Pair-wise comparison of categorized open reading frames from human milk versus infants’ and mothers’ feces. Pair-wise comparisons for the human milk metagenome versus (A) breast-fed infants’ feces, (B) formula-fed infants’ feces and (C) mothers’ feces are shown. For comparison, a plot of breast-fed infants’ feces and formula-fed infants’ feces (D) is also shown. Each point represents a different SEED subsystem and its relative abundance within the human milk metagenome compared to the fecal metagenomes. Points lying on or near the dotted line have equal or similar abundance in both metagenomes. Points closer to the x-axis are more abundant in the feces metagenome, whereas points closer to the y-axis are more abundant in the human milk metagenome. Red dots signify those with significantly different proportions between the two metagenomes (Student’s t-test, P < 0.05). Breast-fed and formula-fed infants’ feces values are an average of five individuals, and mothers’ feces values are an average of three individuals. All subjects are unrelated.