COVID-19 testing involves collection of swabs from nasopharyngeal cavities where the SARS-CoV-2 virus replicates. Many other commensal and pathogenic microbes may be found in the same host niche. Collectively, these microbes are called the microbiome. We hypothesize that the colonizing microbiome at the time of diagnosis may provide leads for early stratification of cases into risk categories, future clinical manifestations of the disease, and insights into treatment strategies.