**Background:** The intestinal mucosa is critical for immune homeostasis, and metabolites in the intestinal chyme serve as signaling molecules that influence host immunity. Saba (SB) pigs, a native breed from Yunnan, China, are known for disease resistance and rough feeding tolerance, while Landrace (LA) pigs are fast-growing but more susceptible to stress and disease. The jejunum is a key site for nutrient absorption and immune function, yet jejunal metabolites in SB pigs have been understudied. This study aimed to compare jejunal immune phenotypes and metabolite profiles between SB and LA piglets to identify potential biomarkers of intestinal health.
**Methods:** Three pregnant SB sows and three LA sows with similar parity were housed identically and fed an antibiotic-free diet. At 35 days of age, two piglets per sow (n=6 per breed, 12 total) were randomly selected for slaughter. Jejunal tissue was collected for histomorphology (H&E staining, PAS staining for goblet cells) and immunohistochemistry for immune markers (IL-10, IL-6, IL-1β, TLR-2, TLR-4, MUC2, ZO-1). Jejunal chyme was collected for untargeted metabolomics using UHPLC-QE Orbitrap MS in both positive and negative ion modes. Multivariate analysis (PCA, OPLS-DA) and univariate analysis (t-test, VIP ≥ 1, P < 0.05) identified differential metabolites. Spearman rank correlations were calculated between metabolites and immune/histomorphological parameters.
**Key Results:** SB piglets showed significantly higher jejunal villus height and villus height/crypt depth ratio (P < 0.05) compared to LA piglets. Immunohistochemistry revealed that SB piglets had markedly higher levels of IL-10, MUC2, and ZO-1 (P < 0.01), and higher goblet cell numbers (P < 0.05), while levels of pro-inflammatory factors IL-6, IL-1β, and TLR-2 were significantly lower (P < 0.01). Metabolomics identified 4,939 compounds in negative ion mode and 7,234 in positive ion mode across all samples. In negative mode, 130 metabolites were upregulated and 583 downregulated in SB vs. LA; in positive mode, 407 upregulated and 806 downregulated. Among the top 20 metabolites in negative mode, cholic acid metabolites accounted for 25%. Taurodeoxycholic acid (TDCA) was significantly higher in SB piglets (P < 0.01, VIP = 8.389, Log2_FC = 3.217, FDR = 0.036). Isohyodeoxycholic acid was significantly lower in SB (P = 0.011, VIP = 22.573, Log2_FC = −1.255). Spearman correlation analysis showed TDCA positively correlated with ZO-1 (R = 0.94, P = 0.017), villus height (R = 1, P = 0.003), villus height/crypt depth ratio (R = 0.94, P = 0.017), and goblet cell number (R = 0.94, P = 0.017).
**Clinical Implications:** These findings indicate that SB piglets possess superior jejunal immune function and intestinal barrier integrity compared to LA piglets, consistent with their known disease resistance. TDCA emerges as a potential biomarker for intestinal health, with positive correlations to barrier function markers. The study provides a reference for understanding breed-specific differences in intestinal immunity and suggests that TDCA or related bile acid metabolites could be targets for improving gut health in pig production. Limitations include the small sample size (n=6 per breed) and the observational, cross-sectional design, which precludes causal inference.