{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,1]],"date-time":"2026-10-01T08:20:02Z","timestamp":1790842802973,"version":"4.1.0"},"reference-count":25,"publisher":"American Society for Microbiology","issue":"3","license":[{"start":{"date-parts":[[2026,3,11]],"date-time":"2026-03-11T00:00:00Z","timestamp":1773187200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"},{"start":{"date-parts":[[2026,3,11]],"date-time":"2026-03-11T00:00:00Z","timestamp":1773187200000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/journals.asm.org\/non-commercial-tdm-license"}],"funder":[{"DOI":"10.13039\/100000060","name":"National Institute of Allergy and Infectious Diseases","doi-asserted-by":"publisher","award":["UH2AI083264"],"award-info":[{"award-number":["UH2AI083264"]}],"id":[{"id":"10.13039\/100000060","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000060","name":"National Institute of Allergy and Infectious Diseases","doi-asserted-by":"publisher","award":["K01AI163413"],"award-info":[{"award-number":["K01AI163413"]}],"id":[{"id":"10.13039\/100000060","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000060","name":"National Institute of Allergy and Infectious Diseases","doi-asserted-by":"publisher","award":["T32AI162579"],"award-info":[{"award-number":["T32AI162579"]}],"id":[{"id":"10.13039\/100000060","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000056","name":"National Institute of Nursing Research","doi-asserted-by":"publisher","award":["R01NR015495"],"award-info":[{"award-number":["R01NR015495"]}],"id":[{"id":"10.13039\/100000056","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000865","name":"Bill and Melinda Gates Foundation","doi-asserted-by":"publisher","award":["OPP1189217"],"award-info":[{"award-number":["OPP1189217"]}],"id":[{"id":"10.13039\/100000865","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["journals.asm.org"],"crossmark-restriction":true},"short-container-title":["mBio"],"published-print":{"date-parts":[[2026,3,11]]},"abstract":"<jats:title>ABSTRACT<\/jats:title>\n                  <jats:sec>\n                    <jats:title\/>\n                    <jats:p>\n                      Taxonomic classification alone fails to capture the ecological and functional diversity of vaginal microbiomes, particularly those dominated by\n                      <jats:italic toggle=\"yes\">Gardnerella<\/jats:italic>\n                      species. Using the expanded VIRGO2 gene catalog, we developed the vaginal inference of subspecies and typing algorithm (VISTA), a novel ortholog-based framework that defined metagenomic subspecies and 25 metagenomic community state types (mgCSTs), including six distinct\n                      <jats:italic toggle=\"yes\">Gardnerella<\/jats:italic>\n                      -dominated profiles. The mgCSTs exhibit marked differences in species composition, functional gene content, transcriptional activity, and host immune responses. These findings reveal that\n                      <jats:italic toggle=\"yes\">Gardnerella<\/jats:italic>\n                      predominance does not uniformly equate to dysbiosis and underscore the importance of functional context in shaping host-microbiome interactions. VISTA provides scalable classifiers and an interactive application to support mechanistic studies of vaginal microbiome function and its implications for reproductive health.\n                    <\/jats:p>\n                    <jats:sec>\n                      <jats:title>IMPORTANCE<\/jats:title>\n                      <jats:p>The vaginal microbiome plays a central role in reproductive and gynecologic health, yet its functional diversity and ecological organization remain poorly understood. Traditional 16S rRNA approaches provide only a partial view of this complexity, overlooking the strain-level variation that often determines microbial behavior and host outcomes. By applying metagenomic sequencing and scalable computational modeling, we developed the vaginal inference of subspecies and typing algorithm, a framework that defines gene-based subspecies and community state types across diverse populations. These classifications reveal new insights into the genomic and ecological foundations of vaginal community structure and offer a standardized resource for comparative and translational microbiome research. This work establishes the foundation for functionally informed diagnostics and precision interventions targeting women\u2019s reproductive health.