{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,8,5]],"date-time":"2026-08-05T05:37:36Z","timestamp":1785908256862,"version":"3.56.0"},"reference-count":65,"publisher":"Frontiers Media SA","license":[{"start":{"date-parts":[[2021,11,1]],"date-time":"2021-11-01T00:00:00Z","timestamp":1635724800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":["frontiersin.org"],"crossmark-restriction":true},"short-container-title":["Front. Microbiol."],"abstract":"<jats:p>The microbes in human bile are closely related to gallbladder health and other potential disorders. Although the bile microbial community has been investigated by recent studies using amplicon or metagenomic sequencing technologies, the genomic information of the microbial species resident in bile is rarely reported. Herein, we isolated 138 bacterial colonies from the fresh bile specimens of four cholecystitis patients using a culturome approach and genomically characterized 35 non-redundant strains using whole-genome shotgun sequencing. The bile bacterial isolates spanned 3 classes, 6 orders, 10 families, and 14 genera, of which the members of <jats:italic>Enterococcus<\/jats:italic>, <jats:italic>Escherichia\u2013Shigella<\/jats:italic>, <jats:italic>Lysinibacillus<\/jats:italic>, and <jats:italic>Enterobacter<\/jats:italic> frequently appeared. Genomic analysis identified three species, including <jats:italic>Providencia<\/jats:italic> sp. D135, <jats:italic>Psychrobacter<\/jats:italic> sp. D093, and <jats:italic>Vibrio<\/jats:italic> sp. D074, which are not represented in existing reference genome databases. Based on the genome data, the functional capacity between bile and gut isolates was compared. The bile strains encoded 5,488 KEGG orthologs, of which 4.9% were specific to the gut strains, including the enzymes involved in biofilm formation, two-component systems, and quorum-sensing pathways. A total of 472 antibiotic resistance genes (ARGs) were identified from the bile genomes including multidrug resistance proteins (42.6%), fluoroquinolone resistance proteins (12.3%), aminoglycoside resistance proteins (9.1%), and \u03b2-lactamase (7.2%). Moreover, <jats:italic>in vitro<\/jats:italic> experiments showed that some bile bacteria have the capabilities for bile salt deconjugation or biotransformation (of primary bile acids into secondary bile acids). Although the physiological or pathological significance of these bacteria needs further exploration, our works expanded knowledge about the genome, diversity, and function of human bile bacteria.<\/jats:p>","DOI":"10.3389\/fmicb.2021.739621","type":"journal-article","created":{"date-parts":[[2021,11,1]],"date-time":"2021-11-01T12:46:27Z","timestamp":1635770787000},"update-policy":"https:\/\/doi.org\/10.3389\/crossmark-policy","source":"Crossref","is-referenced-by-count":11,"title":["Cultivation and Genomic Characterization of the Bile Bacterial Species From Cholecystitis Patients"],"prefix":"10.3389","volume":"12","author":[{"given":"Qiulong","family":"Yan","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Siyi","family":"Zhang","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Shenghui","family":"Li","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Guangyang","family":"Wang","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Aiqin","family":"Zhang","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Taiyang","family":"Jin","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yue","family":"Zhang","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Qingbo","family":"Lv","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Manchun","family":"Xiao","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yuanyuan","family":"Sun","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Xiang","family":"Li","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Song","family":"Cui","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Rui","family":"Li","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