Dysbiosis of the oropharyngeal microbiota in COVID-19: distinct profiles in patients with severe respiratory symptoms.

Background: COVID-19 has been strongly associated with alterations in the oropharyngeal microbiota, yet the microbial features linked to disease severity remain unclear. Objective: This study aimed to elucidate the microbial signatures associated with COVID-19 disease severity. Design: 16S rRNA gene sequencing was employed to profile the oropharyngeal microbiota of patients with varying degrees of COVID-19 severity. Results: A significant reduction in alpha diversity suggests a major microbial dysbiosis in critically ill patients compared to less severe cases and healthy individuals, whereas beta diversity analysis revealed a broadly conserved community structure across different groups. Comparative analysis showed significant depletion of the phylum Fusobacteriota and enrichment of bacterial families, including Corynebacteriaceae, Methylobacteriaceae, Acetobacteraceae, Bradyrhizobiaceae, Lactobacillaceae, Staphylococcaceae, Propionibacteriaceae, and Moraxellaceae. Rothia mucilaginosa was notably enriched in patients with severe respiratory symptoms, and many of the enriched taxa are known opportunistic pathogens associated with respiratory infections. Conclusion: The marked dysbiosis and enrichment of opportunistic pathogens in the oropharyngeal microbiota of critically ill patients indicate their possible role in respiratory complications. The identified microbial patterns highlight the potential of microbiome profiling as a tool for disease prognosis and guide further research into the role of microbes in COVID-19 pathogenesis and implications for treatment protocols.