<\/jats:p>\n                    <\/jats:sec>\n                  <\/jats:sec>","DOI":"10.1128\/mbio.03645-25","type":"journal-article","created":{"date-parts":[[2026,2,5]],"date-time":"2026-02-05T14:00:36Z","timestamp":1770300036000},"update-policy":"https:\/\/doi.org\/10.1128\/asmj-crossmark-policy-page","source":"Crossref","is-referenced-by-count":3,"title":["Not all vaginal microbiomes are equal: functional context shapes immune landscapes"],"prefix":"10.1128","volume":"17","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-1343-1101","authenticated-orcid":false,"given":"Amanda","family":"Williams","sequence":"first","affiliation":[{"id":[{"id":"https:\/\/ror.org\/04rq5mt64","id-type":"ROR","asserted-by":"publisher"}],"name":"Center for Advanced Microbiome Research and Innovation, University of Maryland School of Medicine","place":["Baltimore, USA"]},{"id":[{"id":"https:\/\/ror.org\/04rq5mt64","id-type":"ROR","asserted-by":"publisher"}],"name":"Institute for Genome Sciences, University of Maryland School of Medicine","place":["Baltimore, USA"]},{"id":[{"id":"https:\/\/ror.org\/04rq5mt64","id-type":"ROR","asserted-by":"publisher"}],"name":"Department of Microbiology and Immunology, University of Maryland School of Medicine","place":["Baltimore, USA"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0006-4884-1476","authenticated-orcid":true,"given":"Amaury","family":"Maros","sequence":"additional","affiliation":[{"id":[{"id":"https:\/\/ror.org\/04rq5mt64","id-type":"ROR","asserted-by":"publisher"}],"name":"Center for Advanced Microbiome Research and Innovation, University of Maryland School of Medicine","place":["Baltimore, USA"]},{"id":[{"id":"https:\/\/ror.org\/04rq5mt64","id-type":"ROR","asserted-by":"publisher"}],"name":"Institute for Genome Sciences, University of Maryland School of Medicine","place":["Baltimore, USA"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-6029-0201","authenticated-orcid":false,"given":"Michael T.","family":"France","sequence":"additional","affiliation":[{"id":[{"id":"https:\/\/ror.org\/04rq5mt64","id-type":"ROR","asserted-by":"publisher"}],"name":"Center for Advanced Microbiome Research and Innovation, University of Maryland School of Medicine","place":["Baltimore, USA"]},{"id":[{"id":"https:\/\/ror.org\/04rq5mt64","id-type":"ROR","asserted-by":"publisher"}],"name":"Institute for Genome Sciences, University of Maryland School of Medicine","place":["Baltimore, USA"]},{"id":[{"id":"https:\/\/ror.org\/04rq5mt64","id-type":"ROR","asserted-by":"publisher"}],"name":"Department of Microbiology and Immunology, University of Maryland School of Medicine","place":["Baltimore, USA"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-0851-2233","authenticated-orcid":true,"given":"Jacques","family":"Ravel","sequence":"additional","affiliation":[{"id":[{"id":"https:\/\/ror.org\/04rq5mt64","id-type":"ROR","asserted-by":"publisher"}],"name":"Center for Advanced Microbiome Research and Innovation, University of Maryland School of Medicine","place":["Baltimore, USA"]},{"id":[{"id":"https:\/\/ror.org\/04rq5mt64","id-type":"ROR","asserted-by":"publisher"}],"name":"Institute for Genome Sciences, University of Maryland School of Medicine","place":["Baltimore, USA"]},{"id":[{"id":"https:\/\/ror.org\/04rq5mt64","id-type":"ROR","asserted-by":"publisher"}],"name":"Department of Microbiology and Immunology, University of Maryland School of Medicine","place":["Baltimore, USA"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7646-4085","authenticated-orcid":true,"given":"Johanna B.","family":"Holm","sequence":"additional","affiliation":[{"id":[{"id":"https:\/\/ror.org\/04rq5mt64","id-type":"ROR","asserted-by":"publisher"}],"name":"Center for Advanced Microbiome Research and Innovation, University of Maryland School of Medicine","place":["Baltimore, USA"]},{"id":[{"id":"https:\/\/ror.org\/04rq5mt64","id-type":"ROR","asserted-by":"publisher"}],"name":"Institute for Genome Sciences, University of Maryland School of Medicine","place":["Baltimore, USA"]},{"id":[{"id":"https:\/\/ror.org\/04rq5mt64","id-type":"ROR","asserted-by":"publisher"}],"name":"Department of Microbiology and Immunology, University of Maryland School of