Oral antibiotic prophylaxis in colorectal surgery and perioperative microbiota composition: a systematic review

Oral antibiotic bowel prophylaxis (OAP) is used to reduce infectious complications in colorectal surgery, but its effects on perioperative gut microbiota composition remain unclear. This systematic review evaluated the impact of OAP on intestinal microbiota composition in adults undergoing colorectal surgery. A systematic search of PubMed, Cochrane Library, and Google Scholar was conducted up to November 18th, 2025, following PRISMA guidelines. Studies were eligible if they included adult colorectal surgery patients receiving OAP and reported microbiota composition using 16S rRNA sequencing and/or qPCR. Primary outcomes were changes in microbial diversity and taxonomic composition. Secondary outcomes were surgical site infection (SSI) and anastomotic leakage (AL). Eleven studies involving over 1500 microbiota samples met inclusion criteria. OAP regimens varied widely in agents, duration, and combination with mechanical bowel preparation (MBP) or probiotics. Across studies, OAP consistently reduced microbial diversity and altered taxonomic composition, some shifts, such as increased Enterococcus or decreased Bacteroides , persisted postoperatively. Only a minority of studies assessed microbiota recovery beyond the early postoperative phase. Clinical outcomes such as SSI and anastomotic leakage were inconsistently reported, with limited direct correlations to microbiota data. OAP substantially alters perioperative gut microbiota composition in colorectal surgery patients. Heterogeneity in sampling, analysis, and clinical correlation limits definitive conclusions. Standardized study designs are needed to clarify the relationship between OAP and microbiota composition changes.