Fig. 5.

Taxonomical assignment of the resistome at family level. The abundance of antimicrobial resistance genes (ARGs) taxonomically assigned was expressed in counts per million, selecting the 10 most abundant taxonomical families harboring ARGs. a Pie chart distribution of total AMR abundance per antimicrobial class (colors), per taxonomical family, production system and sample type; the size of each pie chart is proportional to the ARGs abundance within each group. b Pie chart distribution of the 20 most abundant ARGs in the 10 most abundant taxonomical families harboring ARGs (colors), per taxonomical family, production system and sample type; the less abundant ARGs were grouped into “others”. n = 105 metagenomes from 38 independent farms. Nineteen metagenomes per sample type per production system were used, with the exception of extensive-slurry (n = 9). MLSP refers to the macrolides-lincosamides-streptogramins-pleuromutilins AMR class