The nasopharyngeal microbiota in patients with viral respiratory tract infections is enriched in bacterial pathogens

  • Sophie Edouard
  • Matthieu Million
  • Dipankar Bachar
  • Grégory Dubourg
  • Caroline Michelle
  • Laetitia Ninove
  • Rémi Charrel
  • Didier RaoultEmail author
Original Article


The nasopharynx is the primary site of colonization by respiratory pathogen that constitutes the port of entrance in the respiratory tract. The role of mucosal respiratory microbiota in infection has been recently emphasized; therefore, we aimed to assess if a specific respiratory microbiota profile was associated with symptomatic infection and/or with presence of respiratory viruses. We performed a case-control study to characterize the healthy respiratory microbiota and its alteration during acute viral infections. Next-generation sequencing of the 16S rRNA gene was applied to 225 nasopharyngeal samples from 177 patients with viral respiratory infection and 48 matched healthy controls. We evidenced an important decrease of bacterial alpha-diversity in patients with symptomatic respiratory infection and a loss of the healthy core microbiota, specifically anaerobes and Prevotella spp. Moreover, eight respiratory pathogens were enriched in these patients, including Staphylococcus aureus, Haemophilus influenzae, Streptococcus pneumoniae, Moraxella catarrhalis, Dol osigranulum pigrum and Corynebacterium propinquum/pseudodiphtheriticum, whose role in respiratory infection is unclear. The asymptomatic carrier of influenza harbors a microbiota similar to healthy subjects, suggesting a critical role of microbiota in the clinical expression of viruses. These data suggest that the commensal microbiota plays a significant role in susceptibility to viral infection. The frequent co-detection of virus and bacteria raises the question of a strategy to prevent bacterial disease, focusing on the prevention of nasopharyngeal colonization through effective antibiotic treatment. In addition to antibiotics, further studies should test preventive or therapeutic interventions for maintaining or restoring a healthy nasopharyngeal microbiota.


Human Respiratory infection Microbiome Microbiota Virus Respiratory tract infection 



This work was supported by the French Government under the “Investissements d’avenir” (Investments for the Future) program managed by the Agence Nationale de la Recherche (ANR, fr: National Agency for Research), (reference: Méditerranée Infection 10-IAHU-03).This work was also supported by Région Provence Alpes Côte d’Azur and European funding FEDER PRIMMI (Fonds Européen de Développement Régional - Plateformes de Recherche et d'Innovation Mutualisées Méditerranée Infection).

Compliance with ethical standards

Conflict of interest

The authors declare that they have no conflict of interest.

Ethical approval

The study was approved by the local Ethics Committee (number 2016-016).

Informed consent

Written informed consent was obtained for all the controls included on a voluntary basis. For cases, metagenomics was performed on excess respiratory sample received in our laboratory for routine diagnosis of viral respiratory infections. Under the French law, patient consent was not required for this type of non-interventional study, provided the patients had received information and retained the right to oppose the use of excess respiratory samples and anonymized medical data (14–15).

Supplementary material

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ESM 1 (DOCX 555 kb)
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Copyright information

© Springer-Verlag GmbH Germany, part of Springer Nature 2018

Authors and Affiliations

  • Sophie Edouard
    • 1
  • Matthieu Million
    • 1
  • Dipankar Bachar
    • 1
  • Grégory Dubourg
    • 1
  • Caroline Michelle
    • 1
  • Laetitia Ninove
    • 2
  • Rémi Charrel
    • 2
  • Didier Raoult
    • 1
    Email author
  1. 1.Aix Marseille Univ, IRD, APHM, MEPHIIHU-Méditerranée InfectionMarseilleFrance
  2. 2.Unité des Virus Émergents, Aix-Marseille Univ, IRD 190, Inserm 1207IHU Méditerranée InfectionMarseilleFrance

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