Organic copper substitution mitigates feed-derived copper emissions by enhancing bioefficacy and redox–microbiota homeostasis in Eriocheir sinensis

Copper supplementation is essential in aquaculture for maintaining growth and physiological functions but poses significant environmental risks due to poor bioavailability and excessive discharge from inorganic copper sources such as copper sulfate (CuSO 4 ·5H 2 O). This study evaluated hydroxy copper methionine (HCM), a highly bioavailable organic copper complex, as a sustainable nutritional alternative in the diet of Eriocheir sinensis using an integrated multi-omics approach combining transcriptomics and 16S rRNA sequencing. Over an 8-week feeding trial, dietary HCM (8, 18, 28, and 38 mg/kg) was compared with conventional CuSO 4 ·5H 2 O (18, 28, and 38 mg/kg) in terms of copper retention, growth performance, antioxidant activity, intestinal microbiota modulation, and estimated unretained copper. Supplementation with 18 mg/kg HCM achieved copper retention and growth performance comparable to those of 28 mg/kg CuSO 4 ·5H 2 O. HCM significantly enhanced antioxidant capacity, as indicated by increased Cu-Zn SOD activity, T-AOC, and GSH levels; upregulated antioxidant genes ( gst , Cu-Zn sod ) and copper homeostasis-related genes ( Ctr1 , mt1 ); and modulated lipid metabolism-related genes ( acox1 , me2 ). Transcriptomic analysis showed enrichment of glutathione metabolism and peroxisomal pathways. 16S rRNA sequencing revealed a marked restructuring of the intestinal microbiota, characterized by selective enrichment of Bacteroides , which was positively associated with antioxidant and immune indices. Mass-balance modeling projected that replacing 28 mg/kg CuSO 4 ·5H 2 O with 18 mg/kg HCM could reduce annual copper additive input by 19,398–22,250 kg and reduce projected unretained copper discharge by 8,588–9,851 kg at the baseline FCR of 2.5. These findings support HCM as a nutritionally effective and environmentally responsible alternative for cleaner and more sustainable crustacean farming.