SARS-CoV-2 differentially alters gut microbiota's composition and metabolism in young-adult and aged hamsters

Aging is a key contributor to SARS-CoV-2 morbidity and mortality in humans. An impaired or dysregulated immune response together with a dysbiotic gut microbiota may contribute to this phenotype. In this study, we used young (2-month-old) and aged (22-month-old) golden hamsters infected with SARS-CoV-2. We compared lung pathology and transcriptional responses, systemic metabolites and whole-genome shotgun metagenomic changes after infection at two time points namely day 7, the peak of disease severity and day 22, a time point corresponding to the resolution phase of infection. Our data reveal age-dependent changes in the compositional structure and metabolomics activity of the gut microbiota.