Abstract
We investigated nasopharyngeal microbial community structure in COVID-19-positive and -negative patients. High-throughput 16S ribosomal RNA gene amplicon sequencing revealed significant microbial community structure differences between COVID-19-positive and -negative patients. This proof-of-concept study demonstrates that: (1) nasopharyngeal microbiome communities can be assessed using collection samples already collected for SARS-CoV-2 testing (viral transport media) and (2) SARS-CoV-2 infection is associated with altered dysbiotic microbial profiles which could be a biomarker for disease progression and prognosis in SARS-CoV-2.
Highlights
Since the appearance of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infections in 2019, cases of coronavirus disease 2019 (COVID-19) have spread rapidly around the world infecting over 152 million people and claiming over 3.2 million lives, as of May 3, 2021
This study is the first to show that COVID-19-positive patients have a dysbiotic nasopharyngeal microbial community characterized by loss of putative nasal commensal bacteria and an increase in putative pro-inflammatory bacteria
Decreased relative abundance of nasal commensal organisms such as Corynebacterium (Actinobacteria) [24] and Streptococcus (Firmicutes), previously shown to be affected by influenza virus infection [25]. These results need to be further evaluated in future studies using metagenomic and metatranscriptomic techniques, but may reflect baseline differences prior to infection leading to susceptibility to SARS-CoV-2 infection or may be a result of SARS-CoV-2 infection, leading to post-infection microbiome alteration
Summary
Since the appearance of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infections in 2019, cases of coronavirus disease 2019 (COVID-19) have spread rapidly around the world infecting over 152 million people and claiming over 3.2 million lives, as of May 3, 2021 (https://covid19.who.int/). COVID-19 is primarily transmitted through the respiratory tract via aerosolized droplets containing viral particles [1]. Two studies found no significant differences in microbial diversity between COVID-19-positive and negative patients [5, 6] whereas two studies did note differences in community structure [7, 8]. The other study observed differences between microbial communities, with a significantly lower abundance of Fusobacterium periodonticum in COVID-19 positive compared to negative patients [8]. These mixed results highlight the critical need for more information
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