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Carassius auratus gibelio, commonly known as crucian carp, is the main species of freshwater aquaculture in China. Due to high-density aquaculture and environmental pollution, various diseases continue to emerge, especially the diseases caused by pathogenic bacteria have seriously restricted the development of freshwater aquaculture. Among these, Aeromonas hydrophila (AH) is the one of the most serious fish disease causing economic losses among fish farmers. An in-depth understanding of the crucian carp's immune system and its genes involved in the response to bacterial infection is necessary for disease control. In this study, the breeding period was divided into the control group (C group) and the Bacillus licheniformis (B. licheniformis) group (BL group). After 4 weeks of culture, the crucian carp was infected with AH and divided into the control group (Cg group) and the B. licheniformis group (BLg group). After the 72-h challenge, the Illumina-based paired-end sequencing approach to analyze the transcriptome profile of the crucian carp gut following AH infection. A total of 472.05 million valid reads were found from the four intestinal samples and 403.18 million reads were mapped successfully, of which 243.34 million were unique. About GO enrichment analysis, significant differentially expressed genes (DEGs) were more in biological process (406 DEGs), regulation of transcription, DNA-templated (345 DEGs), and signal transduction (304 DEGs). In the cell components, membrane (1913 DEGs) and integral component of membrane (1789 DEGs) had a higher number of significantly different genes. In the molecular function, metal ion binding (780 DEGs), ATP binding (535 DEGs), transferase activity (491 DEGs), and nucleotide binding (482 DEGs) have a large number of significantly different genes. Regarding the KEGG enrich analysis section, this study is arranged in ascending P-value order, andthe most significant signaling paths are lysosome, glucose metabolism, cycline cycline receiver interaction, and phagosome. Among them, the cycline cycline receiver interaction has the highest difference in significant genes. In addition, 5 immune-related genes were selected for real-time fluorescence quantitative PCR analysis to verify the RNA-seq data, and the results showed that the expression of all 5 genes was upregulated, which was consistent with the results of our RNA-seq analysis. After analysis, it was found that B. licheniformis can alleviate the inflammatory response and protect the fish body. Our results provide a reference for further analysis of the antagonism and mitigation mechanism of B. licheniformis against AH. [ABSTRACT FROM AUTHOR]