Intensified livestock farming increases antibiotic resistance genotypes and phenotypes in animal feces

We sampled feces from eight Chinese farms, where animals (yak, sheep, pig, and horse) were reared under free range to more intensive conditions, to determine the extent to which intensified farming expands antibiotic resistance in fecal matter, using both genotype and phenotype approaches.The datasets of Ct values from high-throughput qPCR analyses are shown in supplementary Data 1 (*.xlsx). The datasets of TPM values from metagenomic sequencing analyses are shown in Supplementary Data 2 (*.xlsx). All isolated and then identified strains with their sequenced reads are listed in Supplementary Data 3 (*.xlsx). Supplementary Data 4 (*.xlsx) contains all recorded diameters of the inhibition zone (IZD) for these strains tested using the standard disc diffusion assay. Please see the README document for detailed information.