Effects of Different Farming Models on Muscle Quality, Intestinal Microbiota Diversity, and Liver Metabolism of Rice Field Eel (Monopterus albus)

As consumer demand for quality fish products continues to rise, quality has become a key factor in market competition. Ecological aquaculture research is exploring various farming methods to balance high-quality demand with environmental protection. This study compared three aquaculture models-cage culture (CG), recirculating aquaculture (RAG), and rice-fish co-culture (RG)-by analyzing muscle quality (AOAC, GC-MS), intestinal microbiota (16S rRNA), and liver metabolism (LC-MS) to assess their effects on <i>M. albus</i>. In terms of muscle quality, the RG group showed increased levels of EPA and DHA, reduced muscle moisture and crude lipid content, and enhanced crude protein accumulation. The crude protein content was significantly higher in the RAG group than in the CG group (<i>p</i> < 0.05). The RG group also had the highest levels of total, essential, and umami amino acids, followed by the RAG and CG groups. In terms of intestinal microbiota, the RG group had the highest microbial diversity and stability, with increased abundance of Firmicutes and Bacteroidetes and decreased levels of Proteobacteria. Compared to the CG, the RAG group also showed increased microbial diversity and a reduction in pathogenic genera. Liver metabolomics analysis demonstrated that the RG group had significant advantages over the CG group in amino acid, lipid, and energy metabolism. The RAG group exhibited upregulation of glycerophospholipid metabolism and a decrease in oxidative stress marker levels. Overall, the RG group enhanced muscle quality and optimized intestinal and liver metabolism in <i>M. albus</i>.