Nature Communications (2024).
2. Multiple fresh fecal microbiota transplants induces and maintains clinical remission in Crohn’s disease complicated with inflammatory mass. Scientific Reports (2017).
3. Engraftment of essential functions through multiple fecal microbiota transplants in chronic antibiotic-resistant pouchitis—a case study using metatranscriptomics. Microbiome (2023).
4. Fecal microbiota transplantation to maintain remission in Crohn’s disease: a pilot randomized controlled study. Microbiome (2020).
5. Washed microbiota transplantation vs. manual fecal microbiota transplantation: clinical findings, animal studies and in vitro screening. Protein & Cell (2020).
6. Step-up fecal microbiota transplantation strategy: a pilot study for steroid-dependent ulcerative colitis. Journal of Translational Medicine (2015).
7. Fecal microbiota transplantation and bacterial consortium transplantation have comparable effects on the re-establishment of mucosal barrier function in mice with intestinal dysbiosis. Frontiers in Microbiology (2015).