Xiaochi","family":"Ma","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Chao","family":"Wang","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Xiangge","family":"Tian","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Xiaohui","family":"Duan","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yi","family":"Xin","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Xianhai","family":"Mao","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yufang","family":"Ma","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1965","published-online":{"date-parts":[[2021,11,1]]},"reference":[{"key":"B1","first-page":"2241","article-title":"Vibrio cholerae 01 isolated in the gallbladder of a patient presenting with cholecystitis.","volume":"91","author":"Asnis","year":"1996","journal-title":"Am. J. Gastroenterol."},{"key":"B2","doi-asserted-by":"publisher","first-page":"1826","DOI":"10.3390\/ijms19071826","article-title":"Unusual manifestation of live Staphylococcus saprophyticus, Corynebacterium urinapleomorphum, and Helicobacter pylori in the gallbladder with cholecystitis.","volume":"19","author":"Backert","year":"2018","journal-title":"Int. J. Mol. Sci."},{"key":"B3","doi-asserted-by":"publisher","first-page":"455","DOI":"10.2217\/fmb.15.149","article-title":"Identification of virulence factors and antibiotic resistance markers using bacterial genomics.","volume":"11","author":"Bakour","year":"2016","journal-title":"Future Microbiol."},{"key":"B4","doi-asserted-by":"publisher","first-page":"455","DOI":"10.1089\/cmb.2012.0021","article-title":"SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing.","volume":"19","author":"Bankevich","year":"2012","journal-title":"J. Comput. Biol."},{"key":"B5","doi-asserted-by":"publisher","first-page":"543","DOI":"10.1038\/nature17645","article-title":"Culturing of \u2018unculturable\u2019 human microbiota reveals novel taxa and extensive sporulation.","volume":"533","author":"Browne","year":"2016","journal-title":"Nature"},{"key":"B6","doi-asserted-by":"publisher","first-page":"e12457","DOI":"10.1111\/hel.12457","article-title":"Helicobacter Pylori infection of the gallbladder and the risk of chronic cholecystitis and cholelithiasis: a systematic review and meta-analysis.","volume":"23","author":"Cen","year":"2018","journal-title":"Helicobacter"},{"key":"B7","doi-asserted-by":"publisher","first-page":"D694","DOI":"10.1093\/nar\/gkv1239","article-title":"VFDB 2016: hierarchical and refined dataset for big data analysis\u201310 years on.","volume":"44","author":"Chen","year":"2016","journal-title":"Nucleic Acids Res."},{"key":"B8","doi-asserted-by":"publisher","first-page":"i884","DOI":"10.1093\/bioinformatics\/bty560","article-title":"fastp: an ultra-fast all-in-one FASTQ preprocessor.","volume":"34","author":"Chen","year":"2018","journal-title":"Bioinformatics"},{"key":"B9","doi-asserted-by":"publisher","first-page":"977","DOI":"10.1016\/j.gie.2018.11.017","article-title":"Preoperative predictors of choledocholithiasis in patients presenting with acute calculous cholecystitis.","volume":"89","author":"Chisholm","year":"2019","journal-title":"Gastrointest. Endosc."},{"key":"B10","doi-asserted-by":"publisher","first-page":"80","DOI":"10.1016\/j.mimet.2014.05.013","article-title":"Understanding molecular identification and polyphasic taxonomic approaches for genetic relatedness and phylogenetic relationships of microorganisms.","volume":"103","author":"Das","year":"2014","journal-title":"J. Microbiol. Methods"},{"key":"B11","doi-asserted-by":"publisher","first-page":"317","DOI":"10.1128\/MMBR.00031-07","article-title":"Structure, function, and evolution of bacterial ATP-binding cassette systems.","volume":"72","author":"Davidson","year":"2008","journal-title":"Microbiol. Mol. Biol. Rev."},{"key":"B12","doi-asserted-by":"publisher","first-page":"1611","DOI":"10.2217\/fmb-2018-0181","article-title":"Repertoire of bacterial species cultured from the human oral cavity and respiratory tract.","volume":"13","author":"Fonkou","year":"2018","journal-title":"Future Microbiol."