Cholangiocarcinoma and common bile duct stones are associated with dissimilar biliary microbiota

Background: There are clear links between the intestinal microbiota and gastrointestinal diseases. Recent advances in genome sequencing have permitted the identification of microbial communities in tissues that were previously thought to be sterile. The bile duct is one such tissue; however, there have been few studies of the biliary microbiota.Methods: We performed a cross-sectional study that aimed to characterize the microbial profile associated with cholangiocarcinoma and to compare it with that associated with common bile duct stones using 16S rRNA nanopore sequencing. A total of 59 bile samples, 14 from patients with cholangiocarcinoma and 45 from patients with common bile duct stones, were analyzed.Results: We confirmed the presence of bacterial DNA in all the bile samples. Nanopore sequencing revealed that obligate and facultative microbial taxa, including Bacteroides and Peptostreptococcales, were more abundant in cholangiocarcinoma-derived samples than in those associated with common bile duct stones.Conclusions: The present results confirm the presence of a biliary microbiota, and demonstrate that this differs in the presence of biliary diseases, such as cholangiocarcinoma and common bile duct stones.