Composting Restructures Chicken Manure Viral Communities and Attenuates Virus-Associated Antibiotic Resistance...

Composting is widely used to reduce biological risks during manure recycling, but changes in viral communities and virus-associated antibiotic resistance genes (ARGs) remain poorly resolved. This study aimed to assess changes in DNA viral communities, eukaryotic viral protein signals, virus-associated ARGs, and predicted virus-host linkages during chicken manure composting using paired analyses of total-community metagenomes and viral-particle-enriched viromes. Both approaches recovered viral assemblages dominated by Uroviricota and lytic viruses but produced distinct profiles. Viromes yielded more taxonomically assigned viral operational taxonomic units and a higher proportion of relatively complete viral genomes, whereas metagenomes produced a larger predicted virus-host network. Composting restructured viral communities, reducing manure-associated genera and enriching stage-specific groups. Eukaryotic viral protein signals declined during composting. Virus-associated ARGs accounted for 24.83-38.76% of ARG abundance in metagenomes and 5.38-45.09% in viromes, with lower abundance and richness in viromes. Selected virus-associated ARGs showed transient early enrichment, particularly in the virome. By maturity, both overall virus-associated ARG signals and higher-risk ARG signals had declined. Predicted virus-host associations included bacterial groups containing potential opportunistic pathogens. These results show that composting restructures viral communities and attenuates virus-associated ARG signals, while metagenomes and viromes provide complementary but non-interchangeable views of viral ecology and ARG risk.