Multi-Omics Analysis Reveals Age-Dependent Metabolic Remodeling and Immune Maturation in the Cecum of Liangshan Yanying Chickens

Liangshan Yanying chicken is a valuable plateau-adapted indigenous poultry breed in China. The poultry cecum modulates nutrient metabolism, gut microbial colonization and intestinal immune barrier establishment, while the molecular mechanisms driving its age-dependent development during the brooding stage remain unclear. Here, integrated transcriptomic and metabolomic profiling coupled with bioinformatics correlation analysis were conducted on cecal samples collected from chickens at post-hatching days 1, 14 and 28. Significant temporal changes were observed in cecal gene expression and metabolite abundance, and day 14 was identified as a critical window for cecal functional maturation and microbial colonization. In total, 2424 metabolites were annotated, including 600 differentially accumulated metabolites. The cecum exhibited phase-specific metabolic patterns: endogenous energy metabolism dominated at 1–14 d, while lipid biosynthesis prevailed at 14–28 d. The intestinal IgA immune network was verified as the core pathway maintaining cecal immune homeostasis in young chicks. Multi-omics conjoint analysis yielded 53 overlapping KEGG pathways, 14 core pathways, 3 pivotal metabolites and 5 hub genes, based on which three interactive regulatory networks were constructed. Transcriptomic data were validated via qRT-PCR. This study reveals cecal metabolic remodeling and regulatory characteristics during the brooding period, supplementing gut developmental research on plateau indigenous chickens. Notably, these results reflect age-related cecal developmental changes rather than breed-specific high-altitude adaptation mechanisms. Further independent verification is required for metabolomic data and predicted regulatory networks. This finding provides a theoretical basis for scientific breeding and feeding management of Liangshan Yanying chickens.