{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,1]],"date-time":"2026-09-01T10:03:01Z","timestamp":1788256981855,"version":"build-2803163510"},"reference-count":39,"publisher":"Frontiers Media SA","license":[{"start":{"date-parts":[[2022,4,25]],"date-time":"2022-04-25T00:00:00Z","timestamp":1650844800000},"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. Cell. Infect. Microbiol."],"abstract":"<jats:sec><jats:title>Introduction<\/jats:title><jats:p>Cholelithiasis has a high incidence worldwide and limited treatment options due to its poorly understood pathogenesis. Furthermore, the role of biliary microbiota in cholelithiasis remains understudied. To address these questions, we performed microbial sequencing from biliary samples from primary bile duct stone (PBDS) and secondary bile duct stone (SBDS) patients.<\/jats:p><\/jats:sec><jats:sec><jats:title>Results<\/jats:title><jats:p>We analyzed in total 45 biliary samples, including those from cholelithiasis patients with PBDS or SBDS and people with other digestive diseases. 16S rRNA sequencing showed the bacteria family Alcaligenaceae increased in relative abundance in the lithiasis group compared with the non-lithiasis group. In addition, the PBDS group showed significantly lower bacterial diversity than SBDS, with Propionibacteriaceae, Sphingomonadaceae, and Lactobacillaceae as the most significant bacteria families decreased in relative abundance. We further performed whole metagenomic shotgun sequencing (wMGS) and found increased ability of\u00a0biofilm synthesis and the ability to sense external stimuli in PBDS based on functional annotation of mapped reads. From genome-resolved analysis of the samples, we identified 36 high-quality draft bacterial genome sequences with completion \u226570% and contamination \u226410%. Most of these genomes were classified into Proteobacteria, Firmicutes, or Actinobacteria.<\/jats:p><\/jats:sec><jats:sec><jats:title>Conclusions<\/jats:title><jats:p>Our findings indicated that there is a subtle impact on biliary microbiome from cholelithiasis while the difference is more pronounced between the PBDS and SBDS. It was revealed that the diversity of biliary microbiota in PBDS is lower, while some metabolic pathways are up-regulated, including those linked to higher incidence of different types of cancer, providing new insights for the understanding of cholelithiasis with different origin.<\/jats:p><\/jats:sec>","DOI":"10.3389\/fcimb.2022.881489","type":"journal-article","created":{"date-parts":[[2022,4,25]],"date-time":"2022-04-25T10:38:26Z","timestamp":1650883106000},"update-policy":"https:\/\/doi.org\/10.3389\/crossmark-policy","source":"Crossref","is-referenced-by-count":22,"title":["Patients with Primary and Secondary Bile Duct Stones Harbor Distinct Biliary Microbial Composition and Metabolic Potential"],"prefix":"10.3389","volume":"12","author":[{"given":"Ru","family":"Feng","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Tianyu","family":"Zhang","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Masood ur Rehman","family":"Kayani","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Zhengting","family":"Wang","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yao","family":"Shen","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Kenn Liu","family":"Su","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Kouken","family":"Bielike","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Lei","family":"Chen","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1965","published-online":{"date-parts":[[2022,4,25]]},"reference":[{"key":"B1","doi-asserted-by":"publisher","first-page":"852","DOI":"10.1038\/s41587-019-0209-9","article-title":"Reproducible, Interactive, Scalable and Extensible Microbiome Data Science Using QIIME 2","volume":"37","author":"Bolyen","year":"2019","journal-title":"Nat. Biotechnol."