Figure 3.

Early-life malnutrition compromises microbiota development

(A) Bacterial α-diversity calculated by Shannon index, observed features, and Faith’s phylogenetic diversity. Two-tailed Mann-Whitney U test was used. ∗∗∗∗p < 0.0001; data points represent single mice (n = 11).

(B) Bacterial β-diversity. The PCoA plots of microbial β-diversity were generated using unweighted and weighted UniFrac algorithms. PERMANOVA was used. p < 0.001 and p < 0.003, respectively. Data points represent single mice (n = 11).

(C) Phylum relative abundance in CON and MAL 21-day-old mice.

(D) Cladogram for orders and (E) linear discriminant analysis (LDA) scores (log10) for the most discriminant bacterial family identified by linear discriminant analysis effect size (LEfSe) in the cecal microbiota in CON and MAL 21-day-old mice.

(F) Heatmap showing bacterial amplicon sequence variants (ASVs) in the cecal microbiota that discriminate CON and MAL 21-day-old mice. ASVs were selected according to p < 0.05 with Wald test using false discovery rate (FDR) p value correction following DESeq2 read counts normalization. Each line represents one ASV, and each column represents an individual mouse. Mean relative abundances (log10) of ASVs detected in the different experimental groups are shown.