Fig. 2
From: The host genotype actively shapes its microbiome across generations in laboratory mice
Trajectory of host genotype gut microbiome differentiation. A Y-axis is Faith’s phylogenetic diversity. X-axis is mouse generation or control group. Labels on top list numbers of individual mice (i), cages (c), and cage lineages (l) of which samples were aggregated by color: RM, B6J, and C in red, blue, and orange, respectively. B Distances between 6 RM and 303 breeding experiment samples, grouped by host genotype (B6J = blue, C = orange) in terms of weighted UniFrac beta diversity. Green band indicates distance between host genotypes, not to RM. Gray dashed line is the mean pairwise distance between individuals housed in the same cage, i.e., between biological replicates; 103 cages with 268 individuals and 2.6 individuals per cage on average were considered. Magenta dashed line is the mean distance of individuals from two different cages of the same host genotype, same cage lineage and same generation; 1323 pairs of individuals (i-i) were considered with 42.7 i-i pairs on average per cage lineage and generation; considering housing, there are 141 different cage-to-cage (c-c) pairs with 4.4 c–c pairs on average per cage lineage and generation. C Distances between 24 control and 303 breeding experiment plus six RM samples in terms of weighted UniFrac. We grouped control samples into host genotype and Janvier vs. Duesseldorf, such that each group consisted of six mice housed in two cages. D Comparison of similarities between true dam to offspring (= true dams), dam to mice of same generation, other cage lineage (= other cage lineage), and dam to same generation different host genotype (= other genotype) in terms of unweighted UniFrac. Top label indicates the number of pairwise distances. E Impact of maternal microbiome on offspring microbial composition in terms of source tracking for true dam to offspring (= true dams) and dam to mice of same generation, other cage lineage (= other cage lineage), and other host genotype (= other genotype). F Joint analysis with Robertson et al. data. The y-axis is unweighted UniFrac. First three boxes summarize pairwise distances between our C and Robertson’s mice, our B6J and Robertson’s TAC, and our B6J and Robertson’s JAX mice in orange, blue, and red, respectively. Next four boxes relate our B6J mice with Robertson’s P1, F1, and F2 generation, where the latter is split into maternal JAX and maternal TAC mice. Subsetting Robertson’s F2 maternal JAX mice, the last seven boxes summarize distances to our six generations and B6J controls. We used Mann-Whitney-Wilcoxon for all statistical tests with Benjamini-Hochberg correction for multiple testing (ns: not significant, ****p ≤ 0.0001, ***p ≤ 0.001, **p ≤ 0.01, *p ≤ 0.05)