Fig. 3.

Variation in rectal bacteriome and virome composition between CAP patients and controls is captured by unsupervised analysis in Factor 1. Controls have lower Factor 1 values, a score based on the major source of variation in microbiota composition in our study as identified by MOFA, than CAP patients, both at admission and after one month (A). The bacterial (B) and viral (C) weights for Factor 1 illustrating which bacteria and viruses are important for the value of Factor 1. The plus sign indicates a positive correlation with the value of Factor 1, whereas the minus sign indicates a negative correlation with the value of Factor 1. The larger the value of the weight (loading), the stronger the association. The weights with the highest values are showed. 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 the data, p-values were calculated using the Wilcoxon rank sum test. ***= p<0•001–0•0001; ****= p<0•0001.