The relationship between gut and nasopharyngeal microbiome composition can predict the severity of COVID-19

Background: Coronavirus disease 2019 (COVID-19) is a respiratory illness caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) that displays great variability in clinical phenotype. Many factors have been described to be correlated with its severity, and microbiota could play a key role in the infection, progression, and outcome of the disease. SARS-CoV-2 infection has been associated with nasopharyngeal and gut dysbiosis and higher abundance of opportunistic pathogens. Methods: To identify new prognostic markers for the disease, a multicenter prospective observational cohort study was carried out in COVID-19 patients divided into three cohorts based on symptomatology: mild (n=24), moderate (n=51), and severe/critical (n=31). Faecal and nasopharyngeal samples were taken, and the microbiota was analyzed. Results:Linear discriminant analysis identifiedM. salivarium,P. dentalis, andH. parainfluenzaeas biomarkers of severe COVID-19 in nasopharyngeal microbiota, whileP. biviaandP. timonensiswere defined in faecal microbiota. Additionally, a connection between faecal and nasopharyngeal microbiota was identified, with a significant ratio betweenP. timonensis(faeces) andP. dentalisandM. salivarium(nasopharyngeal) abundances found in critically ill patients. Conclusions: This ratio could serve as a novel prognostic tool for identifying severe COVID-19 cases.