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

Abstract

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. To identify new prognostic markers for the disease, a multicentre 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 analysed. Linear discriminant analysis identified <i>Mycoplasma salivarium</i>, <i>Prevotella dentalis</i>, and <i>Haemophilus parainfluenzae</i> as biomarkers of severe COVID-19 in nasopharyngeal microbiota, while <i>Prevotella bivia</i> and <i>Prevotella timonensis</i> were defined in faecal microbiota. Additionally, a connection between faecal and nasopharyngeal microbiota was identified, with a significant ratio between <i>P. timonensis</i> (faeces) and <i>P. dentalis</i> and <i>M. salivarium</i> (nasopharyngeal) abundances found in critically ill patients. This ratio could serve as a novel prognostic tool for identifying severe COVID-19 cases.