Synthetic Kefir Based on Fermentation of Natural Kefir and Koumiss Core Microbial Species Reveals Microbial Interactions and Gene Exchanges in Natural Kefir

ABSTRACT Kefir and koumiss are both traditional alcoholic fermented milk drinks made from the fermentation of various probiotics and yeasts. The complex microbial composition of kefir and koumiss has hindered the expansion of their consumption in global markets. In this study, we first performed a metagenomic analysis of fermented food to explore the core strains of kefir and koumiss. Five strains ( Lactococcus lactis , Lactobacillus helveticus , Lentilactobacillus kefiri , Lactobacillus kefiranofaciens , and Kluyveromyces marxianus) were identified as the core strains shared by both kefir and koumiss. In contrast to the widespread distribution of L. lactis , L. kefiri and L. kefiranofaciens were primarily restricted to kefir and koumiss and certain fermented cheeses. These five strains were subsequently selected for synthetic kefir (sKefir) fermentation. Metagenomic sequencing and metabolomic analyses revealed that, compared with natural kefir, sKefir exhibited a more balanced microbial composition while also harboring metabolites with analogous functional profiles. Functionally, sKefir alleviated DSS‐induced intestinal barrier damage and intestinal inflammation by promoting the expression of gut barrier‐related genes, such as occludin (OCLN). The microbial interaction analysis revealed mutually synergistic growth‐promoting effects among these five strains. In addition, horizontal gene transfer (HGT) was also observed between L. kefiri and L. kefiranofaciens . Our work clarified the core microbial strains of kefir and koumiss through investigation of their evolutionary histories and explored their potential for artificial synthesis.