Gut microbiome in post-COVID-19 patients is linked to immune and cardiovascular health status

Gut microbiome composition stores the imprints of prior infections and other impacts. COVID-19 implies changes in inflammatory status that persist for considerable time after the end of the infection. As the gut microbiome is closely associated with immunity and inflammation, the infection severity might be linked to its community structure dynamics.Using 16S rRNA sequencing of stool samples, we investigated the microbiome 3 months after the end of the disease in 178 post-COVID-19 patients. The cohort included 3 groups: asymptomatic subjects (n=48), subjects who contacted COVID-19 patients with no further infection (n=46) and severe patients (n=86). Using a novel compositional statistical algorithm (nearest balance) and the concept of bacterial co-occurrence clusters (coops), we compared microbiome composition between the groups as well as with multiple categories of clinical parameters: immunity, cardiovascular parameters and markers of endothelial dysfunction and blood metabolites.Although a number of clinical indicators varied drastically across the three groups, no differences in microbiome features were identified between them at this follow-up point. However, there were multiple associations between the microbiome features and clinical data. Among the immunity parameters, relative lymphocytes number was linked to a balance including 14 genera. Cardiovascular parameters were associated with up to 4 bacterial cooperatives. Intercellular adhesion molecule 1 was linked to a balance including 10 genera and to 1 cooperative. Among the blood biochemistry parameters, calcium was the only parameter associated with the microbiome - via a balance of 16 genera.Our results suggest comparable recovery of the gut community structure in post-COVID-19 period independently of the severity or infection status. Multiple identified associations of clinical analyses data with microbiome provide hypotheses about participation of specific taxa in regulating immunity and homeostasis of cardiovascular and other body systems in health, as well as their disruption in SARS-CoV-2 infections and other diseases.