Multi-Omics Analysis of Gut Microbiota and Metabolites Reveals the Effects of Rearing Systems on the Duodenum and Cecum Gut Barriers of Lueyang Black-Bone Chickens

Gut health is a crucial factor influencing poultry growth, immunity, and meat quality, with the gut barrier playing a pivotal role in maintaining gut health. This study used Lueyang Black-Bone chickens as the research subjects. Through animal gut histology analysis, 16S rRNA sequencing, and LC-MS metabolomics, we investigate the effects of caged rearing and cage-free rearing on the gut barrier by influencing the gut microbiota and metabolites in the Duodenum and cecum. Histological results showed that in the duodenum and cecum, the intestinal wall thickness and goblet cell count of the cage-free rearing group were significantly higher than those of the cage-reared group (P<0.0001). Microbiome analysis revealed significant enrichment of fiber-degrading bacteria, such as Bacteroides and Rikenellaceae_RC9_gut_group, in the caged rearing group, whereas pathogenic bacteria, including Acinetobacter and Campylobacter, predominated in the cage-free rearing group. Non-targeted metabolomics analysis indicated a significant upregulation of bile acid and unsaturated fatty acid metabolites in the caged rearing group. The gut levels of lysophosphatidylcholine (LPC) and phosphatidylcholine (PE) were significantly higher in the cage-free rearing group. Correlation analysis between microbiomics and metabolomics revealed a significant positive correlation between Rikenellaceae_RC9_gut_group and the abundance of bile acids, a metabolite linked to inflammation. Odoribacter and Clostridia_UCG-014 exhibited substantial positive correlations with unsaturated fatty acids and Traumatic Acid. In summary, the results suggest that probiotics in the guts of the caged rearing group influence gut morphology and barrier function through bile acid and unsaturated fatty acid metabolites.