{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,21]],"date-time":"2026-10-21T14:18:58Z","timestamp":1792592338509,"version":"4.5.0"},"reference-count":37,"publisher":"Elsevier BV","issue":"8","license":[{"start":{"date-parts":[[2024,11,1]],"date-time":"2024-11-01T00:00:00Z","timestamp":1730419200000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.elsevier.com\/tdm\/userlicense\/1.0\/"},{"start":{"date-parts":[[2024,11,1]],"date-time":"2024-11-01T00:00:00Z","timestamp":1730419200000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.elsevier.com\/legal\/tdmrep-license"},{"start":{"date-parts":[[2025,11,1]],"date-time":"2025-11-01T00:00:00Z","timestamp":1761955200000},"content-version":"vor","delay-in-days":365,"URL":"http:\/\/www.elsevier.com\/open-access\/userlicense\/1.0\/"}],"funder":[{"DOI":"10.13039\/501100009592","name":"Beijing Municipal Science and Technology Commission, Adminitrative Commission of Zhongguancun Science Park","doi-asserted-by":"publisher","award":["Z221100007922020"],"award-info":[{"award-number":["Z221100007922020"]}],"id":[{"id":"10.13039\/501100009592","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100002799","name":"Capital Medical University","doi-asserted-by":"publisher","award":["YNKTQN2021004"],"award-info":[{"award-number":["YNKTQN2021004"]}],"id":[{"id":"10.13039\/501100002799","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["elsevier.com","sciencedirect.com"],"crossmark-restriction":true},"short-container-title":["Microbes and Infection"],"published-print":{"date-parts":[[2024,11]]},"DOI":"10.1016\/j.micinf.2024.105368","type":"journal-article","created":{"date-parts":[[2024,5,24]],"date-time":"2024-05-24T02:38:11Z","timestamp":1716518291000},"page":"105368","update-policy":"https:\/\/doi.org\/10.1016\/elsevier_cm_policy","source":"Crossref","is-referenced-by-count":13,"title":["Machine learning-based characterization of the gut microbiome associated with the progression of primary biliary cholangitis to cirrhosis"],"prefix":"10.1016","volume":"26","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-9911-0215","authenticated-orcid":false,"given":"Qi","family":"Wang","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Xiaomeng","family":"Tang","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Wenying","family":"Qiao","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Lina","family":"Sun","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Han","family":"Shi","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Dexi","family":"Chen","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Bin","family":"Xu","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yanmin","family":"Liu","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Juan","family":"Zhao","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Chunyang","family":"Huang","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-8496-172X","authenticated-orcid":false,"given":"Ronghua","family":"Jin","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"78","reference":[{"issue":"1","key":"10.1016\/j.micinf.2024.105368_bib1","doi-asserted-by":"crossref","first-page":"1","DOI":"10.3350\/cmh.2020.0028","article-title":"Current understanding of primary biliary cholangitis","volume":"27","author":"Tanaka","year":"2021","journal-title":"Clin Mol Hepatol"},{"issue":"1","key":"10.1016\/j.micinf.2024.105368_bib2","doi-asserted-by":"crossref","first-page":"34","DOI":"10.1055\/s-0039-1697617","article-title":"The pathogenesis of primary biliary cholangitis: a comprehensive review","volume":"40","author":"Lleo","year":"2020","journal-title":"Semin Liver Dis"},{"issue":"10","key":"10.1016\/j.micinf.2024.105368_bib3","doi-asserted-by":"crossref","first-page":"1989","DOI":"10.1136\/gutjnl-2020-322362","article-title":"Recent advances in clinical practice: epidemiology of autoimmune liver