Comparative transcriptome analysis reveals pathogenesis of Procambarus clarkii during Black May Disease

Black May Disease (BMD) is a common illness that affects Procambarus clarkii during the spring-to-summer transition. With a complex pathogenesis, it poses a serious threat to aquaculture safety and industry stability. To better understand the progression of BMD, this study integrates key hepatopancreatic enzyme activity data with intestinal transcriptome profiles. We systematically investigated the immune, antioxidant, and metabolic adaptations of P. clarkii across different stages of the disease from both functional and molecular perspectives. The results showed a continuous increase in the relative abundance of Aeromonas , a typical opportunistic pathogen, throughout disease progression. This was accompanied by a gradual decline in the activities of key enzymes such as AKP, ACP, LPS, and SOD, indicating impaired nonspecific immune responses and basal metabolic functions. Several critical pathways—including PI3K-Akt, NOD-like receptor, Toll and Imd, AMPK, and glutathione metabolism—were significantly activated in the early disease stage (S2), sustained in the mid-stage (S3), and declined during the terminal stage (S4), reflecting a typical “early activation–mid-stage maintenance–late-stage decline” pattern. Pathways related to endocytosis, autophagy, and cell adhesion were consistently downregulated in the later stage, suggesting a systemic weakening of the intestinal barrier function. This study reveals a regulatory framework in which the accumulation of pathogens and external stress jointly disrupt the immune, metabolic, and structural defense systems. These findings offer theoretical insights and foundational data for understanding the pathogenesis of BMD and developing health management strategies for P. clarkii . • This study explores pathogenesis of BMD from multiple perspectives for the first time. • Many important genes and pathways related to BMD are found for the first time. • Immune response and impaired basal metabolic function are main mechanisms. • These findings offer theoretical insights for understanding pathogenesis of BMD.