Altered infective proficiency of the gut microbiome in COVID-19

The effects of SARS-CoV-2 infections comprise of many heterogeneous symptoms including several involving the human gastrointestinal tract. Reports, thus far, have shown pronounced effects of COVID-19 on the gastrointestinal microbiome. However, these studies report differences between severe cases of infection compared to healthy controls, where in particular the loss of commensal taxa are reported. However, it remains unclear whether microbiome alterations including functional shifts are a common effect of COVID-19. Here, we used high-resolution, systematic multi-omic analyses to resolve differences in the gut microbiome following COVID-19. We find an increase in the overall abundance and expression of both virulence factors and antimicrobial resistance genes in COVID-19 patients. Importantly, these genes are encoded and expressed by taxa from families such as Acidaminococcaceae and Erysipelatoclostridiaceae, which we found to be enriched in COVID-19 patients. We also found an enrichment in the expression of rotavirus C genes in COVID-19 patients compared to healthy controls. Collectively, our analyses identify an altered and increased infective proficiency of the gut microbiome in COVID-19 patients, which may cause acute and possibly future burden conferred by other infective agents.