Assessment of the bacterial community of the human upper respiratory tract in patients affected by Covid-19.

Given the challenges posed by the 2019 coronavirus disease (COVID-19), understanding the role of the microbiota is crucial. The analysis of this microbial community in the body not only expands our understanding of health, but also provides insights into the interaction between viruses, microbiota, and the human host. In this study, we aimed to identify possible variations in bacterial diversity caused by Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2). The study involved 45 volunteers, divided into the Positive Group (PG) consisting of 14 patients and the Negative Group (NG) consisting of 31 individuals. Both groups were stratified by biological sex to ensure sample homogeneity. Samples were collected using nasopharyngeal and oropharyngeal swabs, and total DNA was extracted and stored. The V4 region of the 16S rRNA gene was sequenced, and bioinformatics tools were used to assess the composition and diversity of the respiratory microbiota. In our results, the most abundant bacterial phyla were: Firmicutes, Bacteroidetes, and Proteobacteria. There was a notable reduction in the frequency of Firmicutes in the PG, suggesting a potential compromise in the immune response to viral infection. Beta diversity analysis did not reveal significant variations between the communities of the groups. Additionally, the analysis indicated subtle changes in some taxa, such as an increase in the abundance of Neisseriaceae in patients affected by COVID-19. These findings contribute to a deeper understanding of the complex interaction between the virus, the microbiota, and the host during infection with SARS-CoV-2, highlighting the importance of the respiratory microbiota in the context of COVID-19.