Fig. 2

The microbiome clusters with stage of liver disease in Mdr2 −/− mice. Microbiome diversity and taxonomy at each stage of liver injury/disease (baseline/WT, n = 6; liver inflammation/Mdr2−/−, n = 6; liver cirrhosis/Mdr2−/−, n = 9 and hepatocellular carcinoma (HCC)/Mdr2−/−, n = 10) showing differences in (a) β-diversity by Bray–Curtis dissimilarity as displayed in the Principal Coordinates Analysis (PCoA) (b) α-diversity by Shannon index, box plots indicate median (middle line), 25th, 75th percentile (box) and 10th and 90th percentile (whiskers) as well as outliers (single points) and (c) relative taxonomic abundance at the phylum level. Permutational multivariate analysis of variance (PERMANOVA) was performed to visualize the phylogenetic distance between groups (a). Differences in Shannon’s index (b) and relative abundance (c) were assessed by Kruskal-Wallis for overall comparison and Dunn’s test for 2 group comparison with Benjamini-Hochberg multiple test correction, * P < 0.05, ** P < 0.01, ^a P < 0.05 in baseline/WT mice compared to all other groups. Detailed data is shown in Supporting Table 1, Additional File 2