Functional evaluation of synbiotic combination of Kluyveromyces marxianus and Lentilactobacillus kefiri derived from milk kefir using multi-omics approaches

Milk kefir is a fermented dairy product composed of a complex consortium of microorganisms, including lactic acid bacteria (LAB), yeasts, and acetic acid bacteria. Despite growing interest in its health-promoting properties, the synergistic interactions among the diverse microbial constituents of kefir remain insufficiently characterized. This study investigated the probiotic potential of milk kefir through a multi-omics approach. Two strains, <i>Kluyveromyces marxianus</i> SLAM 005Y and <i>Lentilactobacillus kefiri</i> SLAM 023B, were isolated from Korean household milk kefir. Both strains exhibited key probiotic properties, including antibacterial activity, adherence to intestinal epithelial cells, and resistance in simulated gastrointestinal conditions. Supplementation with SLAM 005Y, SLAM 023B, or their synergistic combination (SYN) significantly enhanced lifespan and immune function in <i>Caenorhabditis elegans</i>. Transcriptomic analysis further revealed upregulation of genes involved in longevity and antimicrobial defense, suggesting the activation of conserved stress-response pathways. In a dextran sulfate sodium (DSS)-induced murine colitis model, SYN administration led to marked improvement in clinical outcomes. SYN also restored the expression of inflammatory and anti-inflammatory cytokines and tight junction proteins, indicating improved intestinal barrier function and immune regulation. Importantly, multi-omics analysis revealed that SYN altered both gut microbial composition and fecal metabolite profiles, supporting a mechanistic link between microbiota modulation and host health. Taken together, milk kefir strains SLAM 005Y and SLAM 023B, particularly in combination, exhibit strong probiotic properties. Our findings highlight the therapeutic potential of milk kefir-originated probiotics as a functional food for improving intestinal health.