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Vaccines (Basel). 2017 Nov 3;5(4). pii: E40. doi: 10.3390/vaccines5040040.

Impact of the Respiratory Microbiome on Host Responses to Respiratory Viral Infection.

Author information

1
Hospices Civils de Lyon, Centre National de Reference des virus des Infections Respiratoires France Sud, Laboratoire de Virologie, Institut des Agents Infectieux, Groupement Hospitalier Nord, F-69317 Lyon CEDEX 04, France. maxime.pichon01@chu-lyon.fr.
2
Université de Lyon, Faculté de Médecine Lyon Est, Centre International de Recherche en Infectiologie (CIRI), Inserm U1111, Centre National de la Recherche Scientifique (CNRS) UMR5308, Ecole Nationale Supérieure de Lyon (ENS), équipe Virpath, F-69372 Lyon CEDEX 08, France. maxime.pichon01@chu-lyon.fr.
3
Hospices Civils de Lyon, Centre National de Reference des virus des Infections Respiratoires France Sud, Laboratoire de Virologie, Institut des Agents Infectieux, Groupement Hospitalier Nord, F-69317 Lyon CEDEX 04, France. bruno.lina@chu-lyon.fr.
4
Université de Lyon, Faculté de Médecine Lyon Est, Centre International de Recherche en Infectiologie (CIRI), Inserm U1111, Centre National de la Recherche Scientifique (CNRS) UMR5308, Ecole Nationale Supérieure de Lyon (ENS), équipe Virpath, F-69372 Lyon CEDEX 08, France. bruno.lina@chu-lyon.fr.
5
Hospices Civils de Lyon, Centre National de Reference des virus des Infections Respiratoires France Sud, Laboratoire de Virologie, Institut des Agents Infectieux, Groupement Hospitalier Nord, F-69317 Lyon CEDEX 04, France. laurence.josset@chu-lyon.fr.
6
Université de Lyon, Faculté de Médecine Lyon Est, Centre International de Recherche en Infectiologie (CIRI), Inserm U1111, Centre National de la Recherche Scientifique (CNRS) UMR5308, Ecole Nationale Supérieure de Lyon (ENS), équipe Virpath, F-69372 Lyon CEDEX 08, France. laurence.josset@chu-lyon.fr.

Abstract

Viruses are responsible for most of both upper and lower acute respiratory infections (ARIs). The microbiome-the ecological community of microorganisms sharing the body space, which has gained considerable interest over the last decade-is modified in health and disease states. Even if most of these disturbances have been previously described in relation to chronic disorders of the gastrointestinal microbiome, after a short reminder of microbiome characteristics and methods of characterization, this review will describe the impact of the microbiome (mainly respiratory) on host responses to viral ARIs. The microbiome has a direct environmental impact on the host cells but also an indirect impact on the immune system, by enhancing innate or adaptive immune responses. In microbial infections, especially in viral infections, these dramatic modifications could lead to a dramatic impact responsible for severe clinical outcomes. Studies focusing on the microbiome associated with transcriptomic analyses of the host response and deep characterization of the pathogen would lead to a better understanding of viral pathogenesis and open avenues for biomarker development and innovative therapeutics.

KEYWORDS:

16S; NGS; respiratory microbiome; respiratory tract; viral infections; whole genome sequencing

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