Figure 3.

Bacterial richness and alpha- and beta-diversity results are plotted for each of the COVID-19 severity groups. Each box represents the median and interquartile range, and the mean is shown by the white diamond. Individual points are shown as open circles. In the first three facets, bacterial richness and alpha-diversity are shown for each of the patient groupings. Richness and alpha-diversity (Shannon and Simpson indices) were lowest in the uninfected control participants and generally increased as COVID-19 severity increased. Alpha-diversity (Shannon and Simpson indices) decreased in patients in the ICU with very severe COVID-19. The last facet shows within-group pairwise Bray–Curtis dissimilarities plotted on the y-axis for each of the COVID-19 groups. Larger values indicate that the URT microbial community between the two samples was more dissimilar, while smaller values indicate the opposite. Uninfected control participants had the most similar URT microbiome to each other, while the URT microbiome within each group became more dissimilar as COVID-19 severity increased. The URT microbiomes among those with very severe COVID-19 were very dissimilar to each other.