Fig. 4: Antibiotic treatment had longer-lasting effects on the adult gut microbiome than on the infant gut microbiome, as reflected in microbial composition, ARG and MGE profiles, and plasmid abundance.

Duration of the effect of antibiotic administration on the β-diversity (Bray–Curtis distance) of microbiome, ARG and MGE compositions in the adult gut (a) and in the infant gut (b). Adult subjects were divided into four groups depending on when they had taken antibiotics: within 6 months of sampling, 6 to 12 months prior, 1 to 2 years prior, or 2 to 6 years prior to sampling; the corresponding control groups had not received antibiotics in those periods. Infant subjects were divided into four groups depending on when they had taken antibiotics: within 15 days of sampling, 15 to 30 days prior, 1 to 3 months prior, and 3 to 6 months prior; the corresponding control groups had not received antibiotics in those periods. P-value obtained from the PERMANOVA test and red indicates P < 0.05 (significant difference). Duration of the effect of antibiotic administration on total plasmid abundance in the adult gut (c) and in the infant gut (d). The four studied periods are the same as in a or in b. “+” represents antibiotics administered in a given period, and “−” represents antibiotics not administered in a given period. P-value from the Wilcoxon test and red indicates P < 0.05 (significant difference). The box plots (c, d) display 25th, 50th (median), and 75th percentiles, with whiskers extending 1.5 * IQR. All P-values were derived from two-sided tests.