Spatial heterogeneity determines the gastrointestinal microbiome signatures in Pekin ducks

The gastrointestinal tract (GIT) hosts a complex and abundant microbial ecosystem that is essential for maintaining animal health and optimizing production performance. However, most studies have been confined to individual intestinal segments, underscoring the need for a more holistic understanding of microbial communities across various GIT segments in animals, including Pekin ducks which is important to global poultry meat production. Here, we conducted 16S rRNA sequencing to characterize the microbial landscape along four GIT segments in 313 Pekin ducks (raised with commercial diet) and correlated them with blood biochemical indicators at day 42. Analyses of microbial composition, diversity, functional potential, and co-occurrence networks revealed significant spatial heterogeneity in microbial colonization patterns along the GIT. The small intestine exhibited higher α-diversity than the cecum, and the most complex co-occurrence network presented in ileum. Besides, segment-specific functional specialization of intestinal microbiota reflected their adaptation to local environments. This compartmentalization of GIT microbial communities into functional units underscores regionally encoded functional heterogeneity. These findings enhance our understanding of GIT microbiota in Pekin ducks, informing strategies for feed optimization and breeding improvements.