SARS-CoV-2 infection reduces commensal nasopharyngeal microbiomes with inclusion of opportunistic pathogens Metagenomic assembly

Recent studies have revealed that the gut microbiome of healthy individuals differ remarkably from gut microbiota of COVID-19 patients. However, no studies have examined the relationships of nasopharyngeal microbial communities among healthy individual, COVID-19 confirmed and recovered patients. We hypothesized the possible dysbiosis of microbiome composition and genomic features in nasopharyngeal samples are associated with different pathophysiological conditions of Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) infections. To address this hypothesis, we employed RNASeq analysis of 22 nasopharyngeal samples (including COVID-19 = 8, Recovered = 7 and Healthy = 7) to decipher the microbiome composition, diversities, interrelation, and relevant metabolic functions. These data mapped to 2281 bacterial species showing distinct microbiome dysbiosis (COVID-19>Recovered>Healthy).