Metabolomics and Transcriptomics Reveal the Effects of Fermented Lycium barbarum (Goji) Berry Residue on Muscle Nutrition and Flavor Quality in Fattening Tan Sheep

Background/Objectives: In the context of increasing consumer demand for high-quality meat, this study aimed to evaluate the effects of 4% fermented goji berry residue supplementation on meat quality and flavor characteristics in finishing Tan sheep. Methods: Thirty-six male lambs were randomly assigned to a control and FGB group and fed for 68 days. Results: FGB supplementation significantly enhanced Longissimus Dorsi (LD) brightness (L*), redness (a*), and crude protein content, while reducing crude fat (p < 0.05). Amino acid analysis revealed significant increases in lysine, methionine, histidine, glycine, proline, arginine, cysteine, and total sweet-tasting amino acids in the FGB group (p < 0.05). Lactate and inosine monophosphate (IMP) levels were significantly elevated, whereas hypoxanthine levels decreased (p < 0.05). Metabolomics identified 189 metabolites, with 12 differentially expressed, mainly enriched in butanoate metabolism, glycolysis/gluconeogenesis, PI3K-Akt, and HIF-1 signaling pathways. Transcriptomics revealed 382 differentially expressed genes, including key regulators of lipid metabolism (FOXO1, SLC2A4, LPIN1, IGF1, SPP1) and amino acid metabolism (COL3A1, GLUL, PSMC1). Conclusions: Fermented goji residue altered amino acid and lipid metabolism in the LD muscle of Tan sheep, affecting meat quality and flavor traits. However, effects on color (L*, a*, b*), protein content, and shear force varied across the four muscles studied, indicating that responses to supplementation are muscle-specific. These findings offer a sustainable strategy for improving meat quality and provide insights into the molecular mechanisms underlying flavor development in ruminants.