REVIEW article
Front. Microbiol.
Sec. Microorganisms in Vertebrate Digestive Systems
This article is part of the Research TopicMicrobiome and its Roles in Disease Diagnosis and Treatment: Pathogen Resistance Spectrum, Metabolism, Risk Model, and Vaccine DesignView all 14 articles
The Gut Resistome in Poultry Production: Microbial Ecology, Antibiotic Use, and Sustainable Control Approaches
Provisionally accepted
Zonghui Jian1*
Yuwei Qian2
Shichun He1
Ruohan Zhao1Ke Li3Jinlong Cha1Zhijun Ning1Yanlin Ye1Zhipeng Bao1Kun Wang2
Changrong Ge2Junjing Jia2Tengfei Dou2Yuanyuan Hu1Xiaoming He1*
Shaoxiong Lu2*- 1Yunnan Vocational and Technical College of Agriculture, Kunming, China
- 2Yunnan Agricultural University, Kunming, China
- 3Institute of Poultry Science, Yunnan Academy of Animal Husbandry and Veterinary Sciences, Kunming 650201, Yunnan Province, China, China
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Antibiotics remain central to modern poultry production, but their long-term and sometimes poorly managed use has markedly altered gut microbial ecology, effectively transforming the intestine into a substantial reservoir of antibiotic resistance genes (ARGs). In poultry, the composition of ARGs reflects not only resistant bacterial taxa but also the activity of mobile genetic elements, shifts in gut metabolic conditions, and features of the surrounding production system. This review synthesizes current understanding of both the structural and functional features of the poultry resistome, with particular attention to key bacterial hosts and the mobile genetic elements they carry. We further evaluate how different antibiotic-use patterns and additional co-selective pressures alter microbial communities and contribute to the persistence of ARGs. We also delineate the major transmission pathways that link breeder flocks, hatcheries, production facilities, and manure management, and interpret these connections within a One Health perspective. Particular emphasis is placed on microbial and nutritional interventions that influence gut microbial interactions, epithelial barrier integrity, and metabolic signaling. Drawing on these findings, we propose a resistome–microbiome– metabolome axis that links microbial taxa, resistance elements, and key metabolic signals, offering a conceptual framework for developing more targeted antimicrobial resistance mitigation strategies in poultry systems.
Keywords: antibiotic resistance genes, gut microbiome, Mobile geneticelements, Poultry gut resistome, Resistome–microbiome–metabolome axis
Received: 16 Dec 2025; Accepted: 30 Jan 2026.
Copyright: © 2026 Jian, Qian, He, Zhao, Li, Cha, Ning, Ye, Bao, Wang, Ge, Jia, Dou, Hu, He and Lu. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) or licensor are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.
* Correspondence:
Zonghui Jian
Xiaoming He
Shaoxiong Lu
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