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Yet it is largely unknown which human genetic variants shape a person\u2019s oral microbiome and potentially promote its dysbiosis\n                    <jats:sup>3\u20135<\/jats:sup>\n                    . We characterized the oral microbiomes of 12,519 people by re-analysing whole-genome sequencing reads from previously sequenced saliva-derived DNA. Human genetic variation at 11 loci (10 new) associated with variation in oral microbiome composition. Several of these related to carbohydrate availability; the strongest association (\n                    <jats:italic>P<\/jats:italic>\n                    \u2009=\u20093.0\u2009\u00d7\u200910\n                    <jats:sup>\u2212188<\/jats:sup>\n                    ) involved the common\n                    <jats:italic>FUT2<\/jats:italic>\n                    \u2009W154X loss-of-function variant, which associated with the abundances of 58 bacterial species. Human host genetics also seemed to powerfully shape genetic variation in oral bacterial species: these 11 host genetic variants also associated with variation of gene dosages in 68 regions of bacterial genomes. Common, multi-allelic copy number variation of\n                    <jats:italic>AMY1<\/jats:italic>\n                    , which encodes salivary amylase, associated with oral microbiome composition (\n                    <jats:italic>P<\/jats:italic>\n                    \u2009=\u20091.5\u2009\u00d7\u200910\n                    <jats:sup>\u221253<\/jats:sup>\n                    ) and with dentures use in UK Biobank (\n                    <jats:italic>P<\/jats:italic>\n                    \u2009=\u20095.9\u2009\u00d7\u200910\n                    <jats:sup>\u221235<\/jats:sup>\n                    ,\n                    <jats:italic>n<\/jats:italic>\n                    \u2009=\u2009418,039) but not with body mass index (\n                    <jats:italic>P<\/jats:italic>\n                    \u2009=\u20090.85), suggesting that salivary\u00a0amylase abundance impacts health by influencing the oral microbiome. Two other microbiome composition-associated loci,\n                    <jats:italic>FUT2<\/jats:italic>\n                    and\n                    <jats:italic>PITX1<\/jats:italic>\n                    , also significantly associated with dentures risk, collectively nominating numerous host\u2013microbial interactions that contribute to tooth decay.\n                  <\/jats:p>","DOI":"10.1038\/s41586-025-10037-7","type":"journal-article","created":{"date-parts":[[2026,1,28]],"date-time":"2026-01-28T16:02:19Z","timestamp":1769616139000},"page":"429-439","update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":21,"title":["Human and bacterial genetic variation shape oral microbiomes and health"],"prefix":"10.1038","volume":"651","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-0614-0189","authenticated-orcid":false,"given":"Nolan","family":"Kamitaki","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3128-3547","authenticated-orcid":false,"given":"Robert E.","family":"Handsaker","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-9116-1712","authenticated-orcid":false,"given":"Margaux L. 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