Comprehensive transcriptomic, proteomic, and intestinal microbiota analyses of largemouth bass (Micropterus salmoides) intestines reveal new insights into immune responses to Aeromonas hydrophila infection.

This study investigates the immune responses of largemouth bass (Micropterus salmoides) to infection by Aeromonas hydrophila, a pathogen responsible for significant economic losses in freshwater aquaculture due to bacterial enteritis. We employed transcriptomic sequencing, label-free LC-MS/MS quantitative proteomics, and 16S RNA sequencing to evaluate the transcriptomic, proteomic, and intestinal microbiota changes in infected fish compared to healthycontrols. Each fish (approximately 60 g) in the infection group was injected with 0.5 ml of an A. hydrophila suspension (1.0 × 10 CFU/mL), while the control group received 0.5 ml of phosphate buffer. Samples were collected 72 h post-injection, with three biological replicates made from an equal mix of tissue samples from six fish each. A total of 1666 differentially expressed genes (DEGs) and 2477 differentially expressed proteins (DEPs) were identified. Integrated analysis revealed that the up-regulated DEGs/DEPs in the intestines of infected largemouth bass were primarily associated with immune-related pathways including "antigen processing and presentation", "MAPK signaling pathway", "ECM-receptor interaction", and "leukocyte transendothelial migration". Notable upregulated immune-related proteins included complement or antigen-presenting proteins like complement C1, complement C3, complement C6, ɑ-2-macroglobulin, laminin, serotransferrin, leukocyte cell-derived chemotaxin-2, immunoglobulin C1-set domain-containing protein, and the MHC class I alpha antigen. 16S RNA sequencing indicated a significant increase in Proteobacteria and a decrease in Fusobacteria in the intestines of infected fish compared to controls. Collectively, these findings demonstrate that A. hydrophila infection significantly alters gene and protein expression as well as intestinal microbiota in largemouth bass, providing insights into their immune defense mechanisms against infection.