Comparative Analysis of Meat Quality and Hindgut Microbiota of Cultured and Wild Bighead Carp (Hypophthalmichthys nobilis, Richardson 1845) from the Yangtze River Area

Wild fish are often considered more nutritionally valuable than cultured fish. This study aimed to elucidate the relationship between the gut microbiota and meat quality through the gut–muscle axis. Therefore, cultured and wild bighead carp (Hypophthalmichthys nobilis, Richardson 1845) from the Yangtze River were investigated to compare the differences in the meat quality and gut microbiota composition. Cultured bighead carp were collected from four intensive ponds along the Yangtze River area, while wild bighead carp were obtained from three different sites in the Yangtze River. The results showed that wild bighead carp muscle had significantly higher total saturated fatty acid (∑SFA) and total ω − 3 polyunsaturated fatty acid (∑n − 3 PUFA) content and water-holding capacity and lower lipid, histidine, and total ω − 6 polyunsaturated fatty acid (∑n − 6 PUFA) content than cultured bighead carp, while the muscle texture was not significantly different between the two groups, with the exception of the resilience. Moreover, the hindgut microbiota was analyzed using 16S rRNA high-throughput sequencing. The alpha and beta diversity differences between the cultured and wild groups were significant. The LEfSe analysis revealed Mycobacterium, Longivirga, and Acetobacteroides as biomarkers in cultured bighead carp, while Clostridium_T and other Firmicutes-associated genera were predominant in wild bighead carp. Regarding the relationship between the hindgut microbiota and meat quality, Mycobacterium exhibited a positive correlation with the muscle n-6 PUFA content and a negative correlation with muscle n − 3 PUFAs, while Clostridium_T exhibited the opposite pattern. According to the ecological network, the abundance of Actinobacteria could serve as a significant indicator of variations in the abundance of Mycobacterium and Clostridium_T. Consequently, differences in meat quality, particularly in the fatty acid composition, were observed between wild and cultured bighead carp. These differences may be associated with variations in the hindgut microbiota, shedding light on the gut–muscle axis.