},{"key":"B13","doi-asserted-by":"publisher","first-page":"566","DOI":"10.1038\/s41586-020-2396-4","article-title":"A metabolic pathway for bile acid dehydroxylation by the gut microbiome.","volume":"582","author":"Funabashi","year":"2020","journal-title":"Nature"},{"key":"B14","doi-asserted-by":"publisher","first-page":"212","DOI":"10.1128\/AAC.01310-13","article-title":"ARG-ANNOT, a new bioinformatic tool to discover antibiotic resistance genes in bacterial genomes.","volume":"58","author":"Gupta","year":"2014","journal-title":"Antimicrob. Agents Chemother."},{"key":"B15","doi-asserted-by":"publisher","first-page":"143","DOI":"10.1038\/s41586-019-1785-z","article-title":"Bile acid metabolites control TH17 and Treg cell differentiation.","volume":"576","author":"Hang","year":"2019","journal-title":"Nature"},{"key":"B16","doi-asserted-by":"publisher","first-page":"523","DOI":"10.1080\/19490976.2018.1458180","article-title":"Bile acid oxidation by Eggerthella lenta strains C592 and DSM 2243(T).","volume":"9","author":"Harris","year":"2018","journal-title":"Gut Microbes"},{"key":"B17","doi-asserted-by":"publisher","first-page":"2647","DOI":"10.1001\/archinte.159.22.2647","article-title":"The continuing importance of bile acids in liver and intestinal disease.","volume":"159","author":"Hofmann","year":"1999","journal-title":"Arch. Intern. Med."},{"key":"B18","doi-asserted-by":"publisher","first-page":"2638","DOI":"10.1099\/ijsem.0.003502","article-title":"Providencia huaxiensis sp. nov., recovered from a human rectal swab.","volume":"69","author":"Hu","year":"2019","journal-title":"Int. J. Syst. Evol. Microbiol."},{"key":"B19","doi-asserted-by":"publisher","first-page":"119","DOI":"10.1186\/1471-2105-11-119","article-title":"Prodigal: prokaryotic gene recognition and translation initiation site identification.","volume":"11","author":"Hyatt","year":"2010","journal-title":"BMC Bioinformatics"},{"key":"B20","doi-asserted-by":"publisher","first-page":"5114","DOI":"10.1038\/s41467-018-07641-9","article-title":"High throughput ANI analysis of 90K prokaryotic genomes reveals clear species boundaries.","volume":"9","author":"Jain","year":"2018","journal-title":"Nat. Commun."},{"key":"B21","author":"Jamil","year":"2021","journal-title":"Proteus Mirabilis Infections."},{"key":"B22","doi-asserted-by":"publisher","first-page":"209","DOI":"10.1007\/s12275-018-7457-0","article-title":"Rapid and robust MALDI-TOF MS techniques for microbial identification: a brief overview of their diverse applications.","volume":"56","author":"Jang","year":"2018","journal-title":"J. Microbiol."},{"key":"B23","doi-asserted-by":"publisher","first-page":"D566","DOI":"10.1093\/nar\/gkw1004","article-title":"CARD 2017: expansion and model-centric curation of the comprehensive antibiotic resistance database.","volume":"45","author":"Jia","year":"2017","journal-title":"Nucleic Acids Res."},{"key":"B24","doi-asserted-by":"publisher","first-page":"937","DOI":"10.1002\/mbo3.218","article-title":"Characterization of the bile and gall bladder microbiota of healthy pigs.","volume":"3","author":"Jimenez","year":"2014","journal-title":"Microbiologyopen"},{"key":"B25","doi-asserted-by":"publisher","first-page":"D353","DOI":"10.1093\/nar\/gkw1092","article-title":"KEGG: new perspectives on genomes, pathways, diseases and drugs.","volume":"45","author":"Kanehisa","year":"2017","journal-title":"Nucleic Acids Res."},{"key":"B26","doi-asserted-by":"publisher","first-page":"445","DOI":"10.1016\/j.cmet.2020.02.006","article-title":"Microbiome modulation of the host adaptive immunity through bile acid modification.","volume":"31","author":"Kuipers","year":"2020","journal-title":"Cell Metab."},{"key":"B27","doi-asserted-by":"publisher","first-page":"16203","DOI":"10.1038\/nmicrobiol.2016.203","article-title":"Culture of previously uncultured members of the human gut microbiota by culturomics.","volume":"1","author":"Lagier","year":"2016","journal-title":"Nat. Microbiol."