Inflammation-associated gut microbiome in post-acute sequelae of SARS-CoV-2 points towards new therapeutic targets

Post-acute sequelae of SARS-CoV-2 (PASC), has been associated with sustained elevated levels of SARS-CoV-2-specific T cells, immune activation and inflammation, but little is known about the underlying etiology. Because it is known that the gut microbiome can influence antiviral immunity and inflammation, and that SARS-CoV-2 can infect gut epithelial cells and be shed in stool long after it is undetectable in the upper respiratory tract, we examined the fecal microbiome and systemic inflammatory markers in individuals who were infected with SARS-CoV-2 to determine if the composition of gut microbiome could be involved in PASC. We report that fecal microbes differentiate individuals with PASC from those with resolved COVID-19 (RC) with high accuracy based on the ratio of bacteria in the genus Bacteroides (Bacteroides dorei, Bacteroides massiliensis, and Bacteroides thetaiotaomicron) over Faecalibacterium prausnitzii. Microbiome composition also correlated with plasma levels of the inflammatory markers IL-6 and CRP. These observations indicate that microbiome composition can differentiate individuals with PASC from those with resolved SARS-CoV-2 infection with no lingering symptoms and suggests it could provide a potential target for therapeutic intervention.