Study of microbiome alterations in hospitalized COVID-19 patients and non-infected controls

The clinical course of the 2019 coronavirus disease (COVID-19) is variable and largely unpredictable, especially in persons who have neither been vaccinated nor recovered from previous infection. We hypothesized that disease progression and inflammatory responses were associated with alterations in the microbiome. To test this, we characterized the metagenome of longitudinally collected stool samples and oropharyngeal swabs from hospitalized COVID-19 patients and non-infected controls, as well as tracheobronchial secretions from ventilated patients with COVID-19. Severe COVID-19 was directly associated with a depletion of potentially beneficial intestinal microbes mainly belonging to Clostridiales, whereas oropharyngeal microbiota disturbance appeared to be mainly driven by antibiotic use. Collectively, our study identifies microbiome alterations in severe COVID-19.