Figure 1. Distinct Structure of the Microbial Community in Jax and Tac Mice.
(A) Relative abundance of dominant bacterial families in feces collected from 3-week-old Jax (n = 23) and Tac (n = 20) mice; av, average. Numbers indicate family identities.
(B and C) Average α diversity (B, Shannon diversity, OTU richness, and phylogenetic diversity indexes) and box plot for α diversity (B, Shannon evenness) of fecal microbiota composition from Jax and Tac mice. *p < 0.05; n.s., not significant (two-tailed unpaired t test for Shannon index, OTU richness, and phylogenetic diversity; two-tailed Mann-Whitney U test for Shannon evenness). β diversity (C, Bray-Curtis dissimilarity) of the fecal microbiota within Jax and Tac mice, and that between the two groups. ****p < 0.0001 (Kruskal-Wallis test followed by Dunn’s multiple comparisons test). Data are expressed as mean ± SEM for Shannon diversity, OTU richness, and phylogenetic diversity indexes in (B). Boxes represent the interquartile range between the first and third quartiles (25th and 75th percentiles, respectively), the horizontal line inside the box defines the median, and whiskers represent the lowest and highest values for Shannon evenness in (B) and for Bray-Curtis dissimilarity in (C). Data are pooled from four independent experiments in both (B) and (C).
(D) NMDS plot of β-diversity values (Bray-Curtis dissimilarity indexes) of microbiota in fecal pellets from 3-week-old pups (circles; n = 23 and n = 20 for Jax and Tac, respectively) and mothers (squares; n = 4 each) at weaning is shown with the minimal stress (stress = 0.276383) after 1,000 iterations. Overall, the difference in β diversity between microbiota of Jax (bluish fill) and Tac (reddish fill) pups was statistically significant with p < 0.0001 (permutational multivariate analysis of variance [PERMANOVA]).
(E) The OTUs that were differentially abundant in fecal microbiota of 3-week-old Jax and Tac mice are shown with linear discriminant analysis (LDA) values of LEfSe with p < 0.05, positive false discovery rate q < 0.05, and maximal abundance cut < 1%. Their abundances are depicted by heatmaps. Each colored box represents the abundance of the indicated OTU in individual mice shown with cage identity number at the bottom.