Global panorama of phage-host interactions driving antimicrobial resistance gene transfer in livestock manure anaerobic digestion

Antimicrobial resistance poses a global threat to human health, with livestock manure being a major reservoir of antimicrobial resistance genes (ARGs). Here, we present a global analysis of 205 metagenomic and 36 meta-transcriptomic datasets from anaerobic digestion (AD) systems treating livestock manure. We reveal that pig manure AD harbors the highest ARG abundance (0.709 ARGs/16S rRNA genes), and the expression of ARGs was found to be at a lower level (abundance/transcription < 0.24). A global viral database of livestock manure AD (GVD_LMAD) comprising 59,316 non-redundant DNA viral operational taxonomic units (vOTUs) and 727 non-redundant RNA vOTUs was established. While lytic phages predominantly reduce ARGs by lysing antimicrobial resistant bacteria, the reproduction and transduction role of viral communities on the transfer of ARGs were also elucidated. We further built the global antiviral defense systems (ADS) catalogue of livestock manure AD (GADSC_LMAD), encompassing 33,996 ADS-related genes, which not only protect antimicrobial resistant bacteria from phage predation but also inhibit the transfer of ARGs. Our findings provide actionable insights for enhancing the reduction of ARGs in livestock manure AD, and underscore the need to integrate phage ecology into AMR mitigation strategies.