Integrated transcriptomic and metabolomic analyses reveal host–metabolite interactions underlying cloacal inflammation in laying Pekin ducks

Objective: Cloacal inflammation in laying ducks, often accompanied by prolapse, poses a major threat to animal welfare, productivity, and intestinal health. However, its underlying molecular and metabolic mechanisms remain largely unclear. Methods: Histological examination, transcriptomic sequencing, and metabolomic profiling were performed on cloacal tissues and contents from inflamed and healthy laying Pekin ducks. Cross-omics integration was used to identify coordinated molecular and metabolic changes. Results: Hematoxylin and eosin staining showed a loose and disorganized structure of the cloacal sphincter in inflamed Pekin ducks. Transcriptomic analysis identified differentially expressed genes enriched in immune signaling, inflammatory response, and epithelial repair pathways. Metabolomic profiling revealed significant alterations in taurine- and lipid-related metabolic pathways. Integrated analysis highlighted coordinated changes between immune-related genes (COL6A3, SPARC, PPEF1, HSD17B2, and KCNG2) and key metabolites including Hydroxytyrosol-Ac, Phytol, GG-alcohol, MeCys-SO, Thiazoline, and PEA-glu. Conclusion: These findings provide a multi-omics view of cloacal inflammation in laying Pekin ducks and identify host-metabolite interactions potentially involved in immune activation and epithelial barrier dysfunction.