Lowing lysine (Lys): energy ratio based on corn-soybean diets could increase intramuscular fat (IMF) content, the effectiveness of it in enhancing IMF content when corn is partially substituted by wheat is unclear. This study aimed to determine the effects of dietary wheat levels and standardized ileal digestible (SID) Lys: net energy (NE) ratio on growth performance and meat quality, alteration in gut microbiota and body metabolism, as well as its correlation with meat quality are revealed via combined microbiome and metabolomic methods. A total of 72 pigs were randomly divided into four groups and fed with high SID Lys:NE ratio (HR) diets containing 25% wheat (W25HR), low SID Lys:NE ratio (LR) diets containing 25% wheat (W25LR), HR diets containing 55% wheat (W55HR) or LR diets containing 55% wheat (W55LR). Increasing dietary wheat level impaired feed utilization during 65–90 kg phase (P < 0.05) and enhanced meat color values (P < 0.05) of longissimus dorsi (LD) in finishing pigs. Enhancing dietary wheat level decreased relative abundance of Lactobacillus and Coprococcus (P < 0.05), and inhibited microbial carbohydrate metabolism capacity (P < 0.05) in colon of finishing pigs. Changes in microbial composition and carbohydrate metabolism capacity caused by wheat level led to alteration in meat color. LR diets improved feed utilization (P < 0.05), affected amino acid and lipid metabolism, and increased IMF content in LD (P < 0.05). Reducing SID Lys:NE ratio changed the concentrations of PA, delta-tocopherol, L-arginine, AzA, BA, and L-carnitine at the 25% wheat level and ARA, SDA, Glu, fructose-6-phosphate, and isorhamnetin at the 55% wheat level in the serum (P < 0.05, VIP > 1), which could serve as key biomarkers for predicting meat quality. LR diets upregulated mRNA expression levels of CCAAT/enhancer binding protein (C/EBP) α (P < 0.05), C/EBPβ (P < 0.01), sterol regulatory element-binding transcription factor 1c, fatty acid synthase (FAS) (P < 0.05), while downregulated mRNA abundance of adipose triglyceride lipase (ATGL) (P < 0.05) in liver at the 25% wheat level. The mRNA expression levels of C/EBPβ (P < 0.01), FAS, acetyl-coA carboxylase and fatty acid binding protein 1 (P < 0.05) were higher in the W55LR than W55HR groups, whereas mRNA abundance of ATGL was lower (P < 0.05). These results indicated that lowering SID Lys:NE ratio promoted lipogenesis, inhibited lipolysis and improved IMF deposition in LD via altering serum metabolism in different manner at two wheat level. LR diets containing 25% wheat was recommended to enhance the growth performance of finishing pigs, while concurrently achieving higher IMF content and improved meat color in the LD.
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