Persistent Changes in the Gut Microbiome of Covid-19 Survivors

ABSTRACT

SARS-CoV-2 is detectable in gastrointestinal secretions and has been associated with changes to the gut microbiome during severe infection. However, the majority of individuals with COVID-19 will develop mild infection and remain outpatient for the duration of infection, with a relative paucity of information on the gut microbiome of this group. Furthermore, symptoms can persist for 6 months or longer in some patients, which has presented additional health care burdens given incomplete understanding of the long term impact of SARS-CoV-2 infection. To fill these knowledge gaps, we longitudinally sampled the gut microbial community of subjects infected with SARS-CoV-2 and their household contacts living in San Francisco at varying lengths of time after infection. We report an association between COVID-19 and the gut microbiome. COVID-19 positive subjects exhibited greater variability in the gut microbiome over time. In concordance with this finding, COVID-19 positive gut microbial communities were more self-distinct when compared to COVID-19 negative individuals across sample collections. Population level social distancing practices varied during the time of sample collection in our cohort, and we found an association between population level movement and gut microbial community variation. To better define the impacts of SARS-Cov-2 independent of genetic and environmental variables, are utilizing five SARS-CoV-2 variants (Alpha, Beta, Washington, Delta, and Omicron) in separate mouse models to test the impact of SARSCoV- 2 on the gut microbiome in severe and mild infections to define the impacts of SARS-CoV-2 on gut microbial ecology independent of genetic and environmental variables. We conclude that even mild cases of COVID-19 result in months-long disruption in the gut microbial community, with additional perturbations linked to massive shifts in population level social distancing practices.