Characteristic of upper respiratory tract microbiota in severe covid-19 adult patients in Indonesia

Introduction: Nowadays, new cases of COVID-19 have been found with severe cases and deaths. The upper respiratory microbiota has been associated with susceptibility to viral infection and disease severities. However, the association of respiratory tract microbiota with the modulation of COVID-19 outcomes still raises a question. Therefore, we examined the association between the diversity of upper respiratory microbiota and clinical manifestations of COVID-19. Methods: This research is an observational cross-sectional study. We characterized the microbiota in the upper airway using the 16S ribosomal RNA sequencing method in 74 COVID-19 patients aged 18-64 years. We also examined the association between COVID-19 severities with alpha and beta diversity of upper respiratory microbiota. The alpha and beta diversity was analyzed by QIIME and shown by R software, AMOVA and MRPP testing was done with R software. The t test and diagrams were performed using R software. Bivariate analysis was carried out by t-test and Chi-square test. Results: The top five phyla in the upper respiratory tract of Indonesian COVID-19 patients with age 18-64 years old were Firmicutes (32,3%), Bacteroidota (27,1%), Fusobacteriota (15,2%), Proteobacteria (15,1%) and Actinobacteria (7,1%). Shannon and ACE index analysis showed no decline of microbiota diversity in the upper airway with increased disease severity. However, there were significant beta diversity differences in the upper airway microbiota between mild and severe COVID-19. The Firmicutes phylum and Oribacterium genus abundance were significantly higher in severe COVID-19 than in mild. The quantity of the Fusobacteriota phylum, Neisseria, and Fusobacterium genera was significantly higher in mild COVID-19 than in severe. Conclusion: Our research supports the relationship between the severity of COVID-19 and the diversity of the microbiota in the upper airway in adults. Further studies are needed to examine how microbiota prevents COVID-19 severities.