Role of the upper airway microbiota in respiratory virus and bacterial pathobiont dynamics in the first year of life
Abstract The mechanisms by which respiratory viruses predispose to secondary bacterial infections remain poorly characterized. 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 o...
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| Format: | Article |
| Language: | English |
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Nature Portfolio
2025-06-01
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| Series: | Nature Communications |
| Online Access: | https://doi.org/10.1038/s41467-025-60552-4 |
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| author | Matthew S. Kelly Pixu Shi Sifelane C. Boiditswe Emily Qin Andrew P. Steenhoff Tiny Mazhani Mohamed Z. Patel Coleen K. Cunningham John F. Rawls Kathy Luinstra Jodi Gilchrist Julia Maciejewski Jillian H. Hurst Patrick C. Seed David Bulir Marek Smieja |
| author_facet | Matthew S. Kelly Pixu Shi Sifelane C. Boiditswe Emily Qin Andrew P. Steenhoff Tiny Mazhani Mohamed Z. Patel Coleen K. Cunningham John F. Rawls Kathy Luinstra Jodi Gilchrist Julia Maciejewski Jillian H. Hurst Patrick C. Seed David Bulir Marek Smieja |
| author_sort | Matthew S. Kelly |
| collection | DOAJ |
| description | Abstract The mechanisms by which respiratory viruses predispose to secondary bacterial infections remain poorly characterized. 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 Haemophilus influenzae, Moraxella catarrhalis, and Streptococcus pneumoniae. 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 Corynebacterium and Streptococcus 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. |
| format | Article |
| id | doaj-art-28f4f2cd18f14ec483c3a7ad480ecea0 |
| institution | OA Journals |
| issn | 2041-1723 |
| language | English |
| publishDate | 2025-06-01 |
| publisher | Nature Portfolio |
| record_format | Article |
| series | Nature Communications |
| spelling | doaj-art-28f4f2cd18f14ec483c3a7ad480ecea02025-08-20T02:05:38ZengNature PortfolioNature Communications2041-17232025-06-0116111310.1038/s41467-025-60552-4Role of the upper airway microbiota in respiratory virus and bacterial pathobiont dynamics in the first year of lifeMatthew S. Kelly0Pixu Shi1Sifelane C. Boiditswe2Emily Qin3Andrew P. Steenhoff4Tiny Mazhani5Mohamed Z. Patel6Coleen K. Cunningham7John F. Rawls8Kathy Luinstra9Jodi Gilchrist10Julia Maciejewski11Jillian H. Hurst12Patrick C. Seed13David Bulir14Marek Smieja15Botswana-University of Pennsylvania PartnershipDepartment of Biostatistics and Bioinformatics, Duke UniversityBotswana-University of Pennsylvania PartnershipDepartment of Biostatistics and Bioinformatics, Duke UniversityBotswana-University of Pennsylvania PartnershipUniversity of Botswana School of MedicineUniversity of Botswana School of MedicineDivision of Pediatric Infectious Diseases, University of California, IrvineDepartment of Molecular Genetics and Microbiology, Duke UniversityInfectious Disease Research Group, Research Institute of St. Joe’s HamiltonInfectious Disease Research Group, Research Institute of St. Joe’s HamiltonInfectious Disease Research Group, Research Institute of St. Joe’s HamiltonDivision of Pediatric Infectious Diseases, Duke UniversityDepartment of Pediatrics, Feinberg School of Medicine, Northwestern UniversityDepartment of Chemical Engineering, McMaster UniversityInfectious Disease Research Group, Research Institute of St. Joe’s HamiltonAbstract The mechanisms by which respiratory viruses predispose to secondary bacterial infections remain poorly characterized. 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 Haemophilus influenzae, Moraxella catarrhalis, and Streptococcus pneumoniae. 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 Corynebacterium and Streptococcus 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.https://doi.org/10.1038/s41467-025-60552-4 |
| spellingShingle | Matthew S. Kelly Pixu Shi Sifelane C. Boiditswe Emily Qin Andrew P. Steenhoff Tiny Mazhani Mohamed Z. Patel Coleen K. Cunningham John F. Rawls Kathy Luinstra Jodi Gilchrist Julia Maciejewski Jillian H. Hurst Patrick C. Seed David Bulir Marek Smieja Role of the upper airway microbiota in respiratory virus and bacterial pathobiont dynamics in the first year of life Nature Communications |
| title | Role of the upper airway microbiota in respiratory virus and bacterial pathobiont dynamics in the first year of life |
| title_full | Role of the upper airway microbiota in respiratory virus and bacterial pathobiont dynamics in the first year of life |
| title_fullStr | Role of the upper airway microbiota in respiratory virus and bacterial pathobiont dynamics in the first year of life |
| title_full_unstemmed | Role of the upper airway microbiota in respiratory virus and bacterial pathobiont dynamics in the first year of life |
| title_short | Role of the upper airway microbiota in respiratory virus and bacterial pathobiont dynamics in the first year of life |
| title_sort | role of the upper airway microbiota in respiratory virus and bacterial pathobiont dynamics in the first year of life |
| url | https://doi.org/10.1038/s41467-025-60552-4 |
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