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Despite this, the microbiota of healthy adults remains understudied. To address this gap, we investigated the composition of the nasopharyngeal and oropharyngeal microbiota of healthy adults, focusing on the effect of <jats:italic>Streptococcus pneumoniae<\/jats:italic> carriage, smoking habits, and contact with children.<\/jats:p>\n              <\/jats:sec><jats:sec>\n                <jats:title>Results<\/jats:title>\n                <jats:p>Differential abundance analysis indicated that the microbiota of the oropharynx was significantly different from that of the nasopharynx (<jats:italic>P<\/jats:italic>\u2009&lt;\u20090.001) and highly discriminated by a balance between the classes Negativicutes and Bacilli (AUC of 0.979). Moreover, the oropharynx was associated with a more homogeneous microbiota across individuals, with just two vs<jats:italic>.<\/jats:italic> five clusters identified in the nasopharynx. We observed a shift in the nasopharyngeal microbiota of carriers vs<jats:italic>.<\/jats:italic> noncarriers with an increased relative abundance of <jats:italic>Streptococcus<\/jats:italic>, which summed up to 30% vs<jats:italic>.<\/jats:italic> 10% in noncarriers and was not mirrored in the oropharynx. The oropharyngeal microbiota of smokers had a lower diversity than the microbiota of nonsmokers, while no differences were observed in the nasopharyngeal microbiota. In particular, the microbiota of smokers, compared with nonsmokers, was enriched (on average 16-fold) in potential pathogenic taxa involved in periodontal diseases of the genera <jats:italic>Bacillus<\/jats:italic> and <jats:italic>Burkholderia<\/jats:italic> previously identified in metagenomic studies of cigarettes. The microbiota of adults with contact with children resembled the microbiota of children. Specifically, the nasopharyngeal microbiota of these adults had, on average, an eightfold increase in relative abundance in <jats:italic>Streptococcus<\/jats:italic> sp., <jats:italic>Moraxella catarrhalis<\/jats:italic>, and <jats:italic>Haemophilus influenzae,<\/jats:italic> pathobionts known to colonize the children\u2019s upper respiratory tract, and a fourfold decrease in <jats:italic>Staphylococcus aureus<\/jats:italic> and <jats:italic>Staphylococcus lugdunensis<\/jats:italic>.<\/jats:p>\n              <\/jats:sec><jats:sec>\n                <jats:title>Conclusions<\/jats:title>\n                <jats:p>Our study showed that, in adults, the presence of <jats:italic>S. pneumoniae<\/jats:italic> in the nasopharynx is associated with a shift in the microbiota and dominance of the <jats:italic>Streptococcus<\/jats:italic> genus. Furthermore, we observed that smoking habits are associated with an increase in bacterial genera commonly linked to periodontal diseases. Interestingly, our research also revealed that adults who have regular contact with children have a microbiota enriched in pathobionts frequently carried by children. These findings collectively contribute to a deeper understanding of how various factors influence the upper respiratory tract microbiota in adults.<\/jats:p>\n                \n              <\/jats:sec>","DOI":"10.1186\/s40168-023-01640-9","type":"journal-article","created":{"date-parts":[[2023,9,2]],"date-time":"2023-09-02T02:01:53Z","timestamp":1693620113000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":27,"title":["The upper respiratory tract microbiota of healthy adults is affected by Streptococcus pneumoniae carriage, smoking habits, and contact with children"],"prefix":"10.1186","volume":"11","author":[{"given":"A. 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