},{"key":"B28","doi-asserted-by":"publisher","first-page":"16131","DOI":"10.1038\/nmicrobiol.2016.131","article-title":"The mouse intestinal bacterial collection (miBC) provides host-specific insight into cultured diversity and functional potential of the gut microbiota.","volume":"1","author":"Lagkouvardos","year":"2016","journal-title":"Nat. Microbiol."},{"key":"B29","doi-asserted-by":"publisher","first-page":"W256","DOI":"10.1093\/nar\/gkz239","article-title":"Interactive Tree Of Life (iTOL) v4: recent updates and new developments.","volume":"47","author":"Letunic","year":"2019","journal-title":"Nucleic Acids Res."},{"key":"B30","doi-asserted-by":"publisher","first-page":"79","DOI":"10.1038\/s41467-019-13836-5","article-title":"The mouse gut microbial Biobank expands the coverage of cultured bacteria.","volume":"11","author":"Liu","year":"2020","journal-title":"Nat. Commun."},{"key":"B31","doi-asserted-by":"publisher","first-page":"851 e851","DOI":"10.1016\/j.cmi.2015.05.017","article-title":"Acute cholecystitis associated with infection of Enterobacteriaceae from gut microbiota.","volume":"21","author":"Liu","year":"2015","journal-title":"Clin. Microbiol. Infect."},{"key":"B32","doi-asserted-by":"publisher","first-page":"k3965","DOI":"10.1136\/bmj.k3965","article-title":"Laparoscopic cholecystectomy versus percutaneous catheter drainage for acute cholecystitis in high risk patients (CHOCOLATE): multicentre randomised clinical trial.","volume":"363","author":"Loozen","year":"2018","journal-title":"BMJ"},{"key":"B33","doi-asserted-by":"publisher","first-page":"e0080521","DOI":"10.1128\/mSystems.00805-21","article-title":"Dominant bacterial phyla from the human gut show widespread ability to transform and conjugate bile acids.","volume":"6","author":"Lucas","year":"2021","journal-title":"mSystems"},{"key":"B34","doi-asserted-by":"publisher","first-page":"481","DOI":"10.1080\/19490976.2018.1549420","article-title":"In vitro and in vivo characterization of clostridium scindens bile acid transformations.","volume":"10","author":"Marion","year":"2019","journal-title":"Gut Microbes"},{"key":"B35","doi-asserted-by":"publisher","first-page":"365","DOI":"10.3390\/pathogens9050365","article-title":"Characterizing peri-implant and sub-gingival microbiota through culturomics. first isolation of some species in the oral cavity. a pilot study.","volume":"9","author":"Martellacci","year":"2020","journal-title":"Pathogens"},{"key":"B36","doi-asserted-by":"publisher","first-page":"157","DOI":"10.1080\/10408410902809431","article-title":"Bacterial interactions in biofilms.","volume":"35","author":"Moons","year":"2009","journal-title":"Crit. Rev. Microbiol."},{"key":"B37","doi-asserted-by":"publisher","first-page":"893","DOI":"10.1111\/j.1348-0421.1999.tb01224.x","article-title":"Absence of cecal secondary bile acids in gnotobiotic mice associated with two human intestinal bacteria with the ability to dehydroxylate bile acids in vitro.","volume":"43","author":"Narushima","year":"1999","journal-title":"Microbiol. Immunol."},{"key":"B38","doi-asserted-by":"publisher","first-page":"345","DOI":"10.1089\/sur.2016.232","article-title":"Microbiologic data in acute cholecystitis: ten years\u2019 experience from bile cultures obtained during percutaneous cholecystostomy.","volume":"18","author":"Nitzan","year":"2017","journal-title":"Surg. Infect. (Larchmt.)"},{"key":"B39","doi-asserted-by":"publisher","first-page":"2012","DOI":"10.1128\/JB.01354-13","article-title":"Global metabolic response of Enterococcus faecalis to oxygen.","volume":"196","author":"Portela","year":"2014","journal-title":"J. Bacteriol."},{"key":"B40","doi-asserted-by":"publisher","first-page":"22","DOI":"10.1080\/19490976.2015.1127483","article-title":"Consequences of bile salt biotransformations by intestinal bacteria.","volume":"7","author":"Ridlon","year":"2016","journal-title":"Gut Microbes"},{"key":"B41","doi-asserted-by":"publisher","first-page":"241","DOI":"10.1194\/jlr.R500013-JLR200","article-title":"Bile salt biotransformations by human intestinal bacteria.","volume":"47","author":"Ridlon","year":"2006","journal-title":"J. Lipid Res."