Characterization of the nasopharyngeal microbiota of patients with viral respiratory infection reveals enrichment in pathogenic bacteria and a decrease of Diversity.

The nasopharynx was the primary site of colonization by respiratory pathogen that constitutes the port of entrance in the respiratory tract. The role of mucosal microbiota in infection has been recently emphasized, therefore we aimed to assess if a specific respiratory profile is associated with viral respiratory infection.Nasopharyngeal samples were collected over a 2 months period from 130 virus- positive symptomatic patients with respiratory infection, 47 virus-negative symptomatic patients and 48 controls. All the samples were analyzed by 16S ribosomal RNA sequencing.Microbiota profiles differed between healthy subject and patient with respiratory infection.