The biliary microbiome in obstructive disease: a shotgun metagenomic comparison of benign and malignant conditions

Investigating the contribution of the biliary microbiota is essential for understanding the progression of hepatobiliary diseases, in which persistent inflammation may promote tumorigenesis. The microbiota is a key mediator of the bile acid metabolism, and alterations in its composition and structure may contribute to the onset and progression of severe clinical conditions. Based on this premise, the authors aimed to characterize biliary microbial communities in 48 oncological patients affected by benign (n=24) or malignant (n=24) biliary obstruction (BBO and MBO, respectively). Bile samples were collected by Endoscopic Retrograde Cholangiopancreatography, and Whole-Genome Shotgun Sequencing was performed to characterize the microbial communities. No significant differences were obtained between BBO and MBO in terms of Simpson, richness, and Shannon diversity indices. Overall, 34 common microbial genera were observed between the two populations, whereas several genera were found exclusive to either BBO or MBO. Principal Component Analysis revealed four microbial clusters in both groups. In particular, a topological cluster comprising Shigella, Yersinia, Enterobacter, Photorhabdus, Escherichia, Klebsiella, Vibrio, and Xenorhabdus formed a was found in microbial network of BBO. On the contrary, the topological structure of the MBO network exhibited a higher connected community. The characterization of biliary microbial communities and their structure may improve our understanding of their role in hepatobiliary diseases. Furthermore, the identification of topological characteristics of microbial communities might improve a new insight into host-microbiota interactions.