},{"key":"B2","doi-asserted-by":"crossref","first-page":"966","DOI":"10.1016\/B978-0-7020-3468-8.50196-6","article-title":"CHAPTER 190 - Clostridium Difficile","volume-title":"Principles and Practice of Pediatric Infectious Disease (Third Edition)","author":"Brook","year":"2008"},{"key":"B3","doi-asserted-by":"publisher","first-page":"4536","DOI":"10.3748\/wjg.v27.i28.4536","article-title":"Management of Cholelithiasis With Choledocholithiasis: Endoscopic and Surgical Approaches","volume":"27","author":"Cianci","year":"2021","journal-title":"World J. Gastroenterol."},{"key":"B4","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0067019","article-title":"ANOVA-Like Differential Expression (ALDEx) Analysis for Mixed Population RNA-Seq","volume":"8","author":"Fernandes","year":"2013","journal-title":"PloS One"},{"key":"B5","doi-asserted-by":"publisher","DOI":"10.1186\/2049-2618-2-15","article-title":"Unifying the Analysis of High-Throughput Sequencing Datasets: Characterizing RNA-Seq, 16S rRNA Gene Sequencing and Selective Growth Experiments by Compositional Data Analysis","volume":"2","author":"Fernandes","year":"2014","journal-title":"Microbiome"},{"key":"B6","doi-asserted-by":"publisher","first-page":"46","DOI":"10.1007\/s10096-003-1050-z","article-title":"Haemophilus Parainfluenzae: An Underdiagnosed Pathogen of Biliary Tract Infections","volume":"23","author":"Frankard","year":"2004","journal-title":"Eur. J. Clin. Microbiol. Infect. Dis."},{"key":"B7","doi-asserted-by":"publisher","first-page":"106","DOI":"10.1128\/cmr.00021-11","article-title":"The Malassezia Genus in Skin and Systemic Diseases","volume":"25","author":"Gaitanis","year":"2012","journal-title":"Clin. Microbiol. Rev."},{"key":"B8","doi-asserted-by":"publisher","first-page":"37","DOI":"10.3109\/07853899009147239","article-title":"Lactic Acid Bacteria and Human Health","volume":"22","author":"Gorbach","year":"1990","journal-title":"Ann. Med."},{"key":"B9","doi-asserted-by":"publisher","first-page":"5.3.21","DOI":"10.1128\/microbiolspec.BAD-0010-2016","article-title":"Bifidobacteria and Their Health-Promoting Effects","volume":"5","author":"Hidalgo-Cantabrana","year":"2017","journal-title":"Microbiol. Spectr."},{"key":"B10","doi-asserted-by":"publisher","first-page":"2115","DOI":"10.1093\/molbev\/msx148","article-title":"Fast Genome-Wide Functional Annotation Through Orthology Assignment by eggNOG-Mapper","volume":"34","author":"Huerta-Cepas","year":"2017","journal-title":"Mol. Biol. Evol."},{"key":"B11","doi-asserted-by":"publisher","first-page":"420","DOI":"10.1186\/s12859-016-1278-0","article-title":"FMAP: Functional Mapping and Analysis Pipeline for Metagenomics and Metatranscriptomics Studies","volume":"17","author":"Kim","year":"2016","journal-title":"BMC Bioinf."},{"key":"B12","doi-asserted-by":"publisher","first-page":"11218","DOI":"10.1038\/s41598-018-29571-8","article-title":"Metagenomics of Pigmented and Cholesterol Gallstones: The Putative Role of Bacteria","volume":"8","author":"Kose","year":"2018","journal-title":"Sci. Rep."},{"key":"B13","doi-asserted-by":"publisher","first-page":"4344","DOI":"10.1038\/ncomms5344","article-title":"Tipping Elements in the Human Intestinal Ecosystem","volume":"5","author":"Lahti","year":"2014","journal-title":"Nat. Commun."