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Microbiome disturbance and resilience dynamics of the upper respiratory tract during influenza A virus infection

Author

Listed:
  • Drishti Kaul

    (J. Craig Venter Institute)

  • Raveen Rathnasinghe

    (Pontificia Universidad Católica de Chile)

  • Marcela Ferres

    (Pontificia Universidad Católica de Chile)

  • Gene S. Tan

    (J. Craig Venter Institute
    University of California San Diego)

  • Aldo Barrera

    (Pontificia Universidad Católica de Chile
    Millennium Institute on Immunology and Immunotherapy)

  • Brett E. Pickett

    (J. Craig Venter Institute
    Brigham Young University)

  • Barbara A. Methe

    (J. Craig Venter Institute
    Department of Medicine, University of Pittsburgh)

  • Suman R. Das

    (J. Craig Venter Institute)

  • Isolda Budnik

    (Pontificia Universidad Católica de Chile)

  • Rebecca A. Halpin

    (J. Craig Venter Institute)

  • David Wentworth

    (J. Craig Venter Institute
    Centers for Disease Control and Prevention)

  • Mirco Schmolke

    (Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai
    University of Geneva)

  • Ignacio Mena

    (Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai)

  • Randy A. Albrecht

    (Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai)

  • Indresh Singh

    (J. Craig Venter Institute)

  • Karen E. Nelson

    (J. Craig Venter Institute)

  • Adolfo García-Sastre

    (Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai
    Icahn School of Medicine at Mount Sinai)

  • Chris L. Dupont

    (J. Craig Venter Institute)

  • Rafael A. Medina

    (Pontificia Universidad Católica de Chile
    Millennium Institute on Immunology and Immunotherapy
    Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai)

Abstract

Infection with influenza can be aggravated by bacterial co-infections, which often results in disease exacerbation. The effects of influenza infection on the upper respiratory tract (URT) microbiome are largely unknown. Here, we report a longitudinal study to assess the temporal dynamics of the URT microbiomes of uninfected and influenza virus-infected humans and ferrets. Uninfected human patients and ferret URT microbiomes have stable healthy ecostate communities both within and between individuals. In contrast, infected patients and ferrets exhibit large changes in bacterial community composition over time and between individuals. The unhealthy ecostates of infected individuals progress towards the healthy ecostate, coinciding with viral clearance and recovery. Pseudomonadales associate statistically with the disturbed microbiomes of infected individuals. The dynamic and resilient microbiome during influenza virus infection in multiple hosts provides a compelling rationale for the maintenance of the microbiome homeostasis as a potential therapeutic target to prevent IAV associated bacterial co-infections.

Suggested Citation

  • Drishti Kaul & Raveen Rathnasinghe & Marcela Ferres & Gene S. Tan & Aldo Barrera & Brett E. Pickett & Barbara A. Methe & Suman R. Das & Isolda Budnik & Rebecca A. Halpin & David Wentworth & Mirco Schm, 2020. "Microbiome disturbance and resilience dynamics of the upper respiratory tract during influenza A virus infection," Nature Communications, Nature, vol. 11(1), pages 1-12, December.
    • Handle: RePEc:nat:natcom:v:11:y:2020:i:1:d:10.1038_s41467-020-16429-9
    DOI: 10.1038/s41467-020-16429-9
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