Transcriptomic analysis of immune and metabolic responses in largemouth bass (Micropterus salmoides) challenged with Citrobacter freundii

Abstract Citrobacter freundii , a common zoonotic pathogen affecting humans, livestock and fish, is recognized for its substantial impact on largemouth bass ( Micropterus salmoides ) mortality. However, the mechanisms of C. freundii infection in largemouth bass remain poorly understood. Based on the results of extracellular enzyme activity detection, it was speculated that the production of extracellular enzymes may be related to bacterial pathogenicity. To elucidate the immune response mechanism, transcriptomic analysis was conducted on spleen tissues from largemouth bass infected with C. freundii . Following quality filtering, the control group generated 44.04 million clean reads, while the infected group produced 44.32 million clean reads. A total of 385 differentially expressed genes (DEGs) were identified, comprising 224 up‐regulated and 161 down‐regulated unigenes. Classification using the Gene Ontology and Kyoto Encyclopedia of Genes and Genomes databases further elucidated the biological functions and signalling pathways of the DEGs. Significantly impacted pathways included ‘Galactose metabolism’, ‘ Pyrimidine metabolism’, ‘ Alanine, aspartate and glutamate metabolism’, ‘Ubiquitin‐mediated proteolysis’, ‘Endocytosis’, ‘Phagosome’ and ‘SNARE interactions in vesicular transport’, underscoring their roles in metabolic and immune‐related signalling. Eight DEGs were chosen and validated for their expression levels via real‐time quantitative PCR. This study offered molecular insights into the host defence mechanisms against C. freundii infection, contributing to the formulation of disease prevention and control strategies for largemouth bass aquaculture.