},{"key":"B14","doi-asserted-by":"publisher","first-page":"1674","DOI":"10.1093\/bioinformatics\/btv033","article-title":"MEGAHIT: An Ultra-Fast Single-Node Solution for Large and Complex Metagenomics Assembly via Succinct De Bruijn Graph","volume":"31","author":"Li","year":"2015","journal-title":"Bioinformatics"},{"key":"B15","doi-asserted-by":"publisher","DOI":"10.1097\/MD.0000000000020412","article-title":"Risk Factors of Stone Recurrence After Endoscopic Retrograde Cholangiopancreatography for Common Bile Duct Stones","volume":"99","author":"Lujian","year":"2020","journal-title":"Med. (Baltimore)"},{"key":"B16","doi-asserted-by":"publisher","first-page":"79","DOI":"10.1016\/0039-128x(93)90057-t","article-title":"Bile Acid Transformations by Alcaligenes Recti","volume":"58","author":"Mazumder","year":"1993","journal-title":"Steroids"},{"key":"B17","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0061217","article-title":"Phyloseq: An R Package for Reproducible Interactive Analysis and Graphics of Microbiome Census Data","volume":"8","author":"McMurdie","year":"2013","journal-title":"PloS One"},{"key":"B18","doi-asserted-by":"publisher","first-page":"703","DOI":"10.1093\/gbe\/evu050","article-title":"A Phylogenomic View of Ecological Specialization in the Lachnospiraceae, a Family of Digestive Tract-Associated Bacteria","volume":"6","author":"Meehan","year":"2014","journal-title":"Genome Biol. Evol."},{"key":"B19","doi-asserted-by":"publisher","DOI":"10.1038\/ncomms11257","article-title":"Fast and Sensitive Taxonomic Classification for Metagenomics With Kaiju","volume":"7","author":"Menzel","year":"2016","journal-title":"Nat. Commun."},{"key":"B20","doi-asserted-by":"publisher","first-page":"100","DOI":"10.1186\/s40168-019-0712-8","article-title":"The Human Gallbladder Microbiome Is Related to the Physiological State and the Biliary Metabolic Profile","volume":"7","author":"Molinero","year":"2019","journal-title":"Microbiome"},{"key":"B21","doi-asserted-by":"publisher","first-page":"505","DOI":"10.1038\/s41586-019-1058-x","article-title":"New Insights From Uncultivated Genomes of the Global Human Gut Microbiome","volume":"568","author":"Nayfach","year":"2019","journal-title":"Nature"},{"key":"B22","article-title":"\"Vegan: Community Ecology Package\"","author":"Oksanen","year":"2020","journal-title":"R Package Version 2.5-7"},{"key":"B23","doi-asserted-by":"publisher","first-page":"996","DOI":"10.1111\/1574-6976.12075","article-title":"The First 1000 Cultured Species of the Human Gastrointestinal Microbiota","volume":"38","author":"Rajilic-Stojanovic","year":"2014","journal-title":"FEMS Microbiol. Rev."},{"key":"B24","doi-asserted-by":"publisher","first-page":"18","DOI":"10.4254\/wjh.v4.i2.18","article-title":"Concept of the Pathogenesis and Treatment of Cholelithiasis","volume":"4","author":"Reshetnyak","year":"2012","journal-title":"World J. Hepatol."},{"key":"B25","doi-asserted-by":"publisher","DOI":"10.3389\/fmicb.2019.00846","article-title":"Potential Role of Biofilm Formation in the Development of Digestive Tract Cancer With Special Reference to Helicobacter Pylori Infection","volume":"10","author":"Rizzato","year":"2019","journal-title":"Front. Microbiol."},{"key":"B26","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pntd.0004809","article-title":"Biliary Microbiota, Gallstone Disease and Infection With Opisthorchis Felineus","volume":"10","author":"Saltykova","year":"2016","journal-title":"PloS Negl. Trop. Dis."},{"key":"B27","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":"B28","doi-asserted-by":"publisher","first-page":"R42","DOI":"10.1186\/gb-2012-13-6-r42","article-title":"Composition of the Adult Digestive Tract Bacterial Microbiome Based on Seven Mouth Surfaces, Tonsils, Throat and Stool Samples","volume":"13","author":"Segata","year":"2012","journal-title":"Genome Biol."