Figure 1.

Formula feeding (FF) induces microbiome changes and dysbiosis of f_Enterobacteriaceae and f_Enterococcaceae in the ileum of mouse pups. Neonatal mice [postnatal day (P)0] from multiple litters were subjected to dam feeding (DF) or FF for 2 days. Ileum tissue samples were harvested on P0, P1, and P2 and processed for 16S rRNA gene sequencing followed by bioinformatics analysis. Ileum samples from 2 independent experiments were used for 16S sequencing in each group. A: total number of operational taxonomic units (OTUs) between DF and FF pups on the indicated postnatal days. B and C: Chao-1 index (B) and Shannon index (C) were used to measure the bacterial α-diversity. A–C: statistical significance was calculated by Student’s t test between DF and FF groups on the indicated postnatal days. Data are presented as means ± SD; n = 5 in each group. *P < 0.05 was considered statistically significant. D: β-diversity of the gut microbiota was measured with principal coordinate analysis (PCA) based on unweighted UniFrac distance matrixes between DF (orange) and FF (green) groups on the indicated postnatal days; n = 5 in each group. E–G: fold change (FC log2) in the relative abundance of significantly different (DESeq2) OTUs between groups and their normalized mean counts. A subset of OTUs, grouped by class, family, or genus, with a raw count at least of 100 was kept. The fold changes in microbial abundance at class (E), family (F), and genus (G) levels were calculated between DF and FF pups on P2; n = 5 in each group. Taxonomic units tested with P < 0.05 and FDR < 0.1 were considered significant.