Lymphocyte and neutrophil count combined with intestinal bacteria abundance predict the severity of COVID-19

Early identification of severe 2019 coronavirus disease (COVID-19) cases is of great significance. We included 92 COVID-19 patients and 22 healthy controls and collected their laboratory test data and stool for metagenomic sequencing analysis. We found that the proportion of severe COVID-19 cases was significantly increased in patients with reduced lymphocytes and elevated neutrophils and had unique intestinal microbiota. Pseudothermotoga hypogea and Lachnospiraceae bacterium GAM79 were the species of bacteria that markedly decreased in COVID-19 patients compared to control individuals. For COVID-19 patients, Enterococcus sp. DA9, Caldicellulosiruptor obsidiansis, and Enterococcus faecium were the species of bacteria that significantly altered among patients with normal lymphocytes and neutrophils and patients with decreased lymphocytes and/or increased neutrophils, respectively. Fecal abundances of Enterococcus sp. DA9, Prevotella intermedia, and Bifidobacterium dentium were correlated with COVID-19 disease severity. Decreased lymphocytes and increased neutrophils, combined with decreased Bifidobacterium dentium and Prevotella intermedia, and increased Enterococcus sp. DA9 have the highest power to predict severe cases of COVID-19 patients (area under receiver operating characteristic curve: 0.79). In conclusion, changes in the abundance of intestinal bacteria can reflect the severity of COVID-19 disease, and the combination with lymphocytes and neutrophils might be prognostic factors of COVID-19.IMPORTANCEThe 2019 coronavirus disease (COVID-19) patients had a unique profile of gut bacteria. In this study, we characterized the intestinal bacteria in our COVID-19 cohorts and found that there was an increased incidence of severe cases in COVID-19 patients with decreased lymphocytes and increased neutrophils. Levels of lymphocytes and neutrophils and abundances of intestinal bacteria correlated with the severity of COVID-19. The 2019 coronavirus disease (COVID-19) patients had a unique profile of gut bacteria. In this study, we characterized the intestinal bacteria in our COVID-19 cohorts and found that there was an increased incidence of severe cases in COVID-19 patients with decreased lymphocytes and increased neutrophils. Levels of lymphocytes and neutrophils and abundances of intestinal bacteria correlated with the severity of COVID-19.