Sichuan bream (Sinibrama taeniatu), an endemic small economic fish in the upper Yangtze River, has achieved captive breeding breakthroughs. To advance standardized and large-scale aquaculture, this study investigated intestinal development, enzyme activities, gut microbiota, and its interactions with rearing water microbiota across six developmental stages (G1–G6) from hatching to sexual maturity of Sichuan bream. Results showed its progressive refinement of external morphology and intestinal developing into multiple flexures. Histology examination revealed four foregut layers with continuously increasing villus height. Digestive enzyme analysis revealed significantly higher activity of trypsin compared to that of amylase and lipase (p < 0.05). 16S rRNA sequencing identified Proteobacteria, Firmicutes, Bacteroidota, Actinobacteriota, and Fusobacteria as the dominant phyla in both gut and rearing water microbiota. Gut communities shifted from Proteobacteria-dominance (C₁–C₅) to Firmicutes-dominance (C6). The microbial source tracking analysis indicated water contributed to gut microbiota of Sichuan bream, particularly during G3. This study clarified the intestinal development patterns and gut microbiota colonization dynamics of Sichuan bream. The findings provide reference materials for the research on the growth patterns and host–microbe interaction of Sichuan bream. They lay a theoretical foundation for the protection and utilization of Sichuan bream resources, ultimately aiding in their proliferation and release.

Hybridization is pivotal for germplasm innovation, yet how reciprocal crossing regulates digestive characteristics in sub-cold-water fish remains unclear. This study systematically compared differences in intestinal morphology, physiological function, and microbial community assembly among herbivorous Schizothorax prenanti, carnivorous S. davidi, and their reciprocal hybrids using histological analysis, digestive enzyme assays, and 16S rRNA sequencing. Results indicated that parental intestinal characteristics were highly consistent with their feeding habits. Orthogonal hybrids exhibited a mosaic phenotype, combining the maternal muscular gut structure with high paternal-like lipase activity, and were characterized by an enrichment of the potential probiotic Lactococcus. In contrast, reciprocal hybrids presented a mismatch between morphology and function: despite developed hindgut folds, key digestive enzyme activities were low, and the gut microbiota was dominated by environmental bacteria such as Methylobacterium. Our findings indicate a spatially dependent assembly dynamic: the host genetic background strongly drives microbiome divergence in the anterior segments (foregut and midgut), whereas the long-term administration of a standardized diet ultimately promotes structural convergence in the hindgut. The orthogonal cross yielded a phenotype characterized by an apparent co-occurrence of specific host enzymes and distinct microbiota, suggesting an inferred physiological potential for lipid digestion that requires further multi-omics validation. These findings provide preliminary insights into the associations between genetic background and intestinal traits, providing a theoretical basis for the targeted breeding of Schizothorax species.