BACKGROUND: () type A is a major cause of enteritis in farmed and wild deer populations, leading to significant economic losses in the deer industry. This bacterium produces toxins that damage the intestine. METHODS: In this study, we performed transcriptome analysis by establishing an intestinal circulation model of the intestines of fallow deer () inoculated with type A versus those not inoculated with type A. In a further step, we determined the protein content of immunoinflammation-related molecules by ELISA and the antioxidant capacity of the intestine to investigate the molecular mechanisms of type A-induced enteritis. RESULTS: Transcriptome analysis revealed significant enrichment of pathways related to the haematopoietic system, oxidative stress, the immune system and intestinal tight junctions. Additionally, α-toxin enters the intestine and may be recognized by TLR6, activating the immune system, increasing the secretion of various cytokines and inflammasome components, inducing oxidative stress and damaging the intestine. CONCLUSIONS: This study provides a comprehensive transcriptomic basis for understanding the selective differential expression of genes in deer enteritis induced by type A and provides a broader guide for finding therapeutic approaches to deer enteritis.