Comparative Analysis of Muscle Nutrients, Lipid Metabolism and Intestinal Microbiota in Pelteobagrus fulvidraco from Rice Field and Pond Culture Modes.

Integrated rice-fish farming is increasingly promoted as a sustainable aquaculture model, yet its effects on flesh quality and gut microbial assembly in Pelteobagrus fulvidraco remain insufficiently understood. Here, we compared pond-cultured (PP) and rice-field-cultured (PR) individuals using growth measurements, muscle amino acid and fatty acid profiling, untargeted LC-MS/MS metabolomics and 16S rRNA gene sequencing. Body weight and length did not differ significantly between groups, whereas PP fish showed greater body width and height. PR fish contained higher levels of Ser, Val, Ile and total essential amino acids, together with amino acid and energy-related metabolites. In contrast, PP fish showed higher concentrations of saturated fatty acids, monounsaturated fatty acids, n-3 polyunsaturated fatty acids, total fatty acids and lipid-associated metabolites. The gut microbiota also differed markedly between culture systems. PP fish exhibited higher α-diversity and enrichment of Proteobacteria, Firmicutes, Pseudomonas and Ralstonia, whereas PR fish were characterized by Verrucomicrobiota, Fusobacteriota, Akkermansia and Cetobacterium. Predicted functions suggested enhanced carbohydrate and energy metabolism in PR fish and stronger environmental-response-related functions in PP fish. These findings indicate that pond and rice-field culture promote distinct quality-forming pathways in yellow catfish, providing a basis for optimizing rice-yellow catfish co-culture toward quality-oriented production.