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We investigated whether microbial taxonomic, ecological, and inferred functional features could distinguish LSIL regression from progression and improve risk stratification.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Results<\/jats:title>\n                    <jats:p>\n                      The cervicovaginal microbiome of 90 women with LSIL and known clinical outcomes was profiled using 16S rRNA gene sequencing. Overall microbiome diversity and composition did not differ significantly between regression and progression groups. Instead, microbial profiles clustered primarily by community state type (CST), with CST I-B nominally more frequent among regression cases. Within\n                      <jats:italic>Lactobacillus<\/jats:italic>\n                      -dominated communities, CST I-B exhibited distinct inferred functional profiles characterized by enrichment of carbohydrate metabolism and fermentation pathways and relative depletion of nucleotide biosynthesis pathways compared with CST I-A. Exploratory logistic regression models based on age, or microbiome taxa alone, showed limited discriminatory performance, whereas an integrated model incorporating age, microbiome, and inferred functional pathway features improved apparent discrimination between regression and progression in this cohort (AUC\u2009=\u20090.76, 95% CI 0.66\u20130.86).\n                    <\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Conclusions<\/jats:title>\n                    <jats:p>Differences in microbial community organization and inferred functional profiles were observed to be associated with LSIL clinical trajectories, whereas taxonomic composition alone showed limited discriminatory value. Integrating microbial taxonomic, ecological, and functional features modestly improved the apparent discrimination of LSIL outcomes, suggesting that inferred functional features may provide complementary information that warrants future research.<\/jats:p>\n                  <\/jats:sec>","DOI":"10.1186\/s12866-026-05648-7","type":"journal-article","created":{"date-parts":[[2026,9,12]],"date-time":"2026-09-12T10:33:19Z","timestamp":1789209199000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":2,"title":["Inferred functional microbiome features are associated with clinical trajectories of low-grade cervical lesions"],"prefix":"10.1186","volume":"26","author":[{"given":"Milan","family":"Stosic","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4260-0509","authenticated-orcid":false,"given":"Mariano A.","family":"Molina","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Dhananjay","family":"Mukhedkar","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sadaf Sakina","family":"Hassan","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Anna","family":"Sahlin","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Cristina Ruiz","family":"Ballester","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jiangrong","family":"Wang","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Laila Sara Arroyo","family":"M\u00fchr","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2026,9,12]]},"reference":[{"issue":"2","key":"5648_CR1","doi-asserted-by":"publisher","first-page":"e197","DOI":"10.1016\/S2214-109X(22)00501-0","volume":"11","author":"D Singh","year":"2023","unstructured":"Singh D, Vignat J, Lorenzoni V, Eslahi M, Ginsburg O, Lauby-Secretan B, et al. 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Trends Microbiol. 2025;33(11):1163\u201372.","journal-title":"Trends Microbiol"},{"issue":"2","key":"5648_CR49","first-page":"e01003","volume":"8","author":"A Carter Kayla","year":"2023","unstructured":"Carter Kayla A, Fodor Anthony A, Balkus Jennifer E, Zhang A, Serrano Myrna G, Buck Gregory A, et al. Vaginal Microbiome Metagenome Inference Accuracy: Differential Measurement Error according to Community Composition. mSystems. 2023;8(2):e01003\u201322.","journal-title":"mSystems"},{"issue":"1","key":"5648_CR50","doi-asserted-by":"publisher","first-page":"153","DOI":"10.1186\/s40168-024-01870-5","volume":"12","author":"LW Hugerth","year":"2024","unstructured":"Hugerth LW, Krog MC, Vomstein K, Du J, Bashir Z, Kaldhusdal V, et al. Defining Vaginal Community Dynamics: daily microbiome transitions, the role of menstruation, bacteriophages, and bacterial genes. Microbiome. 2024;12(1):153.","journal-title":"Microbiome"}],"container-title":["BMC Microbiology"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/link.springer.com\/article\/10.1186\/s12866-026-05648-7","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1186\/s12866-026-05648-7.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1186\/s12866-026-05648-7.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,9,12]],"date-time":"2026-09-12T10:46:22Z","timestamp":1789209982000},"score":1,"resource":{"primary":{"URL":"https:\/\/link.springer.com\/10.1186\/s12866-026-05648-7"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,9,12]]},"references-count":50,"journal-issue":{"issue":"1","published-online":{"date-parts":[[2026,12]]}},"alternative-id":["5648"],"URL":"https:\/\/doi.org\/10.1186\/s12866-026-05648-7","relation":{},"ISSN":["1471-2180"],"issn-type":[{"value":"1471-2180","type":"electronic"}],"subject":[],"published":{"date-parts":[[2026,9,12]]},"assertion":[{"value":"30 June 2026","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"9 September 2026","order":2,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"12 September 2026","order":3,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"Ethical approval for this study was obtained from the Regional Ethical Review Board in Stockholm (Dnr 2014\/1242). The study was conducted in accordance with the Declaration of Helsinki and relevant national regulations. Cases were identified through the Swedish National Cervical Screening Registry (NKCx) and subsequently linked to the Stockholm Cervical Screening Biobank using personal identification numbers. Cervical samples were retrieved following this linkage. All data were pseudonymized prior to analysis. Participation in the cervical screening programme includes informed consent for use of samples and data in research, in accordance with Swedish biobank legislation. Individuals who declined consent were not included.","order":1,"name":"Ethics","label":"Ethics approval and consent to participate","group":{"name":"EthicsHeading","label":"Declarations"}},{"value":"Not applicable.","order":2,"name":"Ethics","label":"Consent for publication","group":{"name":"EthicsHeading","label":"Declarations"}},{"value":"The authors declare no competing interests.","order":3,"name":"Ethics","label":"Competing interests","group":{"name":"EthicsHeading","label":"Declarations"}}],"article-number":"802"}}