Multi-omics profiling reveals gut segment-specific and age-associated microbial restructuring linked to host phenotypic maturation in Taihu geese.

Taihu geese are valued for efficient utilization of fibrous feed resources and for desirable meat quality, yet how gut microbial organization varies across intestinal regions and physiological stages, and how these changes relate to host phenotype, remains unclear. We integrated 16S rRNA gene sequencing, ITS sequencing, shotgun metagenomics, and host phenotyping to characterize intestinal microbial ecology in Taihu geese at 160 days of age (D160; physiological stability stage) and 450 days of age (D450; late-laying stage). Spatial profiling of the D160 group across the duodenum, jejunum, ileum, and cecum identified the cecum as the major microbial fermentation niche, with the highest bacterial diversity and enrichment of fiber-associated genera such as Bacteroides and Faecalibacterium. Shotgun metagenomics further showed that the cecum harbored the most extensive repertoire of carbohydrate-active enzymes, especially glycoside hydrolases. Between-stage comparison of the cecum revealed marked age-associated restructuring: the D160 microbiome was characterized by higher abundances of Faecalibacterium and Subdoligranulum, whereas the D450 microbiome was enriched in Bacteroides, Treponema, and several other taxa associated with complex carbohydrate utilization. These taxonomic shifts were accompanied by an expanded CAZyme repertoire and enrichment of pathways related to tryptophan metabolism and ribosome function in the D450 group. At the host level, D450 geese exhibited greater breast muscle weight, altered plasma glucose and lipid indicators, reduced muscle moisture, and increased intramuscular fat in leg muscle. Mantel analysis further linked representative cecal taxa, particularly Bacteroides and Treponema, with breast muscle weight and skeletal traits. The cecum is the principal microbial and functional hub in Taihu geese. Cecal microbiome undergoes pronounced age‑associated restructuring, which co‑occurs with shifts in host metabolic and production‑related phenotypes, providing a foundation for microbiome-informed nutritional strategies in goose production.