Abstract

As a globally important aquaculture species, Litopenaeus vannamei’s freshwater adaptation is of great significance in promoting inland aquaculture. This investigation employed integrated transcriptomic and metabolomic approaches to explore molecular response mechanisms in the intestinal tract of L. vannamei under acute freshwater stress. Transcriptional profiling revealed 218 differentially expressed genes (DEGs) after 24 h freshwater exposure, mainly involved in cysteine and methionine metabolism and sphingolipid metabolism pathways. Metabolomic analysis identified 68 differentially abundant metabolites (DAMs), primarily associated with arginine biosynthesis, glutathione metabolism, and d -amino acid metabolism. Following 96 h of stress, the number of DEGs decreased to 79, showing significant enrichment in nucleotide metabolism and purine metabolism pathways. Metabolite profiling identified 86 differential metabolites at this stage, primarily involved in purine metabolism, nucleotide metabolism, and alanine, aspartate, and glutamate metabolism. Multi-omics integration analysis highlighted the pivotal roles of amino acid metabolism, energy metabolism, and secondary metabolism in stress adaptation. Specifically, amino acid metabolism contributed to osmoregulation and energy supply through the precise modulation of specific amino acids. Energy metabolism displayed temporal dynamics, initially relying on fatty acid oxidation before shifting to purine and nucleotide metabolic pathways. Secondary metabolism enhanced adaptive capacity through the biosynthesis of antimicrobial compounds and osmoprotectants. This study not only fills a critical knowledge gap regarding intestinal functional mechanisms underlying salinity adaptation but also identifies molecular targets for optimizing freshwater aquaculture strategies. These findings are of considerable significance for advancing the sustainable development of aquaculture.