Metagenomic insights into the distribution of antibiotic resistome between the gut-associated environments and the pristine environments

Abstract Antibiotic resistance genes (ARGs) in the environment are promoted by anthropogenic activities, which cause potential risks to human health. However, large-scale quantitative data on antibiotic resistome from the pristine and anthropogenic environments remains largely unexplored. Here, we used metagenome-wide analysis to investigate the share and divergence in ARG profiles and their potential bacterial hosts between the pristine and gut-associated environments. We found that the abundance of total ARGs in gut-associated environments was significantly higher than the pristine environments ( P mcr-1 and tet X, the genes resistant to the last resort antibiotics (colistin and tigecycline, respectively), were in high abundance (4.57 copies/Gb and 3.39 copies/Gb, respectively) in gut-associated environments, suggesting the ARG pollution caused by anthropogenic antibiotics. Metagenomic assembly-based host-tracking analysis identified Escherichia , Bacteroides , and Clostridium as the predominant bacterial hosts of ARGs in gut-associated environments, while Alteromonas , Vibrio , and Proteobacteria as the predominant bacterial hosts of ARGs in pristine environments. We first described the broad diversity of ARG hosts in different environments using metagenome-wide analysis. Our results revealed the heterogeneous distribution of ARGs and their hosts among different microbial niches in gut-associated environments and the pristine environments.