Fig. 5: Genome pairs of identical ARGs in soil and other habitats.

a Workflow for finding genome pairs with identical ARGs. b Proportion of genome pair with identical ARGs between soil-soil and soil-other habitats. Soil indicated that the genome pairs were both from the soil habitat. c SNPs between various genome pairs. The pie chart represented the proportion of SNPs with counts ≥1000 and <1000. All calculations (44,905,050 pairs) were included. d Percentage of VGT (SNP < 1000) and HGT (SNP ≥ 1000) in various habitats. e Phylogenetic tree of genomes isolated from soil and cattle with SNP ≥ 1000. f Phylogenetic tree of genomes isolated from soil and humans with SNP ≥ 1000. g Phylogenetic tree of genomes isolated from soil and chicken with SNP ≥ 1000. h Phylogenetic tree of genomes isolated from soil and swine with SNP ≥ 1000. i Proportion of genome pair with identical ARGs between soil-soil and soil-other habitats in different periods. Soil indicated the genome pairs were both from the soil habitat. In the boxplots of panels, hinges indicate the 25th, 50th, and 75th percentiles, whiskers indicate 1.5× interquartile ranges, and dots indicate the average value from each random sampling (n = 999 rounds of random sampling). Significant comparisons (two-sided t test) between different habitats and different periods were calculated, and detailed p value and T stat were provided in the Supplementary Data 13. j Changes in identical Rank I ARGs copy numbers between soil and human across different periods. The copy numbers of Rank I ARGs was normalized to a range of 0 to 1 in each period.