Gut microbial community assembly exhibits compartment-specific responses to selection for high body weight in female chickens.

Conventional poultry breeding primarily targets host growth traits, yet breeding may also reshape the gut microbiota through host-microbe interactions. Given the spatial heterogeneity of the chicken gastrointestinal tract, whether divergent selection for body weight is associated with compartment-specific microbial assembly and differences in the digestive ecosystem remains unclear. Here, using female primitive line and a high body weight (HBW) selected line, we systematically characterized differences in host gastrointestinal traits and gut microbial ecology associated with divergent selection history. Significant differences in gut morphology and local environmental conditions were observed between the two lines, together with region-specific shifts in microbial community assembly. Specifically, crop weight was greater and microbial assembly exhibited greater stochasticity in the HBW line, potentially reflecting differences in feeding-related gastrointestinal dynamics. In contrast, the small intestine displayed improved villus morphology and altered microbial assembly patterns, accompanied by enrichment of potentially beneficial taxa associated with nutrient utilization, including Monoglobus in the duodenum and Blautia in the ileum, indicating coordinated changes in host intestinal development and microbial ecological adaptation. The cecal community showed relatively stable assembly patterns but was enriched in metabolically relevant taxa such as Lachnospiraceae and Faecalibacterium, together with differences in predicted functional potential related to nutrient metabolism. Overall, this study shows that the HBW line is associated with distinct, compartment-specific patterns of gut microbial assembly, providing a conceptual framework for considering the gut microbiota in poultry breeding strategies.