Integrating Transcriptomics and Gut Microbiota Analysis Reveals Adaptive Mechanisms of Alkaline Stress on the Molting and Intestinal Immune Responses in Pacific White Shrimp, Litopenaeus vannamei

In northwestern China, there is an abundance of saline-alkali water resources, but their high alkalinity severely restricts the development of inland saline-alkali water aquaculture. As an important aquaculture species, the whiteleg shrimp, Litopenaeus vannamei, shows an unclear physiological adaptation mechanism under high-alkaline stress. In this study, multi-omics and physiological methods were used to systematically reveal the effects of high-alkaline stress on the molt, antioxidation response, and immune defense in L. vannamei. The results showed that high-alkaline stress caused damage to the intestinal tissues of the shrimp and weakened the mucous barrier function, which was accompanied by a significant decrease in the activities of antioxidant enzymes (SOD, CAT, and GPx) and non-specific immune indicators (PO and LZM) (p < 0.05). The transcriptome results showed that the expression of genes related to chitin metabolism and calcium ion binding was upregulated, whereas that of genes related to muscle contraction and cell skeleton construction was downregulated. The structure of the intestinal microbiota changed significantly, with a decrease in microbiota diversity, whereas the abundance of potential pathogenic species (e.g., Photobacterium) increased. These results provide a theoretical basis for clarifying the molting response and antioxidant defense mechanism of L. vannamei in high-alkaline environments, with significance for saline-alkali water aquaculture practices.