The intestinal microbiota predicts COVID-19 severity and fatality regardless of hospital feeding method

Intestinal and oral samples from SARS-CoV-2 PCR positive, hospitalized patients collected between April 27 to June 10, 2020. All samples were collected by the doctor or nurse caring for the patient during standard of care rounds to identify oral and intestinal bacteria species that can be used to accurately predict COVID-19 severity in hospitalized patients. SARS-CoV-2 positive patients exhibit gut and oral microbiome dysbiosis which is associated with various aspects of COVID-19 disease. However, little is known about the effect of artificial feeding (through a tube) on the microbiome dysbiosis of hospitalized COVID-19 patients. We used random forest classification (RFC) machine learning models to determine whether specific members of microbiota found to be related to COVID-19 severity are cofounded by the feeding method during hospitalization. The gut, but not the oral microbiota, was a robust predictor of both COVID-19-related fatality and severity, with higher predictive value than most clinical variables. In addition, perturbations of the gut microbiota due to artificial tube feeding (enteral feeding) did not associate with species that were predictive of COVID-19 severity.