diseases","volume":"70","author":"Trivedi","year":"2021","journal-title":"Gut"},{"issue":"2","key":"10.1016\/j.micinf.2024.105368_bib4","doi-asserted-by":"crossref","first-page":"635","DOI":"10.1002\/hep.27744","article-title":"Fibrates and cholestasis","volume":"62","author":"Ghonem","year":"2015","journal-title":"Hepatology"},{"issue":"25","key":"10.1016\/j.micinf.2024.105368_bib5","doi-asserted-by":"crossref","first-page":"7683","DOI":"10.3748\/wjg.v21.i25.7683","article-title":"Primary biliary cirrhosis: clinical and laboratory criteria for its diagnosis","volume":"21","author":"Reshetnyak","year":"2015","journal-title":"World J Gastroenterol"},{"issue":"9","key":"10.1016\/j.micinf.2024.105368_bib6","doi-asserted-by":"crossref","first-page":"1716","DOI":"10.1136\/gutjnl-2018-316723","article-title":"Human gut microbiome: hopes, threats and promises","volume":"67","author":"Cani","year":"2018","journal-title":"Gut"},{"issue":"1","key":"10.1016\/j.micinf.2024.105368_bib7","doi-asserted-by":"crossref","first-page":"4","DOI":"10.1038\/s41423-020-00592-6","article-title":"Gut microbiome, liver immunology, and liver diseases","volume":"18","author":"Wang","year":"2021","journal-title":"Cell Mol Immunol"},{"issue":"3","key":"10.1016\/j.micinf.2024.105368_bib8","doi-asserted-by":"crossref","first-page":"534","DOI":"10.1136\/gutjnl-2016-313332","article-title":"Gut microbial profile is altered in primary biliary cholangitis and partially restored after UDCA therapy","volume":"67","author":"Tang","year":"2018","journal-title":"Gut"},{"issue":"4","key":"10.1016\/j.micinf.2024.105368_bib9","doi-asserted-by":"crossref","first-page":"759","DOI":"10.1136\/gutjnl-2022-328403","article-title":"Longitudinal transkingdom gut microbial approach towards decompensation in outpatients with cirrhosis","volume":"72","author":"Bajaj","year":"2023","journal-title":"Gut"},{"issue":"2","key":"10.1016\/j.micinf.2024.105368_bib10","doi-asserted-by":"crossref","DOI":"10.1111\/eci.13714","article-title":"Alterations in gut microbiota and elevated serum bilirubin in primary biliary cholangitis patients treated with ursodeoxycholic acid","volume":"52","author":"Han","year":"2022","journal-title":"Eur J Clin Invest"},{"issue":"1","key":"10.1016\/j.micinf.2024.105368_bib11","doi-asserted-by":"crossref","first-page":"40","DOI":"10.1038\/s41580-021-00407-0","article-title":"A\u00a0guide to machine learning for biologists","volume":"23","author":"Greener","year":"2022","journal-title":"Nat Rev Mol Cell Biol"},{"issue":"16","key":"10.1016\/j.micinf.2024.105368_bib12","doi-asserted-by":"crossref","first-page":"1521","DOI":"10.1161\/CIRCULATIONAHA.120.050583","article-title":"Machine learning in medicine: will this time Be different?","volume":"142","author":"Deo","year":"2020","journal-title":"Circulation"},{"issue":"5","key":"10.1016\/j.micinf.2024.105368_bib13","doi-asserted-by":"crossref","first-page":"719","DOI":"10.1016\/j.cmet.2022.03.002","article-title":"Early prediction of incident liver disease using conventional risk factors and gut-microbiome-augmented gradient boosting","volume":"34","author":"Liu","year":"2022","journal-title":"Cell Metabol"},{"issue":"7","key":"10.1016\/j.micinf.2024.105368_bib14","doi-asserted-by":"crossref","first-page":"1948","DOI":"10.1053\/j.gastro.2022.02.025","article-title":"Deep learning-based classification of hepatocellular nodular lesions on whole-slide histopathologic images","volume":"162","author":"Cheng","year":"2022","journal-title":"Gastroenterology"},{"issue":"1","key":"10.1016\/j.micinf.2024.105368_bib15","doi-asserted-by":"crossref","first-page":"133","DOI":"10.1002\/hep.31750","article-title":"A\u00a0machine learning approach enables quantitative measurement of liver histology and disease monitoring in NASH","volume":"74","author":"Taylor-Weiner","year":"2021","journal-title":"Hepatology"},{"issue":"3","key":"10.1016\/j.micinf.2024.105368_bib16","doi-asserted-by":"crossref","first-page":"600","DOI":"10.1016\/j.jhep.2021.11.011","article-title":"Stool