Nasopharyngeal Microbiome of COVID-19 Patients Using 16S Amplicon Analysis Revealed Distinct Bacterial Profile in Demised and Recovered Individuals

Abstract

Background COVID-19 pandemic has shaken the entire world and the socio-economic life on the planet. The implications of the bacterial co-infections in SARS-CoV-2 patients remained the least explored subject of clinical manifestations among the COVID-19. Identification and association of the nasopharyngeal microbial community structure within SARS-CoV-2 infected patients could reveal microbiota dynamics that may determine and/or influence the disease outcome in the COVID-19 patients. Results Here, in this study, we present distinct nasopharyngeal microbiome in the demised (N=48) and recovered (N=29) COVID-19 patients as compared to the control group (N=33). The nasal microbiome composition in the three groups vary significantly (PERMANOVA, p-value <0.001), where demised patients showed higher species richness as compared to the recovered and control groups. Pathogenic genera including Corynebacterium (LAD score 5.51), Staphylococcus, Serratia, Klebsiella and their corresponding species were found as biomarkers (p-value <0.05, LDA cutoff 4.0) in the patients those who demised due to SARS-CoV-2 infection. Except for a few pathogenic species in the genera, Ochrobactrum (LDA score 5.79), and Burkholderia (LDA 5.29), the recovered group harbors ordinal bacteria (p-value <0.05, LDA-4.0) as biomarkers. Similarly, Pseudomonas (LDA score 6.19), and several healthy oral/nasal cavity commensal including Veillonella, and Porphyroonas, were biomarkers for the control individuals. Conclusions Dysbiosis in the commensal nasopharyngeal microbiota, especially due to infection of opportunistic pathogens could lead to more complex and severe COVID-19 disease dynamics. Whereas, healthy commensal bacteria may trigger the immune response and alter the viral infection susceptibility and thus, may help in preventing the viral infection and possible recovery which is yet to be explored. The findings in the present study provide key considerations and have significant implications for the COVID-19 treatment and control measures. However, further study is required to address the microbiome based therapeutic aspects.