Pesticide Residues, Gut Microbiota, and Gastrointestinal Outcomes: A Scoping Review of Human Evidence

Vegetables anchor healthy-diet recommendations yet are the principal nonoccupational route by which residues of organophosphate (OP), pyrethroid, neonicotinoid, organochlorine (OC), and glyphosate herbicide enter the diet, with the gut microbiota a plausible mediator linking these residues to functional gastrointestinal (GI) and inflammatory bowel outcomes. We conducted a scoping review following the PRISMA extension for Scoping Reviews (PRISMA-ScR), searching PubMed (2010 to April 2026) with mandatory backward and forward citation tracing for human studies of dietary or biomarker-confirmed pesticide exposure against gut microbiota, intestinal barrier and inflammation, functional GI disorders, or inflammatory bowel disease (IBD). Risk of bias (RoB) was appraised with ROBINS-E and Cochrane RoB 2.0, and evidence was synthesized in a 60-cell pesticide-class × outcome gap matrix. Twenty-eight papers were retained; 20 full-text-extracted human studies entered the synthesis, populating 20 of 60 cells (33%). The strongest convergent within-scope signal was OC exposure × IBD, where three cohorts agreed in direction (hazard ratios 1.56-1.61; Faroese risk ratio 3.04 on 37 cases). As a microbiota-mediation exemplar for an adjacent non-GI endpoint, the MCMC Nanjing pregnancy cohort linked a pesticide environmental risk score to gestational diabetes (adjusted odds ratio 4.5; 95% CI, 1.4-13.8; internal-validation area under the curve 0.83), with a Dorea-branch microbiota mediating part of the path. Glyphosate × IBD and neonicotinoid × any GI outcome remained empty. RoB centered on Moderate (11 of 22 rated cohorts), with six elevated-bias contributors. Biomarker-anchored prospective cohorts targeting the empty cells should be the next research priority.