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

Abstract

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.

Disturbances of the Perioperative Microbiome Across Multiple Body Sites in Patients Undergoing Pancreaticoduodenectomy

“…Klebsiella species (most commonly K. pneumonia and K. oxytoca ) are ubiquitous gram-negative organisms that cause nosocomial infections in humans 25 and commonly harbor genes for antibiotic resistance 26 . Several prior studies of the microbiology of the jejunum 18 , biliary tree 8,27–31 , and pancreas 7 also identified an abundance of Klebsiella in patients with gallstone disease, cholangitis, and cancer. This pattern of results suggests that conditions within the pancreas and biliary tree are favorable for colonization by Klebsiella species, particularly in the setting of disease.…”

The Oral Microbiome of Children: Development, Disease, and Implications Beyond Oral Health

“…The associations between periodontal and systemic disease have been the subject of numerous studies including oral marker links to cardiovascular, respiratory, immune, metabolic, osteopathic and obstetric complications [102–106]. The proposed mechanisms of these oral-systemic links include the spread of infection from the oral cavity in the form of bacteremia or circulating bacterial toxins, triggering increased circulating pro-inflammatory cytokines and a weakened immune system, as well as cross-reactivity (molecular mimicry) between bacterial and self-antigens [104, 107].…”

Analysis of Biliary Microbiota in Hepatobiliopancreatic Diseases Compared to Healthy People [MICROBILIO]: Study Protocol

“…On the other hand, the bile microbiota is still little studied, being sequenced in healthy individuals only recently [23]. Little is known about its composition in malignant diseases [24], with biliary lithiasis being the most studied and best characterized disease [23,25].…”