Fig. 7

Maturation of metabolic functional capacity of gut microbiome as function of postnatal age and antibiotic exposure. A Principal component analysis (PCA) of metabolic pathway composition. Overall composition of metabolic pathway genes and their maturation over 3 weeks was assessed in stools from antibiotic-naïve preterm infants and compared to antibiotic-exposed assessed by unsupervised PCA. Normalized pathway abundance data were subjected to generalized log2 transformation then PCA. Samples were then colored by group membership and an ellipse was drawn at the 95% confidence interval around the group centroid. Arrows were drawn between the centroids to indicate the magnitude and direction of microbiome change in the first two dimensions. MRPP was used to determine significance of the difference in pathway abundance between groups. A. There was a statistically significant difference in metabolic functional capacity at week 1 compared to week 3 in antibiotic-naïve infants (p < 0.001). In contrast, there was a smaller and non-significant change in metabolic pathway composition in antibiotic-exposed infants from week 1 to week 3 (p= 0.064). B Heatmap demonstrating the fold change of metabolic pathways that differ from week 1 to week 3 in antibiotic-naïve and exposed infants. Generalized linear mixed modeling with fixed and random effects (GLMM) was used to identify metabolic pathways that significantly differed from week 1 to week 3 in antibiotic-naïve and exposed infants. After accounting for maternal antibiotics, gestational age, delivery mode, and receipt of breast milk, genes encoding a total of 20 metabolic pathways were significantly different and had fold-change > 2 from week 1 to week 3 in antibiotic-naïve infants. In contrast, 34 metabolic pathways genes were significantly different in infants that received antibiotics