Multi-omics analyses reveal distinct and complementary effects of chlorogenic acid and bile acids on hepatic lipid metabolism and redox homeostasis in juvenile rainbow trout.

Long-term feeding with a commercial basal diet may induce moderate hepatic lipid accumulation and sub-optimal redox status in juvenile rainbow trout (Oncorhynchus mykiss), forming a mutually reinforcing hepatic sub-health cycle. Chlorogenic acid (CGA) and bile acids (BAs) are promising additives for improving hepatic lipid metabolism and redox balance, but their individual and combined effects remain unclear. Here, juvenile rainbow trout were fed four diets for 90 days: basal diet (C), 600 mg/kg CGA (TC), 1000 mg/kg BAs (TB), or both additives (TCB). Unlike previous single-additive studies, this work integrated phenotypic, transcriptomic, metabolomic, and gene-metabolite association analyses to compare additive-specific and combined responses. At day 60, supplementation, especially TCB, improved hepatic histological structure and alleviated lipid accumulation. Compared with C, TCB increased SOD activity and T-AOC by 144.5% and 259.6%, respectively, and decreased MDA content and FAS activity by 56.9% and 53.4%. Oil Red O staining also showed the lowest lipid droplet accumulation in TCB. Multi-omics analyses revealed treatment-specific lipid-redox signatures. CGA was mainly associated with reduced de novo fatty acid biosynthesis, downregulation of acaca and fasn, and altered 5-methylhexanoylcarnitine abundance. BAs were mainly associated with glycerophospholipid metabolism, lipid transport, bile acid-related pathways, altered apoa1 and mfsd2ab expression, and phosphatidylcholine/LysoPE remodeling. Combined supplementation showed broader reprogramming involving fatty acid synthesis, lipid transport, membrane phospholipid turnover, energy metabolism, and stress-responsive genes. Overall, these findings provide an association-based framework for understanding the distinct and complementary roles of CGA and BAs and may support the rational development of functional aquafeed additives for improving hepatic lipid metabolism and redox balance in rainbow trout.