Fig. 5

Effect of prophylactic antibiotic treatment on ARG composition and diversity of the chicken gut microbiome. Chord diagrams showing the relative abundance of ARGs in the intestinal contents collected from A the LAT and B SAT trials. The outmost circle lists the names of intestinal content samples and detected ARG types. The connecting lines inside the circle links ARG types to samples, and the width of the lines is proportional to the relative abundance (%) of each ARG type in the corresponding sample. C Box plots showing total ARGs abundance and Shannon diversity index of the resistome in the cloacal swabs collected from the SAT trial at 25 dph (*P < 0.05, ANOVA, Tukey HSD test). D PCoA plot of the ARG communities in the cloacal swabs collected from the SAT trial at 25 dph based on the Bray–Curtis distances. Below and left boxplots show the overall distribution of PCoA 1 and PCoA 2 scores within each group, and the red asterisk (*) indicates significant difference compared to the NAB-S group (*P < 0.05, **P < 0.01, Wilcoxon rank-sum test)