Fig. 2: Microbiota composition.

a Kernel density plot of antibiotic exposures. The 5 most common antibacterial antibiotic exposures are included. Azithro: azithromycin; CPN 3 + : 3rd or higher generation cephalosporins; Doxy: doxycycline; FQN: fluoroquinolones. b Beta diversity and ordination visualized by principal coordinate analysis. Aitchison’s distance was used to quantify the overall compositional difference between samples. The first two principal coordinates (PC1 and PC2) are shown. Numbers in parentheses indicate percent variation explained by the corresponding axis. Each symbol represents a sample. The centroid of each cluster is shown by a larger symbol. 95% ellipses are shown. A timepoint density plot is added at the bottom border. c Species-level microbiota heatmap visualizing the results of unsupervised hierarchical clustering using centered log-ratio transformed abundances and a ward.D function. Each column is a sample and each row is a species. The blue-red gradient shows species abundances scaled row-wise. Timepoints and sites are added along the top border. d–f Family-level microbiota composition grouped based on site and timepoint, with the 15 most abundant families in each site shown. Less abundant families are grouped together. c: class; o: order (insufficient resolution for family classification).