Fig. 1

Study overview and overall community structure. a Study enrollment of hospitalized patients with confirmed COVID-19 with weekly stool sampling until the time of discharge or death, whichever occurred first. b Marked reduction in species richness and evenness in severe COVID-19 (inverse Simpson ɑ-diversity metric, p-value < 0.0001 from multivariable linear modeling adjusting for age, sex, prior antibiotic use, race, ethnicity, body mass index, Charlson Comorbidity Index, use of remdesivir or corticosteroids, days since admission, SARS-CoV-2 stool viral load, sequencing depth, and a participant-level random effect). Boxes represent median and interquartile range, while whiskers represent 95%ile. c Community-level disturbances in severe vs. moderate COVID-19 as depicted by joint ordination and principal coordinates analysis (PCoA), not fully explained by characteristic trade-offs in Bacteroidetes/Firmicutes or prior antibiotic use. d Ominibus testing of Bray–Curtis distances demonstrates that COVID-19 severity had a modest and statistically significant impact on the overall community structure. Other demographic information, covariates, and hospital course information were not significantly associated (FDR p-value > 0.05)