Multi-Omics Insights into the Effects of Long-Term Faba Bean Feeding on Muscle Quality and Metabolic Reprogramming in Nile Tilapia (Oreochromis niloticus).

While short-term faba bean feeding is known to improve fish texture, its long-term systemic effects and the underlying molecular mechanisms in Nile tilapia remain rarely explored. This knowledge gap is critical, given the potential for extended feeding to induce distinct metabolic reprogramming and trade-offs. Here, we present the first comprehensive study investigating the 180-day impact of a 60% FB-based diet (FBD) on Nile tilapia through an integrated analysis of phenotypic traits, muscle histology, metabolome, and transcriptome. Our results revealed a fundamental trade-off: FBD feeding induced hyperplasia-driven muscle remodeling, significantly enhancing textural properties (hardness, gumminess, chewiness) and increasing intramuscular fat and collagen content, but at the cost of suppressed growth and hepatosomatic index. Metabolomics identified 243 significantly altered metabolites, outlining a systemic metabolic shift characterized by activated lipid synthesis but inhibited amino acid and energy metabolism. This multi-omics integration nominated the chac1 gene as a novel key regulator for FB-induced muscle hyperplasia, a finding not previously reported in this context. We propose a mechanistic model wherein long-term FBD feeding coordinates lipid deposition, collagen accumulation, and chac1-mediated hyperplastic growth to remodel muscle texture. Our work provides new insights into the long-term metabolic trade-offs and molecular drivers of FB-induced flesh quality improvement, offering a theoretical foundation for developing optimized aquafeeds.