The gut resistome in poultry production: microbial ecology, antibiotic use, and sustainable control approaches

Abstract

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.

Key findings

• ▸Long-term and poorly managed antibiotic use transforms the poultry intestine into a significant reservoir of antibiotic resistance genes (ARGs).
• ▸The composition of ARGs is influenced by resistant bacterial taxa, mobile genetic elements, gut metabolic conditions, and production system features.
• ▸Transmission of ARGs occurs through interconnected pathways linking breeder flocks, hatcheries, production facilities, and manure management systems.

Keywords

Identifiers

DOI

10.3389/fmicb.2026.1768747

Journal

Frontiers in Microbiology

Year

2026