Oropharynx microbiome from volunteers following influenza challenge

Secondary bacterial infections are an important cause of morbidity and mortality associated with influenza infection. As bacterial disease can be caused by a disturbance of the host microbiome, we examined the impact of influenza on the upper respiratory tract microbiome in a human challenge study.The dynamics and ecology of the throat microbiome were examined during experimental influenza challenge of 52 previously healthy, seronegative adult volunteers who received Influenza A/Wisconsin/67/2005 (H3N2) by intranasal inoculation; 35 healthy control subjects were not challenged with influenza. Serial oropharyngeal swabs were taken over a 30-day period, and the V1-V3 region of the bacterial 16S rRNA gene was amplified and sequenced to determine the composition of the microbiome.Results: forty three of 52 challenged individuals developed proven influenza infection, of whom 33 became symptomatic. None of the controls developed influenza, although 22% reported symptoms. The diversity of bacterial communities remained remarkably stable following the acquisition of influenza, with no significant differences over time between individuals with influenza and those in the control group. Influenza infection was not associated with perturbation of the microbiome at the level of phylum or genus, and there was no change in colonisation rates with Streptococcus pneumoniae or Neisseria meningitidis.The throat microbiota is resilient to alteration under influenza challenge indicating robustness of the upper airway microbiota.