A global livestock virome catalog links viruses with resistome assembly
Abstract
Livestock manure is a prominent One Health setting for antimicrobial resistance (AMR), yet the contribution of viruses to resistome assembly remains unresolved. Here we compile the Livestock Manure Virus Database (LMVD), a global catalog of 1,330,372 viral operational taxonomic units reconstructed from 4,017 metagenomes. Livestock manure viral communities exhibit restricted biogeographic distributions, and antibiotic use and farming scale show the highest relative predictive importance for viral diversity. Viral genomes contained 78 antibiotic resistance gene (ARG) subtypes, representing 9.1% of resistome diversity in livestock manure, but virus-encoded ARGs were infrequent. Bacteriophages instead showed extensive predicted links to bacterial hosts, with nearly all antibiotic-resistant bacteria linked to viruses, predominantly temperate viruses, and enrichment in pathogenic antibiotic-resistant bacteria. Together, these findings place bounds on the contribution of viruses to direct ARG dissemination and indicate that lysogenic interactions with resistant hosts may shape AMR risk.
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BibTeX
@article{jiang2026global,
title = {{A global livestock virome catalog links viruses with resistome assembly}},
author = {Lan Jiang and Bintao Li and Liusheng Lei and Zishu Liu and Wei Sun and Liping Ma and Chang-Jun Cha and Timothy Johnson and Jing Yu and Zeyou Chen and Yiran Zhang and Guangdong Wang and Chengcheng Yao and Xiaoyu Fan and Fengjia Liu and Wenshan Yang and Wenyan Wang and Haihan Zhang and James Tiedje and Xun Qian},
journal = {Nature Communications},
year = {2026},
month = oct,
doi = {10.1038/s41467-026-78855-5},
url = {https://www.nature.com/articles/s41467-026-78855-5},
note = {CC BY 4.0},
}
RIS
TY - JOUR
TI - A global livestock virome catalog links viruses with resistome assembly
AU - Lan Jiang
AU - Bintao Li
AU - Liusheng Lei
AU - Zishu Liu
AU - Wei Sun
AU - Liping Ma
AU - Chang-Jun Cha
AU - Timothy Johnson
AU - Jing Yu
AU - Zeyou Chen
AU - Yiran Zhang
AU - Guangdong Wang
AU - Chengcheng Yao
AU - Xiaoyu Fan
AU - Fengjia Liu
AU - Wenshan Yang
AU - Wenyan Wang
AU - Haihan Zhang
AU - James Tiedje
AU - Xun Qian
PY - 2026
DA - 2026/10/23
JO - Nature Communications
DO - 10.1038/s41467-026-78855-5
UR - https://www.nature.com/articles/s41467-026-78855-5
AB - Livestock manure is a prominent One Health setting for antimicrobial resistance (AMR), yet the contribution of viruses to resistome assembly remains unresolved. Here we compile the Livestock Manure Virus Database (LMVD), a global catalog of 1,330,372 viral operational taxonomic units reconstructed from 4,017 metagenomes. Livestock manure viral communities exhibit restricted biogeographic distributions, and antibiotic use and farming scale show the highest relative predictive importance for viral diversity. Viral genomes contained 78 antibiotic resistance gene (ARG) subtypes, representing 9.1% of resistome diversity in livestock manure, but virus-encoded ARGs were infrequent. Bacteriophages instead showed extensive predicted links to bacterial hosts, with nearly all antibiotic-resistant bacteria linked to viruses, predominantly temperate viruses, and enrichment in pathogenic antibiotic-resistant bacteria. Together, these findings place bounds on the contribution of viruses to direct ARG dissemination and indicate that lysogenic interactions with resistant hosts may shape AMR risk.
SN - 2041-1723
ER -