Unculturable Microorganisms in Fermented Foods: New Technological Insights and Emerging Health Applications

Abstract

Fermented foods harbor Unculturable Microorganