Fig 7.

Microbiota of infants consuming milk from secretor or non-secretor mothers or those consuming infant formula impacts gene expression in the large intestine. DEGs and activated pathways in the large intestine (colon) of mice transplanted with microbiota from infants consuming milk from secretor or non-secretor mothers or those consuming milk. Each treatment is compared to the germ-free controls. (A) Venn-diagram showing shared and unique DEGs among three groups when compared to germ-free controls, (B–D) Volcano plots showing DEGs in SMM (B), NSM (C), and MFM (D) groups, compared to GF controls. Significantly upregulated genes are represented by red circles (log2 fold change >1.5, adjusted P-value < 0.05, pairwise comparison). (E–G) Barplots showing the significantly activated pathways in SMM (E), NSM (F), and MFM (G) groups compared to GF controls. Pathways are ranked based on NES and significant pathways are shown (pairwise comparison, P-adjusted < 0.05). SMM = mice transplanted with fecal material from infants consuming milk from secretor mothers, N = 6; NSM = mice transplanted with fecal material from infants consuming milk from non-secretor mothers, N = 7; MFM = mice transplanted with fecal material from infants consuming dairy-based formula, N = 4.