Virus-host arms race driving antimicrobial resistance gene transfer in livestock manure anaerobic digestion

Antimicrobial resistance (AMR) poses a critical global health challenge, with livestock manure acting as a significant environmental reservoir for antimicrobial resistance genes (ARGs). Anaerobic digestion (AD) is a pivotal process for mitigating ARG dissemination at the livestock-environment-human interface. This study aims to elucidate the global dynamics of ARGs in AD systems, focusing on virus-host interactions and arms race, to identify actionable strategies for AMR control. We analyzed 205 metagenomic (4.5 Tb) and 36 meta-transcriptomic (640 Gb) datasets, including 15 newly generated datasets, revealing that pig manure AD harbors the highest ARG abundance (0.709 ARGs/16S rRNA), while AD systems generally exhibit limited transcriptional activation of ARGs. We constructed a viral dataset for livestock manure AD (GVD_LMAD), comprising 59,316 DNA and 727 RNA viral operational taxonomic units (vOTUs). Virus-host interactions revealed 542 lytic infections of antimicrobial-resistant bacteria (ARB) compared to only 12 ARG transduction events, underscoring the predominant role of viral communities in reducing ARG abundance. Furthermore, an antiviral defense system catalogue (GADSC_LMAD), derived from 2,760 high-quality metagenome-assembled genomes (MAGs) containing 39,307 ADS genes, showed a higher ADS gene prevalence in ARB (7.8 ± 6.0 per ARB) compared to non-ARB (6.1 ± 4.6; p