},{"key":"B42","doi-asserted-by":"publisher","first-page":"a012427","DOI":"10.1101\/cshperspect.a012427","article-title":"Bacterial quorum sensing: its role in virulence and possibilities for its control.","volume":"2","author":"Rutherford","year":"2012","journal-title":"Cold Spring Harb. Perspect. Med."},{"key":"B43","doi-asserted-by":"publisher","first-page":"80","DOI":"10.1159\/000198691","article-title":"Bile acid transformation by the intestinal flora and cholesterol saturation in bile. Effects of Streptococcus faecium administration.","volume":"23","author":"Salvioli","year":"1982","journal-title":"Digestion"},{"key":"B44","doi-asserted-by":"publisher","first-page":"3920","DOI":"10.1016\/j.jchromb.2009.09.038","article-title":"Rapid quantification of bile acids and their conjugates in serum by liquid chromatography-tandem mass spectrometry.","volume":"877","author":"Scherer","year":"2009","journal-title":"J. Chromatogr. B Analyt. Technol. Biomed. Life Sci."},{"key":"B45","doi-asserted-by":"publisher","first-page":"2068","DOI":"10.1093\/bioinformatics\/btu153","article-title":"Prokka: rapid prokaryotic genome annotation.","volume":"30","author":"Seemann","year":"2014","journal-title":"Bioinformatics"},{"key":"B46","doi-asserted-by":"publisher","first-page":"2304","DOI":"10.1038\/ncomms3304","article-title":"PhyloPhlAn is a new method for improved phylogenetic and taxonomic placement of microbes.","volume":"4","author":"Segata","year":"2013","journal-title":"Nat. Commun."},{"key":"B47","doi-asserted-by":"publisher","first-page":"383","DOI":"10.1084\/jem.20171965","article-title":"Bile acids in glucose metabolism in health and disease.","volume":"215","author":"Shapiro","year":"2018","journal-title":"J. Exp. Med."},{"key":"B48","doi-asserted-by":"publisher","first-page":"17450","DOI":"10.1038\/srep17450","article-title":"Metagenomic sequencing of bile from gallstone patients to identify different microbial community patterns and novel biliary bacteria.","volume":"5","author":"Shen","year":"2015","journal-title":"Sci. Rep."},{"key":"B49","doi-asserted-by":"publisher","first-page":"410","DOI":"10.1038\/s41586-019-1865-0","article-title":"Microbial bile acid metabolites modulate gut RORgamma(+) regulatory T cell homeostasis.","volume":"577","author":"Song","year":"2020","journal-title":"Nature"},{"key":"B50","doi-asserted-by":"publisher","first-page":"9","DOI":"10.1186\/s40168-019-0628-3","article-title":"Taxonomic profiling and populational patterns of bacterial bile salt hydrolase (BSH) genes based on worldwide human gut microbiome.","volume":"7","author":"Song","year":"2019","journal-title":"Microbiome"},{"key":"B51","doi-asserted-by":"publisher","first-page":"977","DOI":"10.1007\/s11605-007-0168-1","article-title":"Gallstones containing bacteria are biofilms: bacterial slime production and ability to form pigment solids determines infection severity and bacteremia.","volume":"11","author":"Stewart","year":"2007","journal-title":"J. Gastrointest. Surg."},{"key":"B52","doi-asserted-by":"publisher","first-page":"1331","DOI":"10.1007\/s10096-016-2669-x","article-title":"Association of diverse bacterial communities in human bile samples with biliary tract disorders: a survey using culture and polymerase chain reaction-denaturing gradient gel electrophoresis methods.","volume":"35","author":"Tajeddin","year":"2016","journal-title":"Eur. J. Clin. Microbiol. Infect. Dis."},{"key":"B53","doi-asserted-by":"publisher","first-page":"1557","DOI":"10.1038\/s41467-018-03968-5","article-title":"Culturing of female bladder bacteria reveals an interconnected urogenital microbiota.","volume":"9","author":"Thomas-White","year":"2018","journal-title":"Nat. Commun."