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Unlike the gut microbiome, the nasal microbiome has not been studied in large numbers of people. Here, we define the nasal microbiome in ~1100 individuals from the CARRIAGE study (ISRCTN: ISRCTN10474633) and combine with\n                    <jats:italic>S. aureus<\/jats:italic>\n                    culture data. We identify seven community state types (CST), including two CSTs more common in females. Approximately 70% of those who are persistently colonised with\n                    <jats:italic>S. aureus<\/jats:italic>\n                    have a CST dominated by\n                    <jats:italic>S. aureus<\/jats:italic>\n                    , while non-carriers are distributed across the other six CSTs. Intermittent carriers are not a unique state but have microbiomes that resemble non- or persistent carriers. Persistent carriage is positively associated with\n                    <jats:italic>S. aureus<\/jats:italic>\n                    abundance, and negatively associated with three\n                    <jats:italic>Corynebacterium<\/jats:italic>\n                    species,\n                    <jats:italic>Dolosigranulum pigrum<\/jats:italic>\n                    ,\n                    <jats:italic>Staphylococcus epidermidis<\/jats:italic>\n                    , and\n                    <jats:italic>Moraxella catarrhalis<\/jats:italic>\n                    ; the microbiome can be exploited with machine learning to accurately predict the persistence of\n                    <jats:italic>S. aureus<\/jats:italic>\n                    colonisation. Finally, we find that certain\n                    <jats:italic>S. aureus<\/jats:italic>\n                    lineages are better adapted to colonisation than others. Our data provides a comprehensive view of the nasal microbiome with respect to\n                    <jats:italic>S. aureus<\/jats:italic>\n                    colonisation, describing two key states: a\n                    <jats:italic>S. aureus<\/jats:italic>\n                    dominated CST in which\n                    <jats:italic>S. aureus<\/jats:italic>\n                    shapes the microbiome, and CSTs in which\n                    <jats:italic>S. aureus<\/jats:italic>\n                    is rare or absent.\n                  <\/jats:p>","DOI":"10.1038\/s41467-025-66564-4","type":"journal-article","created":{"date-parts":[[2025,12,2]],"date-time":"2025-12-02T10:02:39Z","timestamp":1764669759000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":21,"title":["Large-scale characterisation of the nasal microbiome redefines Staphylococcus aureus colonisation status"],"prefix":"10.1038","volume":"16","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-5938-8172","authenticated-orcid":false,"given":"Dinesh","family":"Aggarwal","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-5368-7027","authenticated-orcid":false,"given":"Katherine L.","family":"Bellis","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Beth","family":"Blane","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Marcus C.","family":"de Goffau","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Josef","family":"Wagner","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-1561-8244","authenticated-orcid":false,"given":"Duncan Y. 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