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Despite decades of study, progress in defining\n                    <jats:italic>Gardnerella<\/jats:italic>\n                    diversity has been hindered by inconsistent taxonomy and poor-quality genomic resources. Here we sequenced 392\n                    <jats:italic>Gardnerella<\/jats:italic>\n                    isolates spanning asymptomatic and BV-associated microbiota and integrated this collection with all publicly available genomes to create a curated, high-quality reference set of 312 genomes. We resolved 21 genomic lineages encompassing 11 species and 15 subspecies using phylogenomics, average nucleotide identity (ANI), digital DNA\u2013DNA hybridization (dDDH) and assigned each a provisional taxonomic name. Long-read assemblies enabled construction of a syntenic\n                    <jats:italic>Gardnerella<\/jats:italic>\n                    pangenome, revealing lineage-specific repertoires of virulence, metabolic, and defense, including variable sialidases (NanH), vaginolysin, and amino-acid biosynthetic pathways alongside conserved genomic organization. Comparative methylome profiling uncovered restriction-modification system diversity suggesting barriers to genetic exchange. Finally, we identified native cryptic plasmids in\n                    <jats:italic>Gardnerella<\/jats:italic>\n                    , overturning the assumption that the genus lacks plasmids. Together, these results establish a complete genomic and functional framework for\n                    <jats:italic>Gardnerella<\/jats:italic>\n                    , providing a reproducible foundation for mechanistic and translational studies of BV and a model for resolving taxonomy and functional stratification in other urogenital-associated bacteria.\n                  <\/jats:p>","DOI":"10.1038\/s41467-026-74458-2","type":"journal-article","created":{"date-parts":[[2026,6,20]],"date-time":"2026-06-20T14:34:32Z","timestamp":1781966072000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":2,"title":["A syntenic pangenome of Gardnerella reveals novel plasmids and phage, taxonomic boundaries, and species-level stratification of metabolic and virulence potential"],"prefix":"10.1038","volume":"17","author":[{"given":"Heather K.","family":"Bouzek","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-2408-8719","authenticated-orcid":false,"given":"Martha A.","family":"Zepeda-Rivera","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7267-3859","authenticated-orcid":false,"given":"Sujatha","family":"Srinivasan","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-8323-2795","authenticated-orcid":false,"given":"Elliot M.","family":"Lee","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7845-2013","authenticated-orcid":false,"given":"Susan M.","family":"Strenk","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Dakota S.","family":"Jones","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Elsa F.","family":"McMahon","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Tina L.","family":"Fiedler","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-0590-9734","authenticated-orcid":false,"given":"Marko","family":"Kostovski","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Michael T.","family":"France","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-0851-2233","authenticated-orcid":false,"given":"Jacques","family":"Ravel","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2735-6800","authenticated-orcid":false,"given":"David N.","family":"Fredricks","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-6765-2383","authenticated-orcid":false,"given":"Christopher D.","family":"Johnston","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2026,6,20]]},"reference":[{"key":"74458_CR1","doi-asserted-by":"publisher","first-page":"1899","DOI":"10.1056\/NEJMoa043802","volume":"353","author":"DN Fredricks","year":"2005","unstructured":"Fredricks, D. N., Fiedler, T. L. & Marrazzo, J. M. Molecular identification of bacteria associated with bacterial vaginosis. N. Engl. J. Med. 353, 1899\u20131911 (2005).","journal-title":"N. Engl. J. Med."},{"key":"74458_CR2","doi-asserted-by":"publisher","first-page":"14","DOI":"10.1016\/0002-9343(83)91112-9","volume":"74","author":"R Amsel","year":"1983","unstructured":"Amsel, R. et al. Nonspecific vaginitis: diagnostic criteria and microbial and epidemiologic associations. Am. J. Med. 74, 14\u201322 (1983).","journal-title":"Am. J. Med."},{"key":"74458_CR3","doi-asserted-by":"publisher","DOI":"10.1186\/1471-2164-11-375","volume":"11","author":"MD Harwich","year":"2010","unstructured":"Harwich, M. D. et al. Drawing the line between commensal and pathogenic Gardnerella vaginalis through genome analysis and virulence studies. 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