Fecal microbiota transplantation in inflammatory bowel disease: a systematic review and meta-analysis of randomized...

Fecal microbiota transplantation (FMT) has emerged as a therapeutic strategy for Inflammatory Bowel Disease (IBD) including ulcerative colitis (UC) and Crohn's disease (CD). Although multiple randomized controlled trials (RCTs) have been published in recent years, evidence remains fragmented regarding safety and efficacy. This systematic review and meta-analysis evaluated the efficacy and safety of microbiome-based interventions in Inflammatory Bowel Disease (IBD).

A systematic search of PubMed, Cochrane CENTRAL and Embase was conducted for randomized controlled trials (RCTs) published between January 2020 and May 2025. Eligible studies compared donor FME with placebo, autologous FMT or standard therapy in adult patients with IBD. Primary outcomes were clinical remission and endoscopic improvement; secondary outcomes included maintenance of remission and adverse events. Risk of bias was assessed using the Cochrane RoB-2 tool. Meta-analyses were performed in R using the meta and meta for packages. Pooled odds ratios (ORs) with 95% confidence intervals (CIs) were estimated using common-effects and random-effects models.

Six RCTs involving 220-230 patients were included (majority UC patients, two trials CD). For induction of clinical remission, FMT was associated with significantly higher rates vs controls (OR = 3.24, 95% CI 1.43-7.41, p = 0.005) under a common-effect model; random-effects model showed similar point estimate but wide CI overlapping unity. Endoscopic response was strongly increased with FMT (OR = 6.80, 95% CI 2.96-15.63, p < 0.0001). Serious adverse events were more common in FMT arms but not statistically significant (common-effects OR ~ 2.05, 95% CI 0.72-5.81, p = 0.18). Evidence for maintenance of remission from two trials was limited and inconsistent.

Microbiome-based therapies, particularly FMT, significantly improved clinical and endoscopic remission in IBD (especially in UC) compared with control interventions, but safety signals and maintenance efficacy remain uncertain. Larger and strictly designed UC and CD-specific RCTs are needed to confirm long-term efficacy, clarify safety and define the role of microbiome-targeted therapies in IBD management.