Omics-Guided Construction of Microbial Consortia for Reproducible Traditional Fermented Foods and Beverages

Traditional fermented foods and beverages (TFFB) rely on complex microbial communities that generate distinctive flavors, nutritional attributes, and cultural value, but spontaneous or empirically controlled fermentations often limit reproducibility. Defined microbial consortia (DMCs) provide a promising route for improving fermentation controllability and product consistency, although overly simplified starters may fail to reproduce the ecological robustness and sensory complexity of traditional systems. This review focuses on how multi-omics and culturomics can support rational DMC design in TFFB. We summarize how metagenomics, metatranscriptomics, metaproteomics, metabolomics, and culturomics reveal community structure, functional potential, active expression, metabolic output, and cultivable strain resources. Particular attention is given to translating multi-omics evidence into strain prioritization through the identification of keystone microorganisms that drive core fermentation functions and helper microorganisms that support ecological or metabolic stability. We further propose an Assembly-Assessment-Redesign (A-A-R) framework for iterative DMC optimization, linking strain selection, functional validation, performance evaluation, and consortium redesign. Finally, we discuss key challenges, including cross-omics integration, experimental verification of microbial functions, standardized validation criteria, and the transfer of laboratory-designed consortia to industrial fermentation systems.