Nanopore 16S rRNA sequencing reveals alterations in nasopharyngeal microbiome and enrichment ofMycobacteriumandMycoplasmain patients with COVID 19

The coronavirus disease 2019 (COVID-19) pandemic caused by severe acute respiratory syndrome corona virus 2 (SARS-CoV-2) is a major global health concern. This virus infects the upper respiratory tract and causes pneumonia-like symptoms. So far, few studies have shown that respiratory infections alter nasopharyngeal (NP) microbiome diversity and enrich opportunistic pathogens. In this study, we have sequenced the 16S rRNA variable regions, V1 through V9, extracted from NP samples of control and COVID-19 (symptomatic and asymptomatic) participants using the Oxford Nanopore™ technology. Comprehensive bioinformatics analysis investigating the alpha/beta diversities, non-metric multidimensional scaling, correlation studies, canonical correspondence analysis, linear discriminate analysis, and dysbiosis index analysis revealed control and COVID-19-specific NP microbiomes. We observed significant dysbiosis in COVID-19 NP microbiome with abundance of opportunistic pathogens such asCutibacterium, Corynebacterium, Oerskovia, andCellulomonasin asymptomatic patients, and ofStreptomycesandMycobacteriaceaefamily in symptomatic patients. Furthermore, we observed sharp rise in enrichment of opportunistic pathogens in symptomatic patients, with abundance ofMycobacteriaandMycoplasma, which strongly correlated with the occurrences of chest pain and fever. Our findings contribute novel insights regarding emergence of opportunistic pathogens in COVID-19 patients and their relationship with symptoms, suggesting their potential role in coinfections.