Extended Data Fig. 6: Metagenomic analysis of antimicrobial resistance genes (ARG) during the experiment of preservation of colonization resistance against C. difficile.

a. Analysis of the abundance of ARG reveals significant enrichment in ampicillin-treated mice receiving L. lactis EV but not in mice receiving L. lactis spTEM1. Stacked bar data are presented as reads mapping the different CARD database categories and normalized to the size of the read pool in each sample. Vector-derived ARG in the β-lactam and chloramphenicol classes are presented as a different category to differentiate them from endogenous ARG. Adjusted p-values were calculated with a negative binomial generalized linear model with Tukey’s post hoc test between spTEM1-treated and EV-treated groups. b. Abundance of endogenous and L. lactis spTEM1-derived β-lactamases in the mouse. Elimination of the ampicillin selective pressure by the spTEM1 β-lactamases reduces the enrichment of endogenous β-lactamases in the mouse gut. Rapid elimination from the system of the spTEM1 gene fragments compared to endogenous β-lactamase genes suggests lack of competitive advantage in the spTEM1 strain. n = 8 mice in each L. lactis spTEM1 and L. lactis EV groups. p-value significance corresponds to FDR-corrected two-sided Wilcoxon tests comparing ARG abundance values against baseline values at the pre-treatment timepoint. Means and standard deviations of biological replicates are shown.