Fig. 3

Microbiome comparison in the nested short-term substudy. A Principal coordinates analysis (PCoA) of bacterial taxon abundances, based on Bray–Curtis dissimilarity. The sub-panels are annotated by subject, age at time of first stool sample following antibiotic exposure, breastfeeding status, and timepoint. In the top-left panel, samples collected from the same subject are connected with lines; ellipses represent the 50% confidence interval for each subject where each color represents an individual. B Relative abundance of taxa as a function of baseline age. C Relative abundance of taxa as a function of timepoints in the short-term substudy. The three taxa with the greatest effect size in response to antibiotics or age are presented