},{"key":"B29","doi-asserted-by":"publisher","first-page":"R60","DOI":"10.1186\/gb-2011-12-6-r60","article-title":"Metagenomic Biomarker Discovery and Explanation","volume":"12","author":"Segata","year":"2011","journal-title":"Genome Biol."},{"key":"B30","doi-asserted-by":"publisher","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":"B31","doi-asserted-by":"publisher","first-page":"584","DOI":"10.1111\/j.1462-2920.2004.00590.x","article-title":"Pathogenic Potential of Environmental Klebsiella Pneumoniae Isolates","volume":"6","author":"Struve","year":"2004","journal-title":"Environ. Microbiol."},{"key":"B32","doi-asserted-by":"publisher","first-page":"1075","DOI":"10.1016\/j.bpg.2006.05.009","article-title":"Gallstone Disease: Epidemiology, Pathogenesis, and Classification of Biliary Stones (Common Bile Duct and Intrahepatic)","volume":"20","author":"Tazuma","year":"2006","journal-title":"Best Pract. Res. Clin. Gastroenterol."},{"key":"B33","doi-asserted-by":"publisher","first-page":"1021","DOI":"10.3390\/microorganisms9051021","article-title":"Role of Gut Microbiota and Probiotics in Colorectal Cancer: Onset and Progression","volume":"9","author":"Torres-Maravilla","year":"2021","journal-title":"Microorganisms"},{"key":"B34","doi-asserted-by":"publisher","first-page":"673","DOI":"10.1097\/TA.0000000000003057","article-title":"Outcomes of Same Admission Cholecystectomy and Endoscopic Retrograde Cholangiopancreatography for Common Bile Duct Stones: A Post Hoc Analysis of an Eastern Association for the Surgery of Trauma Multicenter Study","volume":"90","author":"Tracy","year":"2021","journal-title":"J. Trauma Acute Care Surg."},{"key":"B35","doi-asserted-by":"publisher","first-page":"158","DOI":"10.1186\/s40168-018-0541-1","article-title":"MetaWRAP-A Flexible Pipeline for Genome-Resolved Metagenomic Data Analysis","volume":"6","author":"Uritskiy","year":"2018","journal-title":"Microbiome"},{"key":"B36","doi-asserted-by":"publisher","first-page":"470","DOI":"10.1038\/s41564-018-0321-5","article-title":"Genomic Variation and Strain-Specific Functional Adaptation in the Human Gut Microbiome During Early Life","volume":"4","author":"Vatanen","year":"2019","journal-title":"Nat. Microbiol."},{"key":"B37","doi-asserted-by":"publisher","first-page":"156","DOI":"10.1159\/000431071","article-title":"Biliary Mucosal Barrier and Microbiome","volume":"31","author":"Verdier","year":"2015","journal-title":"Viszeralmedizin"},{"key":"B38","doi-asserted-by":"publisher","first-page":"765","DOI":"10.1136\/gutjnl-2016-312317","article-title":"Updated Guideline on the Management of Common Bile Duct Stones (CBDS)","volume":"66","author":"Williams","year":"2017","journal-title":"Gut"},{"key":"B39","doi-asserted-by":"publisher","first-page":"548","DOI":"10.1016\/j.cell.2017.07.008","article-title":"Fusobacterium Nucleatum Promotes Chemoresistance to Colorectal Cancer by Modulating Autophagy","volume":"170","author":"Yu","year":"2017","journal-title":"Cell"}],"container-title":["Frontiers in Cellular and Infection Microbiology"],"original-title":[],"link":[{"URL":"https:\/\/www.frontiersin.org\/articles\/10.3389\/fcimb.2022.881489\/full","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2022,4,25]],"date-time":"2022-04-25T10:38:31Z","timestamp":1650883111000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.frontiersin.org\/articles\/10.3389\/fcimb.2022.881489\/full"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2022,4,25]]},"references-count":39,"alternative-id":["10.3389\/fcimb.2022.881489"],"URL":"https:\/\/doi.org\/10.3389\/fcimb.2022.881489","relation":{},"ISSN":["2235-2988"],"issn-type":[{"value":"2235-2988","type":"electronic"}],"subject":[],"published":{"date-parts":[[2022,4,25]]},"article-number":"881489"}}