The airway microbiota of neonates colonized with asthma-associated pathogenic bacteria

Jonathan Thorsen, Xuan Ji Li, Shuang Peng, Rikke Bjersand Sunde, Shiraz A. Shah, Madhumita Bhattacharyya, Casper Sahl Poulsen, Christina Egeø Poulsen, Cristina Leal Rodriguez, Michael Widdowson, Avidan Uriel Neumann, Urvish Trivedi, Bo Chawes, Klaus Bønnelykke, Hans Bisgaard, Søren J. Sørensen, Jakob Stokholm

Research output: Contribution to journalArticlepeer-review

2 Scopus citations


Culture techniques have associated colonization with pathogenic bacteria in the airways of neonates with later risk of childhood asthma, whereas more recent studies utilizing sequencing techniques have shown the same phenomenon with specific anaerobic taxa. Here, we analyze nasopharyngeal swabs from 1 month neonates in the COPSAC2000 prospective birth cohort by 16S rRNA gene sequencing of the V3-V4 region in relation to asthma risk throughout childhood. Results are compared with previous culture results from hypopharyngeal aspirates from the same cohort and with hypopharyngeal sequencing data from the later COPSAC2010 cohort. Nasopharyngeal relative abundance values of Streptococcus pneumoniae, Haemophilus influenzae, and Moraxella catarrhalis are associated with the same species in the hypopharyngeal cultures. A combined pathogen score of these bacteria’s abundance values is associated with persistent wheeze/asthma by age 7. No other taxa are associated. Compared to the hypopharyngeal aspirates from the COPSAC2010 cohort, the anaerobes Veillonella and Prevotella, which have previously been implicated in asthma development, are less commonly detected in the COPSAC2000 nasopharyngeal samples, but correlate with the pathogen score, hinting at latent community structures that bridge current and previous results. These findings have implications for future asthma prevention efforts.

Original languageEnglish
Article number6668
JournalNature Communications
Issue number1
StatePublished - 20 Oct 2023
Externally publishedYes

Bibliographical note

Publisher Copyright:
© 2023, Springer Nature Limited.


We express our deepest gratitude to the children and families of the COPSAC cohort studies for all their support and commitment. We acknowledge and appreciate the unique efforts of the COPSAC research team. We thank Ulrik Ralfkiær for their graphical assistance. All funding received by COPSAC is listed on . The Lundbeck Foundation (Grant no R16-A1694); The Ministry of Health (Grant no 903516); the Danish Council for Strategic Research (Grant no 0603-00280B) and The Capital Region Research Foundation have provided core support to the COPSAC research center. JS has received funding from the Danish Council for Independent Research (Grant no. 8045-00081B).

FundersFunder number
Capital Region Research Foundation
Strategiske Forskningsråd0603-00280B
Lundbeck FoundationR16-A1694
Danmarks Frie Forskningsfond8045-00081B
Ministeriet Sundhed Forebyggelse903516


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