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Background  Upper respiratory infections (URI) and their complications are a major healthcare burden for pediatric populations. Although the microbiology of the nasopharynx is an important determinant of the complications of URI, little is known of the nasopharyngeal (NP) microbiota of children, the factors that affect its composition, and its precise relationship with URI.    Results  Healthy children ( n  = 47) aged 49–84 months from a prospective cohort study based in Wisconsin, USA, were examined. Demographic and clinical data and NP swab samples were obtained from participants upon entry to the study. All NP samples were profiled for bacterial microbiota using a phylogenetic microarray, and these data were related to demographic characteristics and upper respiratory health outcomes. The composition of the NP bacterial community of children was significantly related prior to the history of acute sinusitis ( R  2  = 0.070,  P  < 0.009). History of acute sinusitis was associated with significant depletion in relative abundance of taxa including  Faecalibacterium prausnitzii  and  Akkermansia  spp. and enrichment of  Moraxella nonliquefaciens . Enrichment of  M. nonliquefaciens  was also a characteristic of baseline NP samples of children who subsequently developed acute sinusitis over the 1-year study period. Time to develop URI was significantly positively correlated with NP diversity, and children who experienced more frequent URIs exhibited significantly diminished NP microbiota diversity ( P  ≤ 0.05).    Conclusions  These preliminary data suggest that previous history of acute sinusitis influences the composition of the NP microbiota, characterized by a depletion in relative abundance of specific taxa. Diminished diversity was associated with more frequent URIs.    Electronic supplementary material  The online version of this article (doi:10.1186/s40168-016-0179-9) contains supplementary material, which is available to authorized users.

Nasopharyngeal microbiota composition of children is related to the frequency of upper respiratory infection and acute sinusitis