Disordered colonic microbiota as a potential contributor to inflammation in diarrheal Jinhua weaned piglets.

Diarrhea is a major cause of mortality in Jinhua piglets, accounting for up to 80% of total piglet deaths and severely restricting the sustainability of pig production systems. In this study, colonic morphology, organ indices, gut microbiota composition, and transcriptomic profiles were compared between diarrheal piglets (DG) and healthy piglets (HG) to identify diarrhea associated bacteria in Jinhua piglets and to explore potential microbial intervention strategies. The results revealed that diarrheal piglets had lower organ indices (p < 0.01) and worse intestinal conditions such as inflammatory factor infiltration, reduced number of goblet cells (p < 0.05), and increased colonic crypt depth (p < 0.05). Transcriptomics analysis of colonic mucosa revealed that differentially expressed genes (DEGs) between two groups (FC > 1.5, p < 0.05) were enriched mainly in Th1 and Th2 cell differentiation and Th17 cell differentiation. Microbiota analysis showed that bacteria such as Clostridium_sensu_stricto_1, which were enriched in the colon of piglets in HG, may contribute to host metabolic and immune modulation via metabolic products such as short chain fatty acids and crosstalk with other microbial taxa. In contrast, potential harmful bacteria, particularly Fusobacterium, were significantly enriched in the colon of piglets in DG. Correlation analysis further identified IL-2Rβ, TBX21, and LCK as key immune related genes associated with differentially abundant microbes. Enriched Fusobacterium showed associations with inflammatory gene expression, whereas Clostridium_sensu_stricto_1 exhibited opposite correlations. In conclusion, harmful bacterial colonization may promote intestinal inflammation and diarrhea in Jinhua piglets, while beneficial bacteria exert protective effects that support piglets’ growth and intestinal health. These beneficial microbes may serve as potential probiotic candidates for improving the health of Jinhua piglets. GRAPHICAL ABSTRACT: [Image: see text] SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s42523-026-00525-0.