Fig. 6: The effects of different antibiotics on ARG and plasmid abundance, and on the relative abundance of bacterial species.

Changes in ARG abundance (a) and plasmid abundance (b) in the gut of adults who had taken one of five major antibiotics or antibiotic combinations in the year before sampling (N = 5, 6, 7, 7, 20, respectively). Individuals who had not taken antibiotics in that period were used as controls (N = 166). P-value obtained from the Wilcoxon test with FDR adjustment and red indicates P < 0.05 (significant difference). The black diamond indicates the mean value. Changes in ARG abundance (c) and plasmid abundance (d) in the gut of infants who had taken one of three major antibiotics in the 15 days before sampling (N = 16, 17, 11, respectively). Infants who had not taken antibiotics within 15 days of sampling were used as controls (N = 605). P-value obtained from the Wilcoxon test with FDR adjustment and red indicates P < 0.05 (significant difference). The black diamond indicates the mean value. The box plots (a–d) display 25th, 50th (median), and 75th percentiles, with whiskers extending 1.5 * IQR. e Members of the 20 most abundant bacterial species whose abundance in the gut differed significantly between (top) adults who had taken tetracycline or macrolide in the year before sampling and those who had not received antibiotic treatment, and (bottom) infants who had taken antibiotics (mixed effects) in the 15 days before sampling and those who had not within the first year. Relative abundance on the x-axis is shown on a logarithmic scale; black dots indicate median value; P-values were generated by the Wilcoxon rank-sum test and adjusted using FDR. All P-values were derived from two-sided tests.