Coronavirus disease 2019 (COVID-19) primarily affects the respiratory tract, but some people experience gastrointestinal symptoms and severe COVID-19 is associated with imbalances of the gut microbiome. However, it’s not clear whether gut microbiome disruption also occurs in milder cases of the disease. To find out, researchers recently investigated the gut microbiome in individuals with asymptomatic-to-moderate COVID-19. The microbiome structures of people with non-severe COVID-19 weren’t drastically different from those of healthy controls, but the microbiome in people with asymptomatic-to-moderate COVID-19 encoded and expressed higher levels of virulence factors and antimicrobial resistance genes indicating that the microbiome is primed for pathogenic function. The virulence factors and antimicrobial resistance genes were expressed predominantly by two bacterial families in the gut that were enriched in COVID-19-positive people. Individuals with COVID-19 also had higher expression of certain betaherpesvirus and rotavirus genes in their gut microbiomes. Although the changes over time need to be examined, the findings reveal that COVID-19 is associated with an altered, pathogenicity-promoting gut microbiome and suggest that the disease might make patients susceptible to other infections.