Academic Journal
Composting Restructures Chicken Manure Viral Communities and Attenuates Virus-Associated Antibiotic Resistance Signals: Paired Metagenome and Virome Analyses.
| Title: | Composting Restructures Chicken Manure Viral Communities and Attenuates Virus-Associated Antibiotic Resistance Signals: Paired Metagenome and Virome Analyses. |
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| Authors: | Liu W; Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang 110016, China., Wang Y; CAS Key Laboratory of Forest Ecology and Silviculture, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang 110016, China.; University of Chinese Academy of Sciences, Beijing 100049, China., Ma J; Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang 110016, China., Liang X; CAS Key Laboratory of Forest Ecology and Silviculture, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang 110016, China.; University of Chinese Academy of Sciences, Beijing 100049, China., Yang L; Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang 110016, China. |
| Source: | Viruses [Viruses] 2026 Jul 19; Vol. 18 (7). Date of Electronic Publication: 2026 Jul 19. |
| Publication Type: | Journal Article |
| Language: | English |
| Journal Info: | Publisher: MDPI Country of Publication: Switzerland NLM ID: 101509722 Publication Model: Electronic Cited Medium: Internet ISSN: 1999-4915 (Electronic) Linking ISSN: 19994915 NLM ISO Abbreviation: Viruses Subsets: MEDLINE |
| Imprint Name(s): | Original Publication: Basel, Switzerland : MDPI |
| MeSH Terms: | Manure*/virology , Manure*/microbiology , Drug Resistance, Microbial*/genetics , Viruses*/genetics , Viruses*/classification , Viruses*/isolation & purification , Viruses*/drug effects , Metagenome* , Composting* , Virome*, Chickens/virology ; Animals ; Metagenomics ; Genome, Viral |
| Abstract: | 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. |
| Grant Information: | 42407182 National Natural Science Foundation of China |
| Contributed Indexing: | Keywords: DNA virus; antibiotic resistance genes; chicken manure; composting; viral particle enrichment; virus–host linkages |
| Substance Nomenclature: | 0 (Manure) |
| Entry Date(s): | Date Created: 20260728 Date Completed: 20260729 Latest Revision: 20260729 |
| Update Code: | 20260730 |
| DOI: | 10.3390/v18070789 |
| PMID: | 42515641 |
| Database: | MEDLINE |
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