Medicine","place":["Baltimore, USA"]}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"235","reference":[{"key":"e_1_3_5_2_2","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.1002611107"},{"key":"e_1_3_5_3_2","first-page":"213","article-title":"Bacterial vaginosis during pregnancy. An association with prematurity and postpartum complications","volume":"86","author":"Eschenbach DA","year":"1984","unstructured":"Eschenbach DA, Gravett MG, Chen KC, Hoyme UB, Holmes KK. 1984. Bacterial vaginosis during pregnancy. An association with prematurity and postpartum complications. Scand J Urol Nephrol Suppl 86:213\u2013222.","journal-title":"Scand J Urol Nephrol Suppl"},{"key":"e_1_3_5_4_2","doi-asserted-by":"publisher","DOI":"10.1177\/0956462415616038"},{"key":"e_1_3_5_5_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.immuni.2016.12.013"},{"key":"e_1_3_5_6_2","doi-asserted-by":"publisher","DOI":"10.1016\/S1473-3099(18)30058-6"},{"key":"e_1_3_5_7_2","doi-asserted-by":"publisher","DOI":"10.1086\/657320"},{"key":"e_1_3_5_8_2","doi-asserted-by":"publisher","DOI":"10.3109\/14767058.2011.565390"},{"key":"e_1_3_5_9_2","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.1002611107"},{"key":"e_1_3_5_10_2","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-020-14677-3"},{"key":"e_1_3_5_11_2","doi-asserted-by":"publisher","DOI":"10.1128\/jcm.20.4.826-827.1984"},{"key":"e_1_3_5_12_2","doi-asserted-by":"publisher","DOI":"10.1128\/jcm.28.12.2761-2764.1990"},{"key":"e_1_3_5_13_2","doi-asserted-by":"publisher","DOI":"10.1186\/s40168-023-01692-x"},{"key":"e_1_3_5_14_2","doi-asserted-by":"publisher","DOI":"10.1186\/s40168-020-00934-6"},{"key":"e_1_3_5_15_2","doi-asserted-by":"publisher","unstructured":"France MT Chaudry I Rutt L Quain M Shirtliff B McComb E Maros A Alizadeh M Hussain FA Elovitz MA Relman DA Rahman A Brotman RM Price J Kassaro M Holm JB Ma B Ravel J. 2025. VIRGO2: unveiling the functional and ecological complexity of the vaginal microbiome with an enhanced non-redundant gene catalog. bioRxiv:2025.03.04.641479. doi:10.1101\/2025.03.04.641479","DOI":"10.1101\/2025.03.04.641479"},{"key":"e_1_3_5_16_2","doi-asserted-by":"publisher","DOI":"10.1128\/msystems.00573-24"},{"key":"e_1_3_5_17_2","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.2005331117"},{"key":"e_1_3_5_18_2","doi-asserted-by":"publisher","DOI":"10.3389\/fcimb.2020.00293"},{"key":"e_1_3_5_19_2","doi-asserted-by":"publisher","DOI":"10.1186\/s40168-025-02039-4"},{"key":"e_1_3_5_20_2","doi-asserted-by":"publisher","DOI":"10.1136\/sextrans-2017-053506"},{"key":"e_1_3_5_21_2","doi-asserted-by":"publisher","DOI":"10.1038\/nrmicro2259"},{"key":"e_1_3_5_22_2","doi-asserted-by":"publisher","DOI":"10.1128\/jb.00393-22"},{"key":"e_1_3_5_23_2","doi-asserted-by":"publisher","DOI":"10.1038\/ncomms3087"},{"key":"e_1_3_5_24_2","doi-asserted-by":"publisher","DOI":"10.3390\/ijms22126487"},{"key":"e_1_3_5_25_2","doi-asserted-by":"publisher","DOI":"10.1136\/sextrans-2014-051601"},{"key":"e_1_3_5_26_2","doi-asserted-by":"publisher","DOI":"10.1186\/s13059-022-02635-9"}],"container-title":["mBio"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/journals.asm.org\/doi\/pdf\/10.1128\/mbio.03645-25","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/journals.asm.org\/doi\/pdf\/10.1128\/mbio.03645-25","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,3,11]],"date-time":"2026-03-11T13:05:00Z","timestamp":1773234300000},"score":1,"resource":{"primary":{"URL":"https:\/\/journals.asm.org\/doi\/10.1128\/mbio.03645-25"}},"subtitle":[],"editor":[{"given":"Katrine","family":"Whiteson","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"editor"}]}],"short-title":[],"issued":{"date-parts":[[2026,3,11]]},"references-count":25,"journal-issue":{"issue":"3","published-print":{"date-parts":[[2026,3,11]]}},"alternative-id":["10.1128\/mbio.03645-25"],"URL":"https:\/\/doi.org\/10.1128\/mbio.03645-25","relation":{},"ISSN":["2150-7511"],"issn-type":[{"value":"2150-7511","type":"electronic"}],"subject":[],"published":{"date-parts":[[2026,3,11]]},"assertion":[{"value":"2025-12-03","order":0,"name":"received","label":"Received","group":{"name":"publication_history","label":"Publication History"}},{"value":"2026-01-07","order":2,"name":"accepted","label":"Accepted","group":{"name":"publication_history","label":"Publication History"}},{"value":"2026-02-05","order":3,"name":"published","label":"Published","group":{"name":"publication_history","label":"Publication History"}}],"article-number":"e03645-25"}}