{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,7,22]],"date-time":"2026-07-22T15:48:31Z","timestamp":1784735311361,"version":"3.55.0"},"reference-count":27,"publisher":"Frontiers Media SA","license":[{"start":{"date-parts":[[2025,3,20]],"date-time":"2025-03-20T00:00:00Z","timestamp":1742428800000},"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>Background<\/jats:title><jats:p>Pigmented gallstone disease (PGS) is prevalent in China. Biliary microbiota is certified to be related to the PGS formation.<\/jats:p><\/jats:sec><jats:sec><jats:title>Methods<\/jats:title><jats:p>We performed 16S sequencing on both bile and gallstone samples in 16 patients with gallstone disease. We analyzed the microbial composition of the biliary tract and identified crucial bacteria related to the formation of PGS.<\/jats:p><\/jats:sec><jats:sec><jats:title>Results<\/jats:title><jats:p>Biliary tract bacterial composition analysis showed heterogeneity of dominated genus among individuals and correlation in bacterial composition between bile and gallstones. We screened 10 prevalent genera with significant abundance in the bile and gallstones. <jats:italic>Actinomyces<\/jats:italic>, <jats:italic>Streptococcus<\/jats:italic>, and <jats:italic>Achromobacter<\/jats:italic> had a significantly higher abundance in gallstones than in bile (<jats:italic>P<\/jats:italic> &amp;lt; 0.05). Furthermore, we identified 32 species that harbored <jats:italic>uidA<\/jats:italic>, <jats:italic>pldA<\/jats:italic>, and <jats:italic>plc<\/jats:italic> genes that encoded <jats:italic>\u03b2<\/jats:italic>-glucuronidase or phospholipase. Finally, we observed an enriched membrane transport for bile resistance through biliary microbiota.<\/jats:p><\/jats:sec><jats:sec><jats:title>Conclusion<\/jats:title><jats:p><jats:italic>\u03b2<\/jats:italic>-glucuronidase-producing <jats:italic>Streptococcus<\/jats:italic> spp., including <jats:italic>Streptococcus dysgalactiae<\/jats:italic> and <jats:italic>Streptococcus agalactiae<\/jats:italic>, and <jats:italic>Parabacteroides merdae<\/jats:italic>, harbored both <jats:italic>uidA<\/jats:italic> and <jats:italic>pldA<\/jats:italic> genes and were found to be crucial bacterial species in PGS formation.<\/jats:p><\/jats:sec>","DOI":"10.3389\/fcimb.2025.1532512","type":"journal-article","created":{"date-parts":[[2025,3,20]],"date-time":"2025-03-20T09:46:31Z","timestamp":1742463991000},"update-policy":"https:\/\/doi.org\/10.3389\/crossmark-policy","source":"Crossref","is-referenced-by-count":11,"title":["Preliminary study of biliary microbiota and identification of bacterial species associated with pigmented gallstone formation"],"prefix":"10.3389","volume":"15","author":[{"given":"Riyuan","family":"Zhang","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Chong","family":"Chen","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Suhua","family":"Zheng","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jianwei","family":"Zhang","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Weiling","family":"Chen","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Zhimin","family":"Chen","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1965","published-online":{"date-parts":[[2025,3,20]]},"reference":[{"key":"B1","doi-asserted-by":"publisher","DOI":"10.1155\/2019\/1092563","article-title":"A preliminary study of biliary microbiota in patients with bile duct stones or distal cholangiocarcinoma","volume":"2019","author":"Chen","year":"2019","journal-title":"BioMed. 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