Biliary Microbiota and Bile Acid Remodeling in Common Bile Duct Stone Patients: A Pilot Multi-Omics Analysis of ERCP-Acquired Human Bile.

BACKGROUND: Gallstone disease is increasingly recognized as involving host-microbe-metabolite interactions. Although biliary microbial communities have been detected in biliary obstruction, their relationship with bile acid remodeling in common bile duct (CBD) stone disease remains unclear. METHODS: ERCP-acquired bile samples from 25 patients, including 12 with CBD stones and 13 patients with non-stone pancreatobiliary diseases, including malignant and benign conditions, were analyzed using 16S rRNA sequencing and targeted bile acid metabolomics. Between-group comparisons and exploratory microbe-bile acid correlation analyses were performed. RESULTS: Bile samples contained detectable microbial communities dominated by Pseudomonadota and Bacillota. Alpha diversity and overall community structure were comparable between groups, with no significant beta-diversity separation (PERMANOVA R2 = 0.0483, p = 0.259). No taxa remained significant after multiple-testing correction, although several genera showed nominal between-group differences. Targeted metabolomics showed only mild separation between groups. TUDCA/THDCA and UDCA were higher in the CBD stone group at the nominal p < 0.05 level, whereas 12-O-CDCA showed a nonsignificant increasing trend; none remained significant after FDR correction. Exploratory multi-omics analysis suggested nominal microbe-bile acid associations, but these correlations were also not significant after FDR correction. CONCLUSION: This pilot multi-omics study identified detectable biliary microbial communities and exploratory bile acid remodeling trends in ERCP-acquired bile from patients with CBD stones. However, key taxonomic, metabolomic, and association findings did not survive multiple-testing correction and should be interpreted as hypothesis-generating observations requiring validation in larger, well-characterized cohorts.