SARS-CoV-2 infection is associated with intestinal permeability, systemic inflammation and microbial dysbiosis in hospitalized patients

Coronavirus disease 2019 (COVID-19) and associated severity has been linked to uncontrolled inflammation and may be associated with changes in the microbiome of mucosal sites including the gastrointestinal tract and oral cavity. These sites play an important role in host-microbe homeostasis and disruption of epithelial barrier integrity during COVID-19 may potentially lead to exacerbated inflammation and immune dysfunction. Outcomes in COVID-19 are highly disparate, ranging from asymptomatic to fatal, and the impact of microbial dysbiosis on disease severity is unclear. Here, we obtained plasma, rectal swabs, oropharyngeal swabs, and nasal swabs from 86 patients hospitalized with COVID-19 and 12 healthy volunteers. We performed V3V4 16S rRNA sequencing to characterize the microbial communities in the mucosal swabs and compared the microbiomes of healthy controls, COVID-19 patients who had survived by the end of study enrollment, and those who had unfortunately died. We further performed a correlation analysis to understand the relationships between differentially abundant taxa and plasma biomarkers. The primary goal of this study was to understand how microbial dysbiosis and translocation contribute to COVID-19 severity.