Many of the foods we eat everyday are sprayed with pesticides during production (1). Among these, organophosphate insecticides are commonly used worldwide to protect crops from insect damage (2). They are designed to kill insects through the inhibition of acetylcholinesterase (2). Humans are exposed to organophosphate insecticides through various routes including through the ingestion of residues in food (2). As a result, metabolites of these insecticides have been detected in human urine samples globally (3). Chronic, low-level exposure to organophosphate insecticides has been linked to neurodegenerative disease and impaired neurological development (4,5). Although the underlying mechanisms are incompletely understood, alterations in the gut microbiome may play a role, with research in mice showing that organophosphate exposure can induce gut dysbiosis resembling that observed in Alzheimer's disease (6). Research to date has been in observational human studies as well as experimental studies using in vitro systems and animal models. The aim of this study is to investigate the impact of organophosphate insecticides on the composition and diversity of the gut microbiome. This study consisted of a systematic review and meta-analysis. Studies were assessed for inclusion according to predefined eligibility criteria. Eligible studies used Illumina-based 16S rRNA sequencing technology to analyse changes in the gut microbiome following organophosphate insecticide exposure using animal models. The collected raw data comprised three overlapping 16S rRNA hypervariable regions (V3/V4, V4 and V4/V5). Analysis was performed using sequence data from the hypervariable regions targeted in the original studies, as well as from the shared, trimmed V4 region. This enabled cross-study comparisons and also allowed evaluation of the extent to which hypervariable region choice influenced measures of microbial composition and diversity. A unified QIIME2 pipeline was applied in the re-analysis of all data. Microbiome diversity was assessed using alpha and beta diversity metrics. Alpha diversity was evaluated using the Shannon index and beta diversity was evaluated using the Bray–Curtis dissimilarity index. Differential abundance analysis was performed to identify bacterial taxa associated with organophosphate insecticide exposure. Findings from the meta-analysis were compared with reported outcomes from human observational studies and in-vitro models investigating associations between pesticide exposure and gut microbiome composition and diversity. To our knowledge, this is the first meta-analysis investigating the effects of organophosphate insecticides on the gut microbiome. By integrating data from multiple studies and reanalysing the data using a unified pipeline, this study increases statistical power while reducing methodological variation between studies arising from differences in hypervariable region selection, sequence processing, and microbiome analysis methods. Furthermore, comparisons between animal and human studies provide insight into the translational relevance of animal models for understanding pesticide-associated alterations in the gut microbiome.