Integrated metagenomics and metabolomics reveal geographical signatures in the microbiome and metabolome of Jiaoke from Inner Mongolia, China.

Jiaoke is a traditional fermented dairy product from Inner Mongolia, China, and its characteristic flavor and quality attributes are shaped by region-specific microbial communities. In this study, shotgun metagenomic sequencing combined with untargeted metabolomics was used to systematically characterize Jiaoke samples collected from three distinct ecological production regions: Hulun Buir (HLB), Xilingol (XLG), and Bayan Nur (BYN). The results demonstrated pronounced regional specificity in both microbial composition and metabolite profiles across the three regions. BYN samples were dominated by Lactococcus lactis and Bifidobacterium spp. with enrichment of lipid-derived metabolites. HLB samples were characterized by Lactococcus raffinolactis and psychrotolerant bacteria, together with elevated levels of sphingolipids. In contrast, XLG samples were dominated by Streptococcus macedonicus and exhibited high abundances of amino acids and dipeptides. Correlation analysis indicated that Lactococcus raffinolactis and Streptococcus macedonicus may contribute to Jiaoke flavor formation by promoting milk protein hydrolysis and dipeptide accumulation. These findings provide a basis for understanding regional flavor formation, developing tailored starter cultures, and establishing geographically indicated products in the future.