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

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 Schmolke, Ignacio Mena, Randy A. Albrecht, Indresh Singh, Karen E. Nelson, Adolfo García-Sastre, Chris L. Dupont () and Rafael A. Medina ()
Additional contact information
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
Aldo Barrera: Pontificia Universidad Católica de Chile
Brett E. Pickett: J. Craig Venter Institute
Barbara A. Methe: J. Craig Venter Institute
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
Mirco Schmolke: Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai
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
Chris L. Dupont: J. Craig Venter Institute
Rafael A. Medina: Pontificia Universidad Católica de Chile

Nature Communications, 2020, vol. 11, issue 1, 1-12

Abstract: 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.

Date: 2020
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DOI: 10.1038/s41467-020-16429-9

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