@article{5301940cf13a41278cea9ba2fef31512,
title = "Microbiome disturbance and resilience dynamics of the upper respiratory tract during influenza A virus infection",
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.",
author = "Drishti Kaul and Raveen Rathnasinghe and Marcela Ferres and Tan, {Gene S.} and Aldo Barrera and Pickett, {Brett E.} and Methe, {Barbara A.} and Suman Das and Isolda Budnik and Halpin, {Rebecca A.} and David Wentworth and Mirco Schmolke and Ignacio Mena and Albrecht, {Randy A.} and Indresh Singh and Nelson, {Karen E.} and Adolfo Garc{\'i}a-Sastre and Dupont, {Chris L.} and Medina, {Rafael A.}",
note = "Funding Information: The authors would like to thank research nurse Claudia Marco and the following clinical fellows and pediatricians that contributed to the recruitment of patients and the collection of samples used in this study: Marta Aravena, Catalina Gutierrez, Tania Lopez, Regina Perez, and Cecilia Vizcaya from the Department of Pediatric Infectious Diseases and Immunology, Facultad de Medicina, Pontificia Universidad Cat{\'o}lica de Chile, Santiago, Chile. This project has been partly funded with federal funds from the National Institute of Allergy and Infectious Diseases, National Institutes of Health, Department of Health and Human Services under Contract Number HHNS272200900007C/ HHSN266200700010C and Grant Number U19AI110819 (to JCVI), grants from the Comisi{\'o}n Nacional de Investigaci{\'o}n Cient{\'i}fica y Tecnol{\'o}gica (FONDECYT 1121172 and 1161791 to R.A.M.; and PIA ACT 1408 to R.A.M. and M.F.), and the Chilean Ministry of Economy, Development and Tourism (P09/016-F to R.A.M.). This study was also partially supported by CRIP (Center for Research in Influenza Pathogenesis), an NIAID funded Center of Excellence for Influenza Research and Surveillance (CEIRS, contract # HHSN272201400008C) and by NIAID grant U19AI135972 (to A.G.-S. and R.A.M.). Publisher Copyright: {\textcopyright} 2020, The Author(s).",
year = "2020",
month = dec,
day = "1",
doi = "10.1038/s41467-020-16429-9",
language = "English",
volume = "11",
journal = "Nature Communications",
issn = "2041-1723",
publisher = "Nature Publishing Group",
number = "1",
}