Sex Differences in the Gastric Mucosal Microbiome Across Gastric Carcinogenesis Are Stage-Specific and Most Pronounced at Intraepithelial Neoplasia

Gastric cancer is a multistage disease and a major global health concern with numerous identified risk factors. It also exhibits sex-associated differences in incidence and prognosis, with males generally experiencing a higher disease burden and worse clinical outcomes. While recent studies have identified gastric microbiome alterations associated with gastric carcinogenesis, the influence of biological sex on these changes remains unexplored. This study investigated whether biological sex modifies gastric microbiome composition and functional profiles across histopathological stages of disease progression. Using a 16S rRNA sequencing dataset of 310 gastric mucosal biopsy samples from patients in Northern China, we analyzed alpha and beta diversity, core microbiome composition, differential abundance, indicator taxa, and predicted functional pathways, stratified by disease stage and biological sex. Sex-associated differences were identified across multiple analyses, with the most pronounced differences at the intraepithelial neoplasia stage. Alpha diversity revealed higher phylogenetic diversity in females at the chronic gastritis stage, whereas beta diversity showed sex-specific compositional differences only at the intraepithelial neoplasia stage. Moreover, core microbiome analysis showed a progressive decrease in the richness of abundant and prevalent taxa across disease stages. Differential abundance analysis identified sex-associated differences in a small number of taxa exclusively at the intraepithelial neoplasia stage. Brevundimonas and Rhodococcus were the only significant indicator genera, both detected as male-specific at the intraepithelial neoplasia stage. Functional profiling identified 27 pro-inflammatory and oncogenic-associated pathways, and 20 tumour-suppressive or oncogenic-associated pathways enriched in males at the intraepithelial neoplasia stage. Overall, these findings indicate that biological sex may influence changes in the gastric microbiome during later stages of gastric carcinogenesis, highlighting the importance of considering biological sex as a host factor in gastric microbiome research associated with disease progression.