Multi-omics profiling identifies intestinal microbial shifts and tissue-specific immunometabolic changes associated with experimental Nocardia seriolae challenge in hybrid sturgeon (Acipenser baerii♀ × Acipenser schrenckii♂)

Introduction Nocardia seriolae is an important bacterial pathogen in aquaculture, but the intestinal microbial, transcriptional, and metabolic responses of hybrid sturgeon ( Acipenser baerii ♀ × Acipenser schrenckii ♂) to infection remain poorly understood. Methods Hybrid sturgeons were experimentally challenged with N. seriolae. PBS-injected control fish were sampled at 0 days post-infection (dpi) as the baseline reference, whereas infected fish were sampled at 7 and 14 dpi for microbiome, transcriptome, and metabolome profiling. Full-length 16S rRNA gene and ITS sequencing were used to characterize intestinal microbial communities, while RNA-seq and untargeted LC–MS metabolomics were performed on liver and spiral valve intestine tissues. Results Compared with the baseline control group, fish sampled at 7 and 14 dpi showed differences in intestinal bacterial community composition, whereas bacterial alpha diversity did not differ significantly among the three sampled groups. ITS profiling also showed differences in fungal diversity and community composition among groups, although no fungal genus remained significant after false discovery rate (FDR) correction. RNA-seq revealed tissue-specific transcriptional responses, with the liver showing a larger number of differentially expressed genes than the spiral valve intestine. Hepatic pathways were mainly related to immune recognition, complement and coagulation cascades, antigen processing, and stress-related responses, whereas intestinal transcriptional changes involved phagosome, cell adhesion, and mucosal immune-related pathways. Metabolomic analysis showed tissue- and stage-related metabolic changes, with clearer pathway-level evidence in the spiral valve intestine at 14 dpi, particularly involving amino acid metabolism and protein digestion and absorption. Representative metabolites related to lipid and bile acid metabolism, carnitine-associated lipid utilization, energy metabolism, and purine/nicotinamide metabolism also showed sampling-stage-related variation. Genus–metabolite association analysis further identified candidate relationships between intestinal bacterial genera and representative metabolites. Discussion These findings provide a multi-omics view of intestinal microbial and tissue-specific immunometabolic changes associated with experimental N. seriolae challenge in hybrid sturgeon. The candidate genus–metabolite relationships provide a basis for future targeted validation of microbial and metabolic features associated with nocardial infection.