Fig. 5: Lung and Gut Microbiota Associations with COVID-19 Severity in Two Independent Cohorts.

A Application of the dysbiosis index in lung (ETA) microbiota profiles in the UPMC-COVID cohort classified subjects in three clusters, with significant differences in Shannon index and bacterial load by 16S qPCR. B The low diversity cluster in lung samples from UPMC-COVID subjects was significantly associated with higher ETA levels of sTNFR1 and plasma levels of Ang-2. C COVID-19 patients classified to the low diversity cluster had numerically worse time-to-liberation from invasive mechanical ventilation and survival. D, E Application of the dysbiosis index models in lung (sputum or ETA) and gut (stool) samples in the MGH-COVID cohort classified subjects in three clusters, with significant differences in Shannon index and anaerobe abundance between clusters. F, G Cluster assignments in the MGH cohort were strongly associated with clinical severity. Membership in the Low-Diversity cluster in the lungs was associated with an odds ratio of 18.07 (1.92-922.5) for severe disease (black belt connecting the Low-Diversity cluster and Severe Disease perimetric zones in the chord diagram). Membership in the low diversity gut cluster was also significantly associated with clinical severity of COVID-19 pneumonia (odds ratio of 4.08 [1.56–11.2]). Source data are provided as a Source Data file. Displayed data include 47 baseline lung samples from UPMC-COVID, and 75 baseline lung and 88 stool samples from MGH-COVID cohort. Data displayed as boxplots with individual dots have their median as the line inside the box, interquartile range (25th–75th percentile) as the box itself, whiskers extend to 1.5 times the interquartile range, and individual dots beyond whiskers signify outlier observations.