Fig. 3

Stack maps of species distributions representing the relative abundance of the top 10 taxa of BALF (A) and fecal (B) microorganisms, expressed at the phylum level; Venn diagrams of the lung (C) and gut (D) microbiota of the two groups are given, showing shared genera between survivor and deceased populations in overlapping regions, and unique genera in non-overlapping regions; Heatmap of hierarchical clustering of lung (E) and gut (F) microbiota, with each row representing a species and each column representing survivors and deceased in both groups. The color indicates the abundance of the species, with dark blue indicating lower abundance and red indicating higher abundance; Paired differential abundance analysis of lung (G, H) and gut (I, J) microbes stratified by survivors and deceased. Natural log transformed sampling-bias corrected observed abundances, as used in ANCOM-BC, were used here to generate the boxplots. The boxplots show the distribution of data for survivors (red) and deceased (blue). Each sample is plotted based on the abundance of its species. The left, center, and right vertical boundaries of each box represent the first, second (median), and third quartiles of the data. W: test statistics. W = lfc/se. p_val: p-values. P-values are obtained from a two-sided Z-test using the test statistic W. q_val: adjusted p-values. Adjusted p-values are obtained by applying p_adj_method to p_val. lfc: log fold changes obtained from the ANCOM-BC log-linear (natural log) model. **p < 0.01,***p < 0.001