Metagenomic profiling of biliary microbiota reveals distinct microbial and functional features in cholelithiasis and cholecystic polyps

Cholelithiasis and cholecystic polyps are common gastrointestinal conditions, and recent studies suggest that biliary microbiota dysbiosis may be closely associated with their pathogenesis. In this small cohort (n = 11), bile samples were aseptically collected during surgery from 6 patients with cholelithiasis and 5 patients with cholecystic polyps. Metagenomic sequencing was performed to investigate differences in the microbial composition and functional profiles between the 2 groups. The results revealed that the microbial α diversity of bile from patients with cholelithiasis was significantly greater than that of the polyp group, with significant differences in the Richness, Chao1, ACE, and Shannon indices (P < .05). β-diversity analysis further revealed distinct differences in microbial community composition across the groups. Linear discriminant analysis effect size analysis revealed Pseudomonadota as the only phylum enriched in the polyp group, whereas the cholelithiasis group was enriched with multiple phyla, such as Campylobacterota, Bacillota, and Fusobacteriota, and 35 genera, such as Bacteroides, Mucilaginibacter, and Pedobacter. Kyoto Encyclopedia of Genes and Genomes functional enrichment analysis indicated that the microbial community in the cholelithiasis group was significantly associated with neurodegenerative disease-related pathways, while the microbial community in the polyp group was enriched in pathways related to ribosomes and fluid shear stress. This study highlights the potential role of biliary microecological imbalances in the development of biliary diseases and provides a theoretical basis for exploring pathogenesis and microbiota-based therapeutic strategies.