{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,23]],"date-time":"2026-09-23T21:46:27Z","timestamp":1790199987007,"version":"4.1.0"},"reference-count":53,"publisher":"Public Library of Science (PLoS)","issue":"3","license":[{"start":{"date-parts":[[2021,3,9]],"date-time":"2021-03-09T00:00:00Z","timestamp":1615248000000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"UFR Sante-Paris12"},{"name":"UPEC Creteil-France"}],"content-domain":{"domain":["www.plosone.org"],"crossmark-restriction":false},"short-container-title":["PLoS ONE"],"abstract":"<jats:p>Extrahepatic cholangiocarcinoma (CCA) accounts for 3% of digestive cancers. The role of biliary microbiota as an environment-related modulator has been scarcely investigated in CCA, and the putative impact of associated diseases has not been yet assessed. We characterized the biliary microbiota in CCA patients in order to identify a specific CCA-related dysbiosis. The biliary effluents were collected through an endoscopic retrograde pancreatic cholangiography (ERCP) examination involving 28 CCA and 47 patients with gallstones, herein considered as controls. The biliary effluents were submitted to bacterial DNA extraction and 16S rRNA sequencing, using Illumina technology. Overall, 32% of CCA and 22% of controls displayed another associated disease, such as diabetes, pancreatitis, inflammatory bowel disease, or primary sclerosing cholangitis. Such associated diseases were considered in the comparisons that were made. Principal coordinate analysis (PCoA) detected a significant disparity of biliary microbiota composition between CCA patients and controls without an associated disease. Amongst the most abundant phyla,<jats:italic>Proteobacteria<\/jats:italic>did not significantly differ between CCA patients and controls, whereas<jats:italic>Firmicutes<\/jats:italic>levels were lower and<jats:italic>Bacteroidetes<\/jats:italic>higher in CCAs\u2019 biliary microbiota than in the controls\u2019 microbiota. The most abundant genera were<jats:italic>Enterococcus<\/jats:italic>,<jats:italic>Streptococcus<\/jats:italic>,<jats:italic>Bacteroides<\/jats:italic>,<jats:italic>Klebsiella<\/jats:italic>, and<jats:italic>Pyramidobacte<\/jats:italic>r in CCA\u2019s biliary microbiota. Additionally, levels of<jats:italic>Bacteroides<\/jats:italic>,<jats:italic>Geobacillus<\/jats:italic>,<jats:italic>Meiothermus<\/jats:italic>, and<jats:italic>Anoxybacillus<\/jats:italic>genera were significantly higher in CCA patients\u2019 biliary microbiota, without an associated disease, in comparison with controls. A specific CCA-related dysbiosis was identified as compared to controls independently from associated diseases. This suggests that a microorganism community may be involved in CCA pathogenesis.<\/jats:p>","DOI":"10.1371\/journal.pone.0247798","type":"journal-article","created":{"date-parts":[[2021,3,9]],"date-time":"2021-03-09T18:28:11Z","timestamp":1615314491000},"page":"e0247798","update-policy":"https:\/\/doi.org\/10.1371\/journal.pone.corrections_policy","source":"Crossref","is-referenced-by-count":72,"title":["Characterization of biliary microbiota dysbiosis in extrahepatic 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Cancer Prev"},{"key":"pone.0247798.ref003","doi-asserted-by":"crossref","first-page":"679","DOI":"10.1016\/S0002-9610(02)00853-X","article-title":"Analysis of the relationships between clinicopathologic factors and survival time in intrahepatic cholangiocarcinoma","volume":"183","author":"Y Kawarada","year":"2002","journal-title":"Am J Surg"},{"key":"pone.0247798.ref004","doi-asserted-by":"crossref","first-page":"1488","DOI":"10.1007\/s11605-007-0282-0","article-title":"Trends in survival after surgery for cholangiocarcinoma: a 30-year population-based SEER database analysis","volume":"11","author":"H Nathan","year":"2007","journal-title":"J Gastrointest Surg"},{"key":"pone.0247798.ref005","first-page":"748","article-title":"The diagnosis and treatment of cholangiocarcinoma","volume":"111","author":"A Vogel","year":"2014","journal-title":"Dtsch Arztebl Int"},{"issue":"Suppl 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and disease","volume":"7","author":"KJ Pflughoeft","year":"2012","journal-title":"Annu Rev Pathol"},{"key":"pone.0247798.ref010","doi-asserted-by":"crossref","first-page":"643","DOI":"10.1002\/em.21878","article-title":"The potential role of lung microbiota in lung cancer attributed to household coal burning