},{"key":"B54","doi-asserted-by":"publisher","first-page":"e00129","DOI":"10.1128\/CMR.00129-19","article-title":"State of the art in the culture of the human microbiota: new interests and strategies.","volume":"34","author":"Tidjani Alou","year":"2020","journal-title":"Clin. Microbiol. Rev."},{"key":"B55","doi-asserted-by":"publisher","first-page":"36","DOI":"10.1093\/gastro\/gov015","article-title":"Nationwide trends of hospital admissions for acute cholecystitis in the United States.","volume":"5","author":"Wadhwa","year":"2017","journal-title":"Gastroenterol. Rep. (Oxf.)"},{"key":"B56","doi-asserted-by":"publisher","first-page":"e84","DOI":"10.1097\/RLU.0000000000003317","article-title":"Gallbladder perforation into the peritoneal cavity.","volume":"46","author":"Wang","year":"2021","journal-title":"Clin. Nucl. Med."},{"key":"B57","doi-asserted-by":"publisher","first-page":"508","DOI":"10.1038\/nrmicro.2016.83","article-title":"Metagenome-wide association studies: fine-mining the microbiome.","volume":"14","author":"Wang","year":"2016","journal-title":"Nat. Rev. Microbiol."},{"key":"B58","doi-asserted-by":"publisher","first-page":"103","DOI":"10.1016\/0039-128x(80)90115-4","article-title":"Bile acid induction specificity of 7 alpha-dehydroxylase activity in an intestinal Eubacterium species.","volume":"35","author":"White","year":"1980","journal-title":"Steroids"},{"key":"B59","doi-asserted-by":"publisher","first-page":"265","DOI":"10.1128\/jcm.40.1.265-267.2002","article-title":"Identification by 16S rRNA gene sequencing of Lactobacillus salivarius bacteremic cholecystitis.","volume":"40","author":"Woo","year":"2002","journal-title":"J. Clin. Microbiol."},{"key":"B60","doi-asserted-by":"publisher","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":"Wu","year":"2013","journal-title":"BMC Genomics"},{"key":"B61","doi-asserted-by":"publisher","first-page":"474","DOI":"10.1007\/s13238-018-0543-6","article-title":"The association of diet, gut microbiota and colorectal cancer: what we eat may imply what we get.","volume":"9","author":"Yang","year":"2018","journal-title":"Protein Cell"},{"key":"B62","doi-asserted-by":"publisher","first-page":"e11234","DOI":"10.1097\/MD.0000000000011234","article-title":"Clinical aspects of bile culture in patients undergoing laparoscopic cholecystectomy.","volume":"97","author":"Yun","year":"2018","journal-title":"Medicine (Baltimore)"},{"key":"B63","doi-asserted-by":"publisher","first-page":"2640","DOI":"10.1093\/jac\/dks261","article-title":"Identification of acquired antimicrobial resistance genes.","volume":"67","author":"Zankari","year":"2012","journal-title":"J. Antimicrob. Chemother."},{"key":"B64","doi-asserted-by":"publisher","first-page":"11827","DOI":"10.1038\/s41598-017-12304-8","article-title":"Genome characterization of two bile-isolated Vibrio fluvialis strains: an insight into pathogenicity and bile salt adaption.","volume":"7","author":"Zheng","year":"2017","journal-title":"Sci. Rep."},{"key":"B65","doi-asserted-by":"publisher","first-page":"179","DOI":"10.1038\/s41587-018-0008-8","article-title":"1,520 reference genomes from cultivated human gut bacteria enable functional microbiome analyses.","volume":"37","author":"Zou","year":"2019","journal-title":"Nat. Biotechnol."}],"container-title":["Frontiers in Microbiology"],"original-title":[],"link":[{"URL":"https:\/\/www.frontiersin.org\/articles\/10.3389\/fmicb.2021.739621\/full","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2021,11,1]],"date-time":"2021-11-01T12:46:31Z","timestamp":1635770791000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.frontiersin.org\/articles\/10.3389\/fmicb.2021.739621\/full"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2021,11,1]]},"references-count":65,"alternative-id":["10.3389\/fmicb.2021.739621"],"URL":"https:\/\/doi.org\/10.3389\/fmicb.2021.739621","relation":{},"ISSN":["1664-302X"],"issn-type":[{"value":"1664-302X","type":"electronic"}],"subject":[],"published":{"date-parts":[[2021,11,1]]},"article-number":"739621"}}