Alterations in the upper respiratory bacterial microbiome in critically ill COVID-19 patients

The upper respiratory tract (URT) microbiome is a potential contributor to the acquisition and severity of respiratory viral infections. Associations between URT microbiota and severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection have been described but are limited at microbiota genus level and lack of functional interpretation. In this study, we performed whole metagenome sequencing to characterize the URT microbiome including bacterial communities and their encoded pathways, which was correlated to the presence of SARS-CoV-2 infection and clinical parameters.