exposures","volume":"55","author":"HD Hosgood","year":"2014","journal-title":"Environ Mol Mutagen"},{"key":"pone.0247798.ref011","doi-asserted-by":"crossref","first-page":"e98741","DOI":"10.1371\/journal.pone.0098741","article-title":"Changes in abundance of oral microbiota associated with oral cancer","volume":"9","author":"BL Schmidt","year":"2014","journal-title":"PLoS ONE"},{"key":"pone.0247798.ref012","doi-asserted-by":"crossref","first-page":"462","DOI":"10.1007\/s00248-013-0245-9","article-title":"Dysbiosis signature of fecal microbiota in colorectal cancer patients","volume":"66","author":"N Wu","year":"2013","journal-title":"Microb Ecol"},{"key":"pone.0247798.ref013","doi-asserted-by":"crossref","first-page":"26","DOI":"10.1002\/hep.28135","article-title":"Could gut microbiota protect against sclerosing cholangitis?","volume":"63","author":"HU Marschall","year":"2016","journal-title":"Hepatology"},{"key":"pone.0247798.ref014","doi-asserted-by":"crossref","first-page":"91","DOI":"10.1016\/B978-0-12-800100-4.00003-9","article-title":"The Role of Short-Chain Fatty Acids in Health and Disease","volume":"121","author":"J Tan","year":"2014","journal-title":"Advances in immunology"},{"issue":"no. 2","key":"pone.0247798.ref015","doi-asserted-by":"crossref","first-page":"178. e11","DOI":"10.1016\/j.cmi.2015.10.008","article-title":"Microbiota studies in the bile duct strongly suggest a role for Helicobacter pylori in extrahepatic cholangiocarcinoma","volume":"vol. 22","author":"F. Avil\u00e9s-Jim\u00e9nez","year":"2016","journal-title":"Clinical Microbiology and Infection"},{"key":"pone.0247798.ref016","doi-asserted-by":"crossref","first-page":"893","DOI":"10.1002\/hep.30852","article-title":"Characterization of Gut Microbiota, Bile Acid Metabolism, and Cytokines in Intrahepatic Cholangiocarcinoma","volume":"71","author":"X. Jia","year":"2020","journal-title":"Hepatology"},{"issue":"no. 1","key":"pone.0247798.ref017","article-title":"e microbiota continuum along the female reproductive tract and its relation to uterinerelated diseases Nature","volume":"vol. 8","author":"C. Chen","year":"2017","journal-title":"Communications"},{"key":"pone.0247798.ref018","article-title":"Profiling the urinary microbiota in male patients with bladder cancer in China Frontiers in Cellular and Infection","volume":"vol. 8","author":"P. Wu","year":"2018","journal-title":"Microbiology"},{"key":"pone.0247798.ref019","doi-asserted-by":"crossref","first-page":"1533","DOI":"10.1099\/jmm.0.014092-0","article-title":"Effect of bile salts on the DNA and membrane integrity of enteric bacteria","volume":"58","author":"ME Merritt","year":"2009","journal-title":"J Med Microbiol"},{"key":"pone.0247798.ref020","first-page":"156","article-title":"Biliary Mucosal Barrier and Microbiome","volume":"31","author":"J Verdier","year":"2015","journal-title":"Viszeralmedizin"},{"key":"pone.0247798.ref021","doi-asserted-by":"crossref","first-page":"669","DOI":"10.1186\/1471-2164-14-669","article-title":"Gut microbiota dysbiosis and bacterial community assembly associated with cholesterol gallstones in large-scale study","volume":"14","author":"W Tao","year":"2013","journal-title":"BMC Genomics"},{"key":"pone.0247798.ref022","doi-asserted-by":"crossref","first-page":"937","DOI":"10.1002\/mbo3.218","article-title":"Characterization of the bile and gall bladder microbiota of healthy pigs","volume":"3","author":"E Jim\u00e9nez","year":"2014","journal-title":"MicrobiologyOpen"},{"key":"pone.0247798.ref023","doi-asserted-by":"crossref","first-page":"4799","DOI":"10.1128\/AEM.65.11.4799-4807.1999","article-title":"Direct analysis of genes encoding 16S rRNA from complex communities reveals many novel molecular species within the human gut","volume":"65","author":"A Suau","year":"1999","journal-title":"Appl Environ Microbiol"},{"key":"pone.0247798.ref024","doi-asserted-by":"crossref","first-page":"e1","DOI":"10.1093\/nar\/gks808","article-title":"Evaluation of general 16S ribosomal RNA gene PCR primers for classical and next-generation sequencing-based diversity studies","volume":"41","author":"A Klindworth","year":"2013","journal-title":"Nucleic acids research"},{"key":"pone.0247798.ref025","unstructured":"Illumina. 16S Metagenomic Sequencing Library Preparation 2015. https:\/\/web.uri.edu\/gsc\/files\/16s-metagenomic-library-prep-guide-15044223-b.pdf."