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Using 2,409 nasopharyngeal swabs from 300 infants enrolled in a prospective cohort study in Botswana, we perform a detailed analysis of factors that influence the dynamics of bacterial pathobiont colonization during infancy. We quantify the extent to which viruses increase the acquisition of\n                    <jats:italic>Haemophilus influenzae<\/jats:italic>\n                    ,\n                    <jats:italic>Moraxella catarrhalis<\/jats:italic>\n                    , and\n                    <jats:italic>Streptococcus pneumoniae<\/jats:italic>\n                    . We provide evidence of cooperative interactions between these pathobionts while identifying host characteristics and environmental exposures that influence the odds of pathobiont colonization during early life. Using 16S rRNA gene sequencing, we demonstrate that respiratory viruses result in losses of putatively beneficial\n                    <jats:italic>Corynebacterium<\/jats:italic>\n                    and\n                    <jats:italic>Streptococcus<\/jats:italic>\n                    species that are associated with a lower odds of pathobiont acquisition. These findings provide important insights into viral-bacterial relationships in the upper respiratory tract of direct relevance to respiratory infections and suggest that the bacterial microbiota is a potentially modifiable mechanism by which viruses promote bacterial respiratory infections.\n                  <\/jats:p>","DOI":"10.1038\/s41467-025-60552-4","type":"journal-article","created":{"date-parts":[[2025,6,4]],"date-time":"2025-06-04T12:02:15Z","timestamp":1749038535000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":10,"title":["Role of the upper airway microbiota in respiratory virus and bacterial pathobiont dynamics in the first year of life"],"prefix":"10.1038","volume":"16","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-8819-2315","authenticated-orcid":false,"given":"Matthew S.","family":"Kelly","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Pixu","family":"Shi","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sifelane C.","family":"Boiditswe","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Emily","family":"Qin","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-9002-8207","authenticated-orcid":false,"given":"Andrew P.","family":"Steenhoff","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Tiny","family":"Mazhani","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Mohamed Z.","family":"Patel","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7725-3052","authenticated-orcid":false,"given":"Coleen K.","family":"Cunningham","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5976-5206","authenticated-orcid":false,"given":"John F.","family":"Rawls","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Kathy","family":"Luinstra","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jodi","family":"Gilchrist","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Julia","family":"Maciejewski","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-5079-9920","authenticated-orcid":false,"given":"Jillian H.","family":"Hurst","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Patrick C.","family":"Seed","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"David","family":"Bulir","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Marek","family":"Smieja","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2025,6,4]]},"reference":[{"key":"60552_CR1","unstructured":"Bender, R. 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