Nasal microbiota exhibit neither reproducible nor orderly dynamics following rhinoviral infection

BackgroundHow human-associated microbial communities resist and respond to perturbations remains incompletely understood. Viral challenge provides one opportunity to test how human microbiota respond to disturbance. MethodsUsing an experimental human rhinovirus infection challenge model, we explored how viral infection may alter microbiota of the upper respiratory tract (URT). Healthy human volunteers were inoculated with HRV serotype 39. Samples were collected by lavage before and after inoculation from healthy (sham inoculated, n=7) and infected (n=15) individuals and subjected to 16S rRNA gene sequencing through amplification of the V4 hypervariable region. ResultsNo evidence for differences in community alpha-diversity between cohorts was observed. The composition of microbiota of sham-treated and infected subjects did not appear distinguishable and no taxa were significantly associated with infection status. We did not observe support for a correlation between microbial dynamics and counts of specific monocytes. Subject identity was found to be the strongest determinant of community structure in our dataset. ConclusionsOverall, our findings do not suggest a consistent nasopharyngeal microbiota response to rhinovirus challenge. We support the conclusion that this microbial community is individualized. Broadly, our findings contribute to our understanding of how and when immune responses to viruses affect bacterial communities in the URT.