Integrated Multi-Omics Analysis Reveals Molecular Features Associated with Energy Metabolism Adaptations in Brooding Taihe Black-Bone Silky Fowls

Abstract

Simple Summary Broodiness is an inherent characteristic of female poultry, regulated by genetic, hormonal and environmental factors. This study was conducted using Taihe Black-Boned Silky Fowl (TBSF), a native Chinese chicken breed with a strong brooding tendency. The results indicate that brooding hens had significantly decreased feed intake and body weight, accompanied by altered lipid profiles in liver tissue and serum, as well as variations in hepatic gene expression, gut microbial pathways and serum metabolite levels. Furthermore, significant correlations were detected between gut microbial phyla, circulating metabolites and hepatic gene expression. Multiple lipid and amino acid metabolites were positively associated with specific microbes and genes responsible for lipid and amino acid synthesis. These findings deepen our understanding of key gut–liver axis metabolic targets regulating energy metabolism during broodiness, and provide strategies to improve reproductive performance and production efficiency in poultry. Abstract Broodiness is a natural behavior whereby female birds stop laying eggs to sit on and hatch them. This behavior is regulated through genetic, hormonal, and environmental factors. The Taihe Black-Boned Silky Fowl (TBSF), a Chinese traditional domestic breed, exhibits a strong brooding tendency; however, the molecular mechanisms underlying this trait remain unclear. In this study, we performed an integrated multi-omics analysis to characterize differences between two groups of TBSF hens: 8 individuals undergoing 30 days of active brooding (BR30) and 8 individuals in the normal laying egg stage (NB), selected from a total group of 230 hens. We combined 16S rRNA sequencing, untargeted metabolomics, and hepatic transcriptome sequencing, with statistical analyses including QIIME 1.9.1, OPLS-DA (VIP > 1), Student’s t-test (p ≤ 0.05), and DESeq2 (|log2FC| ≥ 1, FDR < 0.05) for differentially expressed genes (DEGs), respectively, and Pearson’s correlation analysis for multi-omics integration. Phenotypically, brooder hens showed significantly reduced feed intake, body weight, and main digestive tissue indices, alongside altered liver and blood biochemical parameters. Hepatic transcriptome analysis identified 1582 DEGs between groups, enriched in pathways related to fatty acid oxidation and the amino acid degradation pathway. In addition, 16S rRNA sequencing revealed distinct gut microbial community structures: the NB group was enriched in Bacilliota and Pseudomonadota, while the BR30 group was enriched in Spirochaetota and Synergistota. Metabolomic profiling identified a total of 143 differential metabolites, which were enriched in lipid and amino acid metabolites, including alpha-linolenic acid and pyruvate metabolites. Multi-omics correlation analysis revealed tight associations between gut microbial taxa, circulating metabolites, and hepatic gene expression. Specifically, beneficial lipid metabolites, including phospholipids, lysophosphatidylcholines, and sphingomyelins, were positively correlated with Synergistes and the Christensenellaceae R-7, as well as with key hepatic lipid metabolism genes FABP1, LPL, and FADS2. In summary, this study reveals that the gut–liver axis plays a critical part in the modulation of energy metabolism during broodiness, and further highlights new insights into metabolic targets that could optimize reproductive behavior and enhance poultry production.