Fig. 4

Impact of postnatal antibiotic exposure on skin and gut microbiome diversity and maturation. A Microbiuome diversity. Box and whisker plot of microbiome diversity by Shannon Index using the median and interquartile ranges for each cohort. Stool samples showed a decrease in diversity during the first and third weeks after antibiotic therapy, while skin samples from the groin demonstrated decreased diversity by the third week post-antibiotic use (p<0.001, week 1: axilla (n=43), groin (n=43), and stool (n=46) samples in antibiotic-naïve infants vs axilla (n=21), groin (n=21), and stool (n=22) samples in antibiotic-exposed infants; week 3: axilla (n=40), groin (n=43), and stool (n=43) samples in antibiotic-naïve infants vs axilla (n=21), groin (n=21), and stool (n=22) samples in antibiotic-exposed infants). B Microbiome composition. PCA was applied to generalized log2 transformed microbiome composition data from antibiotic-naïve and exposed infants at week 1 and week 3. Samples were then colored by group membership and an ellipse was drawn at the 95% confidence interval around the group centroid. PCA calculation and graphing in the first two dimensions is the same for A and B. Dotted arrows were drawn between the centroids to indicate the magnitude and direction of microbiome difference in the first two dimensions between antibiotic-exposed and antibiotic-naïve infants. MRPP was used to assess the significance of difference in microbiome composition between groups. A At week 1, the composition of gut microbiome was significantly different among antibiotic-exposed infants when compared to antibiotic-naïve infants. At week 3, the composition of groin and gut microbiome was significantly different in antibiotic-exposed and antibiotic-naïve infants. C Overlay of week 1 and week 3 data reveals that antibiotic exposure (dotted arrows) tends to drive microbiome composition in a direction opposite or perpendicular to postnatal age (solid arrows), suggesting that antibiotics blunt the impact of postnatal age on microbiome composition. D Mean Bray-Curtis distances for all pairwise comparisons from week 1 to week 3 were determined in samples from the axilla, groin, and stool in antibiotic-naïve and antibiotic-exposed infants. The mean Bray-Curtis distance is indicated as a solid line. There was a statistically significant decrease in mean Bray-Curtis distance at each body site in antibiotic-exposed infants compared to antibiotic-naïve infants (unpaired t-test p < 0.05) indicating that antibiotic exposure blunts microbiome differentiation from week 1 to week 3 at all three body sites