Fig. 1.

Rectal bacteriome diversity of CAP patients differs from controls. Lower richness (A) and α-diversity (B) of the bacterial microbiota in CAP patients at admission and after one month, compared to controls. Significant differences are seen in beta-diversity of CAP patients at both timepoints, compared to controls (C). No significant changes in richness, α-diversity or β-diversity of viral microbiota were observed between groups (D–F). In the boxplots, the rectangle spans the first quartile to the third quartile (the interquartile range or IQR), the horizontal black line inside the rectangle shows the median, and whiskers above and below the box. Given the non-normal distribution of these data, p-values were calculated using the Wilcoxon rank sum test. β-diversity as depicted by Bray-Curtis dissimilarity index in a principal coordinate analysis (PCoA). Each dot represents a sample, coloured by group. Shaded area spans all samples per group. Dissimilarities in gut microbiota composition (R²) and p-values are determined using permutational multivariate analysis of variance. **= p<0•01–0•001; ****= p<0•0001.