Saliva microbiome in SARS-CoV-2 infection

The clinical outcomes of SARS-CoV-2 infection vary substantially in their severity. Since such differences could be related to the state of the resident human microbiota, we used saliva specimens as a sentinel to assess upper respiratory track microbiome variation. Early in 2020, we assembled a cohort of 831 adults without known SARS-CoV-2 infection to assess occurrence and natural history of the expected wave of SARS-CoV-2 infection over a six-month period. In this pre-vaccination, immunologically naïve population, the infections that occurred produced generally mild illnesses, with little hospitalization and antibiotic use. From 81 participants before, during, and after SARS-CoV-2 infection and from 57 matched SARS-CoV-2 negative controls, we examined 748 serial saliva samples to assess the extent to which the acute infection perturbed the salivary microbiome, measuring total bacterial abundance, composition, population structure, and gene function. In the controls, the salivary microbiome was stable over six months by all metrics used. There was similar stability in the samples from participants with mild to moderate SARS-CoV-2, throughout and after their infection. However, we report significant reductions in microbiome diversity in SARS-CoV-2-positive participants with severe symptoms early after their infection, which then recovered. These findings highlight microbiome resilience in relation to SARS-CoV-2 infection, but also indicate its limits with severe infection.