Fig. 4: A reference protein catalog and resistance genes.

a The non-redundant proteins were annotated based on four functional categories (COGs, KOs, and CAZy). Percentages of identified genes in the specified functional categories are shown. b The distribution shows carbohydrate enzyme classifications. c All ARGs were classified according to the antimicrobial for which they showed resistance. d The abundances and numbers of ARGs are presented for each sample. e The abundance of 22 core ARGs in each of pig populations, and their corresponding antimicrobial classes and resistance mechanisms. The ARGs existing in at least 95% of samples were defined as core ARGs in pig feces. Two color bars on the left of the heatmap represent the resistance mechanism and corresponding antimicrobial class of each resistance gene, respectively. f The identification shows the number of non-redundant proteins classified as various types of mobile elements. g We define and annotate ARG-MGE contigs, and subsequently integrate the analysis with the differential results between high-intensity and low-intensity farming communities. h MGCs of the UPGG are compared between kSGBs and uSGBs. All the MGCs were separated into eight classes. i The relative frequency of MGC types across dominant phyla shows that MGC genes are predominantly identified in Bacteroidota, Firmicutes, Proteobacteria and Actinobacteria. j The largest hybrid MGC predicted by gutSMASH harbored three MGC functional domains, potentially encoding different metabolic pathways. PDU pdu operon, NADHD Threonine to propionate; PROP, Threonine to propionate.