Cecal microbiota-host phenotype associations in young White Leghorn and Silky Fowl chickens

Genetic background and intestinal region both shape the gut microbiota, yet their relative contributions before the onset of laying remain poorly defined. This study compared intestinal traits and luminal microbiota of the duodenum, jejunum, ileum, and cecum between White Leghorn (WL) and Silky Fowl (SF) chickens at 42 days of age (20 birds per breed; 160 samples). Microbiota were characterized by 16S rRNA gene sequencing, followed by diversity, differential abundance, co-occurrence network, functional prediction, and microbiota-phenotype association analyses. Body weight did not differ between breeds, whereas WL showed higher liver, spleen, and bursa of Fabricius indices and greater length and relative length in all four segments (P < 0.05); SF showed a higher eviscerating rate (P < 0.05). Intestinal segment explained more community variation than breed, with Lactobacillus dominating the small intestine and richness and phylogenetic diversity highest in the cecum. Community composition differed between breeds in the duodenum, jejunum, and cecum (q < 0.05) but not in the ileum. Cecal richness was higher in WL, whereas Shannon diversity did not differ between breeds. In the cecum, Bacteroides was enriched in SF and Megamonas and Lactobacillus in WL (P < 0.05). Co-occurrence networks and predicted functions were breed- and segment-specific, with pathways showing higher predicted abundance in WL concentrated in the duodenum and jejunum and predicted glycan- and carbohydrate-degradation pathways showing higher abundance in SF in the ileum and cecum. Of the four segments, only the cecal predicted functional profile was associated with the measured host phenotypes (RDA P = 0.022), with Bacteroides associated with body weight and eviscerating rate and Megamonas associated with intestinal length traits. Breed-associated microbial differences were therefore detectable at 42 days of age, well before the onset of laying, and were distributed unevenly along the intestinal tract, with the cecum the only compartment in which microbial composition, richness, and predicted functional profiles showed associations with the measured host phenotypes.