Background Under the "One Health" framework, untreated livestock waste serves as a critical vector for the cross-domain proliferation of antibiotic resistance genes (ARGs). While integrated anaerobic digestion-composting systems are increasingly adopted for agricultural waste treatment, the dynamic succession of ARGs and the regulatory roles of quorum sensing (QS) and viral communities during the drastic environmental transitions remain critically unexplored. 

Results We applied comprehensive viromic and metagenomic analyses to track the dynamic fate of ARGs, ARB (antibiotic resistance bacteria), QS, and viral communities across a single campaign of full-scale anaerobic digestion-composting system treating cattle slurry. The relative abundance of total ARG (RPKG) was higher in cattle slurry digestate than in raw cattle slurry and lower in mature compost than in compost feedstock. The relative abundance of VFG-carrying contigs (RPKM) was also lower in mature compost than in compost feedstock. However, specific high-risk ARGs, notably aac(3)-VIIa and sul1, exhibited extreme recalcitrance. At the maturation stage, we revealed that thermotolerant taxa, predominantly Bacillota and Actinomycetota, dominated the ultimate high-risk ARB. Crucially, the carriage of specific QS regulatory genes (LuxR and DGC) within ultimate high-risk ARB exhibited a highly significant positive correlation (R² > 0.82, P < 0.001) with ARG and virulence factor gene (VFG) abundances. Furthermore, while lytic phages dominated the viral community, the thermophilic stage coincided with a marked decoupling of phage and ARB-host abundance trajectories, consistent with reduced viral abundance under thermal stress.

Conclusion Within this campaign, mean ARG abundance (RPKG) was higher in cattle slurry digestate than in raw cattle slurry. Mean ARG and VFG abundances (RPKG) were lower in mature compost than in compost feedstock. Nevertheless, aac(3)-VIIa, sul1, and tet(M), together with ARG-carrying MAGs affiliated with Bacillota and Actinomycetota, remained detectable in mature compost. QS (LuxR and DGC) is associated mainly with persistence and potential horizontal gene transfer, whereas phages act chiefly as ecological predators and rarely carry ARGs, so that resistant-bacteria persistence coincided with weaker virus–host coupling at high temperature, rather than providing evidence for transduction. These observations suggest biologically targeted interventions (e.g., QS inhibitors or sequential phage inoculation) as candidate strategies whose feasibility and efficacy remain to be tested across different feedstocks, seasons, and full-scale operating conditions before any general management recommendation can be made.