Microbiome-related interventions in benign anorectal disease: a systematic review of clinical evidence and implications for colorectal practice

Abstract Purpose Benign anorectal diseases, including haemorrhoids, anal fissures, anal fistulae, and pruritus ani, are common causes of morbidity with variable treatment outcomes. Emerging evidence suggests that microbial factors may contribute to disease pathophysiology and healing. This systematic review evaluates the clinical evidence for microbiome-related interventions in benign anorectal disease and summarises current mechanistic evidence supporting microbial involvement. Method A PRISMA-compliant systematic review was conducted using PubMed, Scopus, Cochrane Library, and Ovid MEDLINE from database inception to October 2025. Randomised controlled trials evaluating microbiome-related interventions were included. Mechanistic and observational microbiological studies were reviewed separately to provide biological context. Risk of bias was assessed using the Cochrane Risk of Bias 2 tool, and certainty of evidence was evaluated using the GRADE framework. Results Six randomised controlled trials ( n = 436) were included across haemorrhoids, anal fissure, and anal fistula. Topical metronidazole improved fissure healing rates (67–83% vs 33–47%) and reduced pain (mean difference −1.8 to −2.6 on visual analogue scale) compared with standard therapy alone. Evidence supporting probiotic use in haemorrhoids was limited to a single small randomised trial in postpartum women. One small trial of oral ciprofloxacin in Crohn’s-related anal fistula demonstrated no significant effect on microbial diversity. No eligible interventional studies were identified for pruritus ani. Observational microbiological studies suggest that local anorectal microbial communities differ from faecal microbiota; however, causal relationships remain uncertain. Conclusions Current evidence suggests that selected microbiome-related interventions, particularly adjunctive topical metronidazole in anal fissure, may improve clinical outcomes. However, the evidence remains limited and heterogeneous. Microbiological studies provide biological plausibility for microbial involvement in benign anorectal disease, but further adequately powered mechanistic and clinical studies are required before routine clinical implementation can be recommended.