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Role of the upper airway microbiota in respiratory virus and bacterial pathobiont dynamics in the first year of life

Author

Listed:
  • Matthew S. Kelly

    (Botswana-University of Pennsylvania Partnership
    Duke University
    Duke University)

  • Pixu Shi

    (Duke University)

  • Sifelane C. Boiditswe

    (Botswana-University of Pennsylvania Partnership)

  • Emily Qin

    (Duke University)

  • Andrew P. Steenhoff

    (Botswana-University of Pennsylvania Partnership
    Children’s Hospital of Philadelphia
    Children’s Hospital of Philadelphia)

  • Tiny Mazhani

    (University of Botswana School of Medicine)

  • Mohamed Z. Patel

    (University of Botswana School of Medicine)

  • Coleen K. Cunningham

    (Irvine)

  • John F. Rawls

    (Duke University)

  • Kathy Luinstra

    (Research Institute of St. Joe’s Hamilton)

  • Jodi Gilchrist

    (Research Institute of St. Joe’s Hamilton)

  • Julia Maciejewski

    (Research Institute of St. Joe’s Hamilton)

  • Jillian H. Hurst

    (Duke University)

  • Patrick C. Seed

    (Northwestern University)

  • David Bulir

    (McMaster University)

  • Marek Smieja

    (Research Institute of St. Joe’s Hamilton
    McMaster University)

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.

Suggested Citation

  • 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, 2025. "Role of the upper airway microbiota in respiratory virus and bacterial pathobiont dynamics in the first year of life," Nature Communications, Nature, vol. 16(1), pages 1-13, December.
  • Handle: RePEc:nat:natcom:v:16:y:2025:i:1:d:10.1038_s41467-025-60552-4
    DOI: 10.1038/s41467-025-60552-4
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    References listed on IDEAS

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    1. Himel Mallick & Ali Rahnavard & Lauren J McIver & Siyuan Ma & Yancong Zhang & Long H Nguyen & Timothy L Tickle & George Weingart & Boyu Ren & Emma H Schwager & Suvo Chatterjee & Kelsey N Thompson & Je, 2021. "Multivariable association discovery in population-scale meta-omics studies," PLOS Computational Biology, Public Library of Science, vol. 17(11), pages 1-27, November.
    2. Masahiro Yoshida & Kaylee B. Worlock & Ni Huang & Rik G. H. Lindeboom & Colin R. Butler & Natsuhiko Kumasaka & Cecilia Dominguez Conde & Lira Mamanova & Liam Bolt & Laura Richardson & Krzysztof Polans, 2022. "Local and systemic responses to SARS-CoV-2 infection in children and adults," Nature, Nature, vol. 602(7896), pages 321-327, February.
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