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A nested case-control study from the Swedish Maternal Microbiome cohort was conducted, including 34 participants who sent at least one vaginal or fecal microbiome sample and questionnaire data before miscarrying (\n                    <jats:italic>n<\/jats:italic>\n                    \u2009=\u200934), and matched controls (\n                    <jats:italic>n<\/jats:italic>\n                    \u2009=\u2009105 for regression models,\n                    <jats:italic>n<\/jats:italic>\n                    \u2009=\u200927 for machine learning models). Non-vaccine type HPV (aOR 3.95, 95%CI 1.04\u201315.06) and vaginal microbiome with community state type (CST) II (aOR 6.52, 95%CI 1.58\u201326.98) or CST-IVB (aOR 4.18, 95%CI 1.08\u201316.18) in early pregnancy were associated with an increased risk of miscarriage. Furthermore, we explored six machine learning algorithms using 70% of the cohort for training and 30% for testing, for the prediction of miscarriage using vaginal (AUROC 85%), fecal (AUROC 81%) and questionnaire (AUROC 82%) data separately and combined (AUROC 82%). Our results highlight the urgency of HPV screening and vaccine development for women\u2019s reproductive health. Despite limitations, including a small number of miscarriage cases, our results indicate the potential for both vaginal and fecal microbiomes in the prediction of miscarriage.\n                  <\/jats:p>","DOI":"10.1038\/s41522-026-00956-2","type":"journal-article","created":{"date-parts":[[2026,3,13]],"date-time":"2026-03-13T18:32:28Z","timestamp":1773426748000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":5,"title":["Machine learning and the role of the vaginal and fecal microbiome in miscarriage: a matched case-control study"],"prefix":"10.1038","volume":"12","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-4663-9921","authenticated-orcid":false,"given":"Unnur","family":"Gudnadottir","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Stefanie","family":"Prast-Nielsen","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Nicole","family":"Wagner","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Luisa W.","family":"Hugerth","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Vilma Kuttainen","family":"Alderheim","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Anusha T.","family":"Antony","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Juan","family":"Du","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jorge Reis","family":"Guerreiro","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Fredrik","family":"Boulund","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Eva","family":"Wiberg-Itzel","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Lars","family":"Engstrand","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ina","family":"Schuppe-Koistinen","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Nele","family":"Brusselaers","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Emma","family":"Fransson","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2026,3,13]]},"reference":[{"key":"956_CR1","doi-asserted-by":"publisher","first-page":"839","DOI":"10.1053\/beog.2000.0123","volume":"14","author":"L Regan","year":"2000","unstructured":"Regan, L. & Rai, R. 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