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Sci Rep. 2015 Dec 2;5:17450. doi: 10.1038/srep17450.

Metagenomic sequencing of bile from gallstone patients to identify different microbial community patterns and novel biliary bacteria.

Shen H1, Ye F2,3, Xie L1, Yang J1, Li Z2,3, Xu P4, Meng F4, Li L4, Chen Y5, Bo X2,3, Ni M2,3, Zhang X1.

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Department of Gastroenterology, Hangzhou First People's Hospital, Hangzhou 310000, People's Republic of China.
Department of Biotechnology, Beijing Institute of Radiation Medicine, Beijing 100850, People's Republic of China.
Genomics Center of Academy of Military Medical Sciences, Beijing 100850, People's Republic of China.
Department of Research Service, Zhiyuan Inspection Medical Institute, Hangzhou 310009, People's Republic of China.
Department of Radiation Toxicology &Oncology, Beijing Institute of Radiation Medicine, Beijing 100850, People's Republic of China.


Despite the high worldwide prevalence of gallstone disease, the role of the biliary microbiota in gallstone pathogenesis remains obscure. Next-generation sequencing offers advantages for systematically understanding the human microbiota; however, there have been few such investigations of the biliary microbiome. Here, we performed whole-metagenome shotgun (WMS) sequencing and 16S rRNA sequencing on bile samples from 15 Chinese patients with gallstone disease. Microbial communities of most individuals were clustered into two types, according to the relative enrichment of different intestinal bacterial species. In the bile samples, oral cavity/respiratory tract inhabitants were more prevalent than intestinal inhabitants and existed in both community types. Unexpectedly, the two types were not associated with fever status or surgical history, and many bacteria were patient-specific. We identified 13 novel biliary bacteria based on WMS sequencing, as well as genes encoding putative proteins related to gallstone formation and bile resistance (e.g., β-glucuronidase and multidrug efflux pumps). Bile samples from gallstone patients had reduced microbial diversity compared to healthy faecal samples. Patient samples were enriched in pathways related to oxidative stress and flagellar assembly, whereas carbohydrate metabolic pathways showed varying behaviours. As the first biliary WMS survey, our study reveals the complexity and specificity of biliary microecology.

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