Distinct gut microbiota signatures in white leghorn and silky fowl are associated with divergent laying performance.

The gut microbiota is a key modulator of nutrient utilization and egg production in laying hens. However, breed-associated differences in gut microbiota during the critical peak laying period, as well as their spatial distribution along the intestinal tract, remain poorly characterized. We compared the microbiota of duodenum, jejunum, ileum, and cecum in high-yielding White Leghorn (WL, n = 20) and niche-adapted Silky Fowl (SF, n = 20) hens at peak lay using 16S rRNA sequencing, with intestinal segments analyzed as within-individual compartments. The small intestinal segments exhibited conserved Lactobacillus dominance in both breeds. In contrast, the cecal microbiota diverged significantly: WL was enriched in Bacteroides (P < 0.05), which was linked to glycan degradation, while SF harbored a higher abundance of Faecalibacterium (P < 0.05), associated with vitamin B12 synthesis. Functional prediction revealed that WL upregulated energy-harvesting pathways such as glycolysis in the small intestines and glycosaminoglycan degradation in the cecum. Conversely, SF prioritized stress-resilience pathways including porphyrin metabolism. These functional profiles aligned with host phenotypes, where Lactobacillus and Bacteroides abundance correlated with hepatic efficiency in WL, and multiple microbiota taxa were associated with maintaining metabolic homeostasis and adaptation in SF. Collectively, our findings demonstrate that breed-specific cecal microbiota and their metabolic functions underlie divergent host resource-allocation strategies during peak lay. These results provide tangible targets for modulating the gut ecosystem through nutritional or breeding strategies, aiming to enhance disease resilience in commercial stocks or improve robustness and productivity in indigenous breeds.