microbiota are superior to saliva in distinguishing cirrhosis and hepatic encephalopathy using machine learning","volume":"76","author":"Saboo","year":"2022","journal-title":"J\u00a0Hepatol"},{"issue":"5","key":"10.1016\/j.micinf.2024.105368_bib17","doi-asserted-by":"crossref","first-page":"901","DOI":"10.1016\/j.cmet.2020.10.015","article-title":"A\u00a0universal gut-microbiome-derived signature predicts cirrhosis","volume":"32","author":"Oh","year":"2020","journal-title":"Cell Metabol"},{"issue":"1","key":"10.1016\/j.micinf.2024.105368_bib18","doi-asserted-by":"crossref","first-page":"145","DOI":"10.1016\/j.jhep.2017.03.022","article-title":"Electronic address eee, European Association for the Study of the L. EASL Clinical Practice Guidelines: the diagnosis and management of patients with primary biliary cholangitis","volume":"67","year":"2017","journal-title":"J\u00a0Hepatol"},{"issue":"1","key":"10.1016\/j.micinf.2024.105368_bib19","doi-asserted-by":"crossref","first-page":"310","DOI":"10.1002\/hep.28906","article-title":"Portal hypertensive bleeding in cirrhosis: risk stratification, diagnosis, and management: 2016 practice guidance by the American Association for the study of liver diseases","volume":"65","author":"Garcia-Tsao","year":"2017","journal-title":"Hepatology"},{"issue":"Suppl 1","key":"10.1016\/j.micinf.2024.105368_bib20","doi-asserted-by":"crossref","first-page":"S67","DOI":"10.1016\/j.jhep.2020.11.013","article-title":"The microbiota in cirrhosis and its role in hepatic decompensation","volume":"75","author":"Trebicka","year":"2021","journal-title":"J\u00a0Hepatol"},{"issue":"7","key":"10.1016\/j.micinf.2024.105368_bib21","doi-asserted-by":"crossref","first-page":"907","DOI":"10.1002\/lt.24754","article-title":"Liver transplant modulates gut microbial dysbiosis and cognitive function in cirrhosis","volume":"23","author":"Bajaj","year":"2017","journal-title":"Liver Transplant"},{"key":"10.1016\/j.micinf.2024.105368_bib22","unstructured":"Kanehisa M, Goto S. KEGG: kyoto encyclopedia of genes and genomes. (0305-1048 (Print))."},{"issue":"2","key":"10.1016\/j.micinf.2024.105368_bib23","doi-asserted-by":"crossref","first-page":"452","DOI":"10.1159\/000494158","article-title":"Plasma MicroRNA-29c levels are associated with carotid intima-media thickness and is a potential biomarker for the early detection of atherosclerosis","volume":"50","author":"Huang","year":"2018","journal-title":"Cell Physiol Biochem"},{"key":"10.1016\/j.micinf.2024.105368_bib24","doi-asserted-by":"crossref","unstructured":"Hiippala K, Jouhten H, Ronkainen A, Hartikainen A, Kainulainen V, Jalanka J, et\u00a0al. The potential of gut commensals in reinforcing intestinal barrier function and alleviating inflammation. LID - 10.3390\/nu10080988 [doi] LID - 988. (2072-6643 (Electronic)).","DOI":"10.3390\/nu10080988"},{"key":"10.1016\/j.micinf.2024.105368_bib25","unstructured":"Lopez-Siles M, Duncan SH, Garcia-Gil LJ, Martinez-Medina M. Faecalibacterium prausnitzii: from microbiology to diagnostics and prognostics. (1751-7370 (Electronic))."},{"key":"10.1016\/j.micinf.2024.105368_bib26","unstructured":"Haber AL, Biton M, Rogel N, Herbst RH, Shekhar K, Smillie C, et\u00a0al. A single-cell survey of the small intestinal epithelium. (1476-4687 (Electronic))."},{"key":"10.1016\/j.micinf.2024.105368_bib27","unstructured":"Wells JM, Brummer RJ, Derrien M, MacDonald TT, Troost F, Cani PD, et\u00a0al. Homeostasis of the gut barrier and potential biomarkers. (1522-1547 (Electronic))."},{"key":"10.1016\/j.micinf.2024.105368_bib28","unstructured":"Cani PD. Interactions between gut microbes and host cells control gut barrier and metabolism. (2046-2166 [Print]."},{"key":"10.1016\/j.micinf.2024.105368_bib29","unstructured":"Wang RA-OX, Lee JA-O, Campbell EL, Colgan SA-O. Microbiota-derived butyrate dynamically regulates intestinal homeostasis through regulation of actin-associated protein synaptopodin. (1091-6490 (Electronic))."},{"key":"10.1016\/j.micinf.2024.105368_bib30","unstructured":"Citi S. Intestinal barriers protect against disease. (1095-9203 (Electronic))."},{"key":"10.1016\/j.micinf.2024.105368_bib31","unstructured":"Tripathi A, Debelius J, Brenner DA, Karin M, Loomba R, Schnabl B, et\u00a0al. The gut-liver axis and the intersection with the microbiome. (1759-5053 (Electronic))."},{"key":"10.1016\/j.micinf.2024.105368_bib32","unstructured":"Liu R, Li X, Huang Z, Zhao D, Ganesh BS, Lai G, et\u00a0al. C\/EBP homologous protein-induced loss of intestinal epithelial stemness contributes to bile duct ligation-induced cholestatic liver injury in mice. (1527-3350 (Electronic))."},{"key":"10.1016\/j.micinf.2024.105368_bib33","unstructured":"Han W, Huang C, Ji Y, Zhou L, Chen J, Hou J. Alterations in the gut microbiota and hepatitis-B-virus infection in southern Chinese patients with coexisting non-alcoholic fatty liver disease and type-2 diabetes mellitus. (2296-858X (Print))."},{"key":"10.1016\/j.micinf.2024.105368_bib34","unstructured":"Sookoian SA-O, Salatino A, Casta\u00f1o GO, Landa MS, Fijalkowky C, Garaycoechea M, et\u00a0al. Intrahepatic bacterial metataxonomic signature in non-alcoholic fatty liver disease. (1468-3288 (Electronic))."},{"key":"10.1016\/j.micinf.2024.105368_bib35","unstructured":"Ren Z, Li A, Jiang J, Zhou L, Yu Z, Lu H, et\u00a0al. Gut microbiome analysis as a tool towards targeted non-invasive biomarkers for early hepatocellular carcinoma. (1468-3288 (Electronic))."},{"key":"10.1016\/j.micinf.2024.105368_bib36","unstructured":"Pace F, Rudolph SE, Chen Y, Bao B, Kaplan DL, Watnick PA-O. The short-chain fatty acids propionate and butyrate augment adherent-invasive Escherichia coli virulence but repress inflammation in a human intestinal enteroid model of infection. (2165-0497 (Electronic))."},{"key":"10.1016\/j.micinf.2024.105368_bib37","unstructured":"Chen Y, Guo J, Qian G, Fang D, Shi D, Guo L, et\u00a0al. Gut dysbiosis in acute-on-chronic liver failure and its predictive value for mortality. (1440-1746 (Electronic))."}],"container-title":["Microbes and Infection"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/api.elsevier.com\/content\/article\/PII:S1286457924001047?httpAccept=text\/xml","content-type":"text\/xml","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/api.elsevier.com\/content\/article\/PII:S1286457924001047?httpAccept=text\/plain","content-type":"text\/plain","content-version":"vor","intended-application":"text-mining"}],"deposited":{"date-parts":[[2025,11,5]],"date-time":"2025-11-05T18:41:44Z","timestamp":1762368104000},"score":1,"resource":{"primary":{"URL":"https:\/\/linkinghub.elsevier.com\/retrieve\/pii\/S1286457924001047"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2024,11]]},"references-count":37,"journal-issue":{"issue":"8","published-print":{"date-parts":[[2024,11]]}},"alternative-id":["S1286457924001047"],"URL":"https:\/\/doi.org\/10.1016\/j.micinf.2024.105368","relation":{},"ISSN":["1286-4579"],"issn-type":[{"value":"1286-4579","type":"print"}],"subject":[],"published":{"date-parts":[[2024,11]]},"assertion":[{"value":"Elsevier","name":"publisher","label":"This article is maintained by"},{"value":"Machine learning-based characterization of the gut microbiome associated with the progression of primary biliary cholangitis to cirrhosis","name":"articletitle","label":"Article Title"},{"value":"Microbes and Infection","name":"journaltitle","label":"Journal Title"},{"value":"https:\/\/doi.org\/10.1016\/j.micinf.2024.105368","name":"articlelink","label":"CrossRef DOI link to publisher maintained version"},{"value":"article","name":"content_type","label":"Content Type"},{"value":"\u00a9 2024 Published by Elsevier Masson SAS on behalf of Institut Pasteur.","name":"copyright","label":"Copyright"}],"article-number":"105368"}}