},{"key":"pone.0247798.ref026","doi-asserted-by":"crossref","first-page":"2114","DOI":"10.1093\/bioinformatics\/btu170","article-title":"Trimmomatic: a flexible trimmer for Illumina sequence data","volume":"30","author":"AM Bolger","year":"2014","journal-title":"Bioinformatics"},{"key":"pone.0247798.ref027","doi-asserted-by":"crossref","first-page":"2957","DOI":"10.1093\/bioinformatics\/btr507","article-title":"FLASH: fast length adjustment of short reads to improve genome assemblies","volume":"27","author":"T Mago\u010d","year":"2011","journal-title":"Bioinformatics"},{"key":"pone.0247798.ref028","doi-asserted-by":"crossref","first-page":"591","DOI":"10.1007\/978-1-4939-9074-0_19","article-title":"Introduction to the Analysis of Environmental Sequences: Metagenomics with MEGAN","volume":"1910","author":"C Ba\u011fc\u0131","year":"2019","journal-title":"Methods Mol Biol"},{"issue":"Database 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microbiology of biliary tract disease","volume":"27","author":"I Brook","year":"1989","journal-title":"J Clin Microbiol"},{"key":"pone.0247798.ref036","doi-asserted-by":"crossref","first-page":"340","DOI":"10.1067\/mge.2001.117547","article-title":"Bacteriologic analyses of bile and brown pigment stones in patients with acute cholangitis","volume":"54","author":"JW Leung","year":"2001","journal-title":"Gastrointest Endosc"},{"key":"pone.0247798.ref037","doi-asserted-by":"crossref","first-page":"345","DOI":"10.1136\/jcp.36.3.345","article-title":"Clostridium perfringens and other anaerobes isolated from bile","volume":"36","author":"Y Sakaguchi","year":"1983","journal-title":"J Clin Pathol"},{"key":"pone.0247798.ref038","first-page":"431","article-title":"Bile anaerobic bacteria detection and antibiotic susceptibility in patients with gallstone","volume":"2","author":"Y Lu","year":"2003","journal-title":"Hepatobiliary & Pancreatic Diseases International: Hbpd INT"},{"key":"pone.0247798.ref039","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1038\/srep04202","article-title":"Stomach microbiota composition varies between patients with non-atrophic gastritis and patients with intestinal type of gastric cancer","volume":"4","author":"F Aviles-Jimenez","year":"2014","journal-title":"Sci Rep"},{"key":"pone.0247798.ref040","doi-asserted-by":"crossref","first-page":"685","DOI":"10.1038\/ni.2608","article-title":"Control of Pathogens and Pathobionts by the Gut microbiota","volume":"14","author":"N Kamada","year":"2013","journal-title":"Nat Immunol"},{"issue":"6","key":"pone.0247798.ref041","doi-asserted-by":"crossref","first-page":"814","DOI":"10.14309\/ajg.0000000000000604","article-title":"Targeting the Gut Microbiome as a Treatment for Primary Sclerosing Cholangitis: A Conceptional Framework","volume":"115","author":"A Shah","year":"2020","journal-title":"Am J Gastroenterol"},{"key":"pone.0247798.ref042","doi-asserted-by":"crossref","first-page":"e00438","DOI":"10.1128\/mSystems.00438-19","article-title":"Association of Flavonifractor plautii, a Flavonoid-Degrading Bacterium, with the Gut Microbiome of Colorectal Cancer Patients in India","volume":"4","author":"A Gupta","year":"2019","journal-title":"mSystems"},{"key":"pone.0247798.ref043","doi-asserted-by":"crossref","first-page":"e16393","DOI":"10.1371\/journal.pone.0016393","article-title":"Microbial Dysbiosis in Colorectal Cancer (CRC) Patients","volume":"6","author":"I Sobhani","year":"2011","journal-title":"PLOS ONE"},{"key":"pone.0247798.ref044","doi-asserted-by":"crossref","first-page":"945","DOI":"10.1172\/JCI118878","article-title":"Normal luminal bacteria, especially Bacteroides species, mediate chronic colitis, gastritis, and arthritis in HLA-B27\/human beta2 microglobulin transgenic rats","volume":"98","author":"HC Rath","year":"1996","journal-title":"J Clin 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Molinero","year":"2019","journal-title":"Microbiome"},{"key":"pone.0247798.ref048","doi-asserted-by":"crossref","first-page":"e0182924","DOI":"10.1371\/journal.pone.0182924","article-title":"Bile microbiota in primary sclerosing cholangitis: Impact on disease progression and development of biliary dysplasia","volume":"12","author":"P Pereira","year":"2017","journal-title":"PLoS ONE"},{"key":"pone.0247798.ref049","first-page":"1","article-title":"A Preliminary Study of Biliary Microbiota in Patients with Bile Duct Stones or Distal Cholangiocarcinoma","volume":"2019","author":"B. Chen","year":"2019","journal-title":"BioMed Res. 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