{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,24]],"date-time":"2026-10-24T01:43:18Z","timestamp":1792806198301,"version":"4.5.0"},"reference-count":26,"publisher":"Public Library of Science (PLoS)","issue":"12","license":[{"start":{"date-parts":[[2021,12,28]],"date-time":"2021-12-28T00:00:00Z","timestamp":1640649600000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"publisher","award":["R01 AI097172"],"award-info":[{"award-number":["R01 AI097172"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["www.plosone.org"],"crossmark-restriction":false},"short-container-title":["PLoS ONE"],"abstract":"<jats:sec id=\"sec001\">\n<jats:title>Background<\/jats:title>\n<jats:p>Distinct bacterial upper airway microbiota structures have been described in pediatric populations, and relate to risk of respiratory viral infection and, exacerbations of asthma. We hypothesized that distinct nasopharyngeal (NP) microbiota structures exist in pediatric populations, relate to environmental exposures and modify risk of acute sinusitis or upper respiratory infection (URI) in children.<\/jats:p>\n<\/jats:sec>\n<jats:sec id=\"sec002\">\n<jats:title>Methods<\/jats:title>\n<jats:p>Bacterial 16S rRNA profiles from nasopharyngeal swabs (n = 354) collected longitudinally over a one-year period from 58 children, aged four to seven years, were analyzed and correlated with environmental variables, URI, and sinusitis outcomes.<\/jats:p>\n<\/jats:sec>\n<jats:sec id=\"sec003\">\n<jats:title>Results<\/jats:title>\n<jats:p>Variance in nasopharyngeal microbiota composition significantly related to clinical outcomes, participant characteristics and environmental exposures including dominant bacterial genus, season, daycare attendance and tobacco exposure. Four distinct nasopharyngeal microbiota structures (Cluster I-IV) were evident and differed with respect to URI and sinusitis outcomes. These clusters were characteristically either dominated by <jats:italic>Moraxella<\/jats:italic> with sparse underlying taxa (Cluster I), comprised of a non-dominated, diverse microbiota (Cluster II), dominated by <jats:italic>Alloiococcus\/Corynebacterium<\/jats:italic> (Cluster III), or by <jats:italic>Haemophilus<\/jats:italic> (Cluster IV). Cluster I was associated with increased risk of URI and sinusitis (RR = 1.18, p = 0.046; RR = 1.25, p = 0.009, respectively) in the population studied.<\/jats:p>\n<\/jats:sec>\n<jats:sec id=\"sec004\">\n<jats:title>Conclusion<\/jats:title>\n<jats:p>In a pediatric population, URI and sinusitis associate with the presence of <jats:italic>Moraxella<\/jats:italic>-dominated NP microbiota.<\/jats:p>\n<\/jats:sec>","DOI":"10.1371\/journal.pone.0261179","type":"journal-article","created":{"date-parts":[[2021,12,28]],"date-time":"2021-12-28T19:21:47Z","timestamp":1640719307000},"page":"e0261179","update-policy":"https:\/\/doi.org\/10.1371\/journal.pone.corrections_policy","source":"Crossref","is-referenced-by-count":32,"title":["Moraxella-dominated pediatric nasopharyngeal microbiota associate with upper respiratory infection and sinusitis"],"prefix":"10.1371","volume":"16","author":[{"given":"Kathryn E.","family":"McCauley","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Gregory","family":"DeMuri","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Kole","family":"Lynch","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Douglas W.","family":"Fadrosh","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Clark","family":"Santee","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Nabeetha N.","family":"Nagalingam","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ellen R.","family":"Wald","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-5695-7336","authenticated-orcid":true,"given":"Susan V.","family":"Lynch","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"340","published-online":{"date-parts":[[2021,12,28]]},"reference":[{"key":"pone.0261179.ref001","doi-asserted-by":"crossref","first-page":"133","DOI":"10.1016\/j.jpeds.2015.12.034","article-title":"Clinical Features, Virus Identification, and Sinusitis as a Complication of Upper Respiratory Tract Illness in Children Ages 4\u20137 Years","volume":"171","author":"GP DeMuri","year":"2016","journal-title":"The Journal of Pediatrics"},{"key":"pone.0261179.ref002","doi-asserted-by":"crossref","first-page":"3","DOI":"10.1177\/00034894041130S502","article-title":"Epidemiology and economic impact of rhinosinusitis.","volume":"193","author":"VK Anand","year":"2004","journal-title":"Ann Otol Rhinol Laryngol Suppl"},{"key":"pone.0261179.ref003","doi-asserted-by":"crossref","first-page":"1045","DOI":"10.1093\/cid\/cix941","article-title":"Dynamics of Bacterial Colonization With Streptococcus pneumoniae, Haemophilus influenzae, and Moraxella catarrhalis During Symptomatic and Asymptomatic Viral Upper Respiratory Tract Infection","volume":"66","author":"GP DeMuri","year":"2018","journal-title":"Clin Infect Dis"},{"key":"pone.0261179.ref004","doi-asserted-by":"crossref","first-page":"34","DOI":"10.1186\/s40168-016-0179-9","article-title":"Nasopharyngeal microbiota composition of children is related to the frequency of upper respiratory infection and acute sinusitis","volume":"4","author":"CA Santee","year":"2016","journal-title":"Microbiome"},{"key":"pone.0261179.ref005","doi-asserted-by":"crossref","first-page":"803","DOI":"10.1097\/INF.0000000000000278","article-title":"Acute bacterial sinusitis complicating viral upper respiratory tract infection in young children","volume":"33","author":"T Marom","year":"2014","journal-title":"Pediatr Infect Dis J"},{"key":"pone.0261179.ref006","article-title":"Illness in the Home. 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childhood multisensitized atopy and T cell differentiation","volume":"22","author":"KE Fujimura","year":"2016","journal-title":"Nat Med"},{"key":"pone.0261179.ref010","doi-asserted-by":"crossref","first-page":"335","DOI":"10.1038\/nmeth.f.303","article-title":"QIIME allows analysis of high-throughput community sequencing data","volume":"7","author":"JG Caporaso","year":"2010","journal-title":"Nat Methods"},{"key":"pone.0261179.ref011","doi-asserted-by":"crossref","first-page":"2460","DOI":"10.1093\/bioinformatics\/btq461","article-title":"Search and clustering orders of magnitude faster than BLAST","volume":"26","author":"RC Edgar","year":"2010","journal-title":"Bioinformatics"},{"key":"pone.0261179.ref012","doi-asserted-by":"crossref","first-page":"266","DOI":"10.1093\/bioinformatics\/btp636","article-title":"PyNAST: a flexible tool for aligning sequences to a template alignment","volume":"26","author":"JG Caporaso","year":"2010","journal-title":"Bioinformatics"},{"key":"pone.0261179.ref013","doi-asserted-by":"crossref","first-page":"5069","DOI":"10.1128\/AEM.03006-05","article-title":"Greengenes, a chimera-checked 16S rRNA gene database and workbench compatible with ARB","volume":"72","author":"TZ DeSantis","year":"2006","journal-title":"Appl Environ Microbiol"},{"key":"pone.0261179.ref014","doi-asserted-by":"crossref","first-page":"2461","DOI":"10.1128\/JCM.00075-14","article-title":"Improved Molecular Typing Assay for Rhinovirus Species A, B, and C","volume":"52","author":"YA Bochkov","year":"2014","journal-title":"J Clin Microbiol"},{"key":"pone.0261179.ref015","first-page":"1","article-title":"The R Package geepack for Generalized Estimating Equations","volume":"15","author":"S H\u00f8jsgaard","year":"2005","journal-title":"Journal of Statistical Software"},{"key":"pone.0261179.ref016","author":"J Oksanen","year":"2016","journal-title":"vegan: Community Ecology 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Kloepfer","year":"2014","journal-title":"J Allergy Clin Immunol"},{"key":"pone.0261179.ref023","doi-asserted-by":"crossref","first-page":"279","DOI":"10.1097\/QCO.0b013e3283298e4e","article-title":"Virulence mechanisms of Moraxella in the pathogenesis of infection","volume":"22","author":"ML Perez Vidakovics","year":"2009","journal-title":"Curr Opin Infect Dis"},{"key":"pone.0261179.ref024","doi-asserted-by":"crossref","first-page":"704","DOI":"10.1016\/j.chom.2015.03.008","article-title":"The Infant Nasopharyngeal Microbiome Impacts Severity of Lower Respiratory Infection and Risk of Asthma Development.","volume":"17","author":"SM Teo","year":"2015","journal-title":"Cell Host & Microbe"},{"key":"pone.0261179.ref025","doi-asserted-by":"crossref","first-page":"2","DOI":"10.1186\/s40168-017-0385-0","article-title":"The association between anterior nares and nasopharyngeal microbiota in infants hospitalized for bronchiolitis","volume":"6","author":"PN 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