Fig. 4: AMR-mediated via integrons in mice administered with antibiotics.

a Anvi’o based visualization of the Akkermansia muciniphila genomes from the pre- and post-treatment (day 0 and day 21 respectively) samples in blue and purple respectively. Annotations on the outer ring indicate the ‘Core’ genome and the ‘Acquired’ genome partially (75%) mediated by integrons. GC: gene clusters; Geo. Homogeneity Ind.: geometric homogeneity index; Func. Homogeneity Ind.: functional homogeneity index; Comb. Homogeneity Ind.: combined homogeneity index. b Boxplots showing the relative abundance of ARGs linked to integrons. n = 8 biological replicates per group. The center line denotes the median value (50th percentile), while the outer lines of the box represent the 25th–75th percentiles. The black whiskers mark the 5th and 95th percentiles. A two-sided Wilcoxon rank sum test was used to assess significance, where, p-values are indicated by *, i.e., * < 0.05, ** < 0.01, *** < 0.001. c Relative abundance of gene cassettes found to be encoded by phages and plasmids across different groups (n = 8 biological replicates) and timepoints. The center line denotes the median value (50th percentile), while the outer lines of the box represent the 25th–75th percentiles. The black whiskers mark the 5th and 95th percentiles. d Alluvial diagram demonstrating the abundance of ‘complete’ integrons linked with observed ARGs in specific taxonomic families. The flow (gray) bars indicate the number of AMR-linked integrons found in each group. Source data are provided as a Source Data file.