Age-related changes in the upper respiratory microbiome are associated with SARS-CoV-2 susceptibility and illness severity

Hurst, J. H.; McCumber, A. W.; Aquino, J. N.; Rodriguez, J.; Heston, S. M.; Lugo, D. J.; Rotta, A. T.; Turner, N. A.; Pfeiffer, T. S.; Gurley, T. C.; Moody, M. A.; Denny, T. N.; Rawls, J. F.; Woods, C. W.; Kelly, M. S.

Children are less susceptible to SARS-CoV-2 and typically have milder illness courses than adults. We studied the nasopharyngeal microbiomes of 274 children, adolescents, and young adults with SARS-CoV-2 exposure using 16S rRNA gene sequencing. We find that higher abundances of Corynebacterium species are associated with SARS-CoV-2 infection and SARS-CoV-2-associated respiratory symptoms, while higher abundances of Dolosigranulum pigrum are present in SARS-CoV-2-infected individuals without respiratory symptoms. We also demonstrate that the abundances of these bacteria are strongly, and independently, associated with age, suggesting that the nasopharyngeal microbiome may be a potentially modifiable mechanism by which age influences SARS-CoV-2 susceptibility and severity.