Global multi-omics reveals that virus–host arms race drives antimicrobial resistance genes attenuation and thermophilic persistence in livestock manure composting

Composting is a widely adopted strategy to mitigate the global burden of antimicrobial resistance (AMR) in livestock manure, yet the biological mechanisms driving resistome dynamics, particularly the role of the viral biosphere, remain a black box. Here, we leverage a massive global dataset of 420 metagenomes (9.1Tb) and 42 (840Gb) viromes (GVD_LMC), coupled with paired meta-transcriptomics, to decipher the phage–host evolutionary arms race in the ecological succession composting systems. We demonstrate that while composting effectively acts as an ecological filter, reducing total antimicrobial resistance genes (ARGs) and horizontal gene transfer risks, the process is bottlenecked by the selective enrichment of thermophilic antimicrobial-resistant bacteria (ARB). These recalcitrant hosts dominate (~60%) the residual resistome in the maturation phase, challenging the traditional reliance on thermal inactivation alone. Crucially, we reveal that bacteriophages function as the primary sanitizing agents in this succession, where lytic interactions (accounting for 39.5% of the virus-host network) quantitatively override transduction events (