Abstract
This study comparatively analyzed the spatial heterogeneity of the gut microbiome across gastrointestinal segments in Changle geese versus yellow-feathered broilers to discover their links with growth and intestinal development. Twelve 63-day-old male yellow-feathered broilers and twelve 70-day-old male Changle geese were selected. Body weight (BW), slaughter weight (SW), absolute lengths of the small intestine (LSI) and cecum (LC), and their relative lengths normalized to body size (RLSI/RLC) were measured. Additionally, 16S rDNA sequencing of crop, proventriculus, gizzard, jejunum, cecum, and rectum microbiota was conducted to assess microbial diversity, composition, and its correlation with phenotypes. Results demonstrated higher BW, SW, LSI, LC and lower RLSI and RLC in geese versus broilers (p < 0.001). Alpha diversity analysis revealed lower microbial richness and diversity in broilers across most gastrointestinal segments (p < 0.05), while beta diversity analysis confirmed distinct community structures between two species (p = 0.001). Firmicutes dominated broiler gut microbiota (94.49%), whereas geese exhibited greater phylum-level diversity (p < 0.05). Random forestry analysis identified Top 15 core Amplicon Sequencing Variants in both the cecum and rectum, with ASV12260 (unclassified Lachnospiraceae) and ASV12412 (uncultured Faecalibacterium sp.) as key biomarkers. Correlation analyses found 21 phenotype-related ASVs (p < 0.05). Specially, two Lactobacillus ingluviei strains showed negatively correlated with LSI and RLSI in the chicken foregut (p < 0.05). And two Gallibacterium anatis strains were associated with RLSI, with one strain also showing an inverse correlation with LSI in the goose foregut (p < 0.05). Interestingly, one Peptococcus strain was negatively correlated with BW and SW, while the other was inversely associated with LC and RLC in the goose hindgut (p < 0.05). These findings provide insights into species-specific distribution patterns of gut microbiota across poultry species and their correlation with growth performance and intestinal development, developing a theoretical foundation for advancing avian digestive physiology research and optimizing feeding strategies.