Cholesterol gallstones and bile host diverse bacterial communities with potential to promote the formation of gallstones

•We identified fourteen bacterial genera in cholesterol gallstones.•Eight bacterial genera were identified in the bile of gallstone patients.•The gallstone microbiome was considered more stable than that of bile.•30% of the isolates from gallstones secreted β-glucuronidase and phospholipase A2.•Pseudomonas aeruginosa may be a major agent in the formation of cholesterol gallstones.

The prevalence of cholesterol gallstones has increased in recent years. Bacterial infection correlates with the formation of gallstones. We studied the composition and function of bacterial communities in cholesterol gallstones and bile from 22 cholesterol gallstone patients using culture-dependent and culture-independent methods. Altogether fourteen and eight bacterial genera were detected in cholesterol gallstones and bile, respectively. Pseudomonas spp. were the dominant bacteria in both cholesterol gallstones and bile. As judged by diversity indices, hierarchical clustering and principal component analysis, the bacterial communities in gallstones were different from those in bile. The gallstone microbiome was considered more stable than that of bile. The different microbial communities may be partially explained by differences in their habitats. We found that 30% of the culturable strains from cholesterol gallstones secreted β-glucuronidase and phospholipase A2. Pseudomonas aeruginosa strains showed the highest β-glucuronidase activity and produced the highest concentration of phospholipase A2, indicating that Ps. aeruginosa may be a major agent in the formation of cholesterol gallstones.