The aim of the present study was therefore to characterize the oral microbiome in a cohort of COVID-19 patients with different symptom levels, to evidence the eventual association between virus induced disease and the microbial environment of the oral cavity.

Background: The new human coronavirus SARS-CoV-2, responsible for the development of COVID-19 disease, has become a global pandemic emergency. Like other respiratory viruses, the primary site of entrance is represented by the oropharynx, and the local microbiome environment may influence its capability to infect and induce the disease. The aim of the present study was therefore to characterize the oral microbiome in a cohort of COVID-19 patients with different symptom levels, to evidence the eventual association between virus induced disease and the microbial environment of the oral cavity. Microbiome features and alterations were assessed by Whole Genome Sequencing (WGS), allowing to evidence all the microbial components (bacteria, mycetes and viruses) of the oral microbiome. In parallel, the local immune response (IgA) and inflammatory cytokine release were ascertained.Results: Overall, 75 oral rinse samples were collected from 39 COVID-19 subjects and 36 controls recruited in the study. WGS results showed significant alterations in the oral microbiome of COVID-19 patients compared with matched controls. In particular, alpha-diversity was significantly different in COVID-19 patients and controls, and lower richness associated with symptoms severity.Oral dysbiosis was associated with increase in local concentration of inflammatory cytokines and decrease of IgA response.Conclusions: The oral microbiome may be important in defining the individual susceptibility to SARS-CoV-2 infection and the subsequent development of symptomatic COVID-19. By contrast, IgA presence associated with mild symptoms and should be considered as an important parameter in therapy and vaccine development.