Effect of Respiratory Tract Microbiome on Susceptibility to Viral Infections

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Investigators assert that the depletion of anaerobes appears to be linked to the onset of viral respiratory disease, suggesting the protective role of commensal anaerobic bacteria.
Investigators assert that the depletion of anaerobes appears to be linked to the onset of viral respiratory disease, suggesting the protective role of commensal anaerobic bacteria.

New data published in the European Journal of Clinical Microbiology & Infectious Diseases suggest that commensal respiratory microbiota play a significant role in susceptibility to viral infection.

Sequencing of the 16S rRNA gene was applied to nasopharyngeal samples from 177 patients with a viral respiratory infection: 26 symptomatic patients positive for influenza A, 27 for influenza B, 26 for respiratory syncytial virus, 28 for metapneumovirus, 23 for rhinovirus, and 47 virus-negative symptomatic patients. These samples were matched with sequencing from 48 healthy control patients to assess whether a specific microbiota profile is associated with symptomatic infection and/or with the presence of respiratory viruses.

Results indicated a significant decrease in bacterial alpha-diversity in symptomatic patients and a loss of healthy core microbiota species, specifically anaerobes and Prevotella spp. Investigators also identified 8 respiratory pathogens as more likely to be found in symptomatic patients, including Staphylococcus aureus, Haemophilus influenzae, Streptococcus pneumoniae, Moraxella catarrhalis, Dolosigranulum pigrum, and Corynebacterium propinquum/pseudodiphtheriticum. Asymptomatic patients had microbiota profiles similar to those of the healthy control patients, suggesting a role for the microbiota in clinical expression of infections.

The investigators report that, "to the best of our knowledge, this is the largest metagenomic study exploring the human nasopharyngeal microbiota of patients with viral respiratory illnesses and controls." However, high interindividual heterogeneity in microbiota composition was observed, meaning large numbers of subjects are required to reveal significant differences between groups. The study had another potential limitation, in that confounding factors correlated with reduced microbiota diversity may be present, such as recent antibiotic use. Information regarding other potential confounders such as vaccination, asthma, allergies, and smoking habitats were also not collected.

The investigators conclude that the observational data here show "the healthy nasopharyngeal microbiota is composed of a diverse and well-balanced aero-anaerobic bacterial core consortium, which is altered during respiratory infection." Along with antibiotics, investigators recommend that future work also focus on preventive or therapeutic interventions for maintaining and restoring healthy microbiota profiles.

Reference

Edouard S, Million M, Bachar D, et al. The nasopharyngeal microbiota in patients with viral respiratory tract infections is enriched in bacterial pathogens [published online July 22, 2018]. Eur J Clin Microbiol Infect Dis. doi: 10.1007/s10096-018-3305-8

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