Molecular and Functional Insights Into the Avian Gut Microbiota: Roles in Health, Disease Resistance, and Microbiome Modulation

The avian gut microbiota constitutes a complex, multiphyla ecosystem that critically shapes host physiology, immune function, disease resistance, and antimicrobial resistance dynamics. Bacteria, archaea, fungi, and viruses collectively regulate nutrient metabolism, mucosal barrier integrity, and immunological maturation, whereas dysbiosis increases susceptibility to pathogens such as Eimeria , Clostridium perfringens , Salmonella sp., and avian pathogenic Escherichia coli (APEC). Despite advances in characterizing microbial composition, major gaps remain in understanding species‐specific microbiota profiles, the mechanistic pathways linking microbes to host immunity, and the dynamics of the resistome under diverse production and environmental conditions. This review is aimed at integrating current knowledge on avian gut microbiota, identifying key research gaps, and providing a mechanistic framework for microbiome‐informed strategies to enhance poultry health, disease resistance, and productivity. We synthesized recent literature from peer‐reviewed studies and multiomics investigations to provide a comprehensive overview of avian gut microbiota and its role in health and disease. This review highlights mechanisms of host–microbe interaction and evaluates strategies for microbiome modulation, including probiotics, prebiotics, synbiotics, postbiotics, phage therapy, and fecal microbiota transplantation. It also discusses emerging computational and functional approaches for predictive microbiome management as scalable tools to enhance disease resistance, vaccine responsiveness, and antimicrobial stewardship in poultry systems. By integrating current research gaps, mechanistic insights, and translational strategies, this review is aimed at providing a framework for advancing poultry health, productivity, and conservation through precision microbiome interventions.