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The interplay of genetic and environmental factors leads to the breakdown of self-tolerance, resulting in hyper-responsiveness, and auto-aggressive immune activation. Emerging evidence links autoimmune liver diseases with alterations of the commensal microbiome configuration and aberrant immune system activation by microbial signals, mainly via the gut-liver axis. Thus, the microbiome is a new frontier to deepen the pathogenetic understanding, uncover biomarkers, and inspire innovative treatments. Herein, we review the current evidence on the role of the microbiome in autoimmune liver diseases from both clinical and basic research. We highlight recent achievements and also bottlenecks and limitations. Moreover, we give an outlook on future developments and potential for clinical applications.<\/jats:p>","DOI":"10.1007\/s00281-022-00936-6","type":"journal-article","created":{"date-parts":[[2022,5,10]],"date-time":"2022-05-10T09:03:46Z","timestamp":1652173426000},"page":"485-507","update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":56,"title":["The intestinal and biliary microbiome in autoimmune liver disease\u2014current evidence and concepts"],"prefix":"10.1007","volume":"44","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-1041-9142","authenticated-orcid":false,"given":"Timur","family":"Liwinski","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Melina","family":"Heinemann","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Christoph","family":"Schramm","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2022,5,10]]},"reference":[{"issue":"Suppl 1","key":"936_CR1","doi-asserted-by":"publisher","first-page":"149","DOI":"10.1111\/liv.14378","volume":"40","author":"B Engel","year":"2020","unstructured":"Engel B, Taubert R, Jaeckel E, Manns MP (2020) The future of autoimmune liver diseases - understanding pathogenesis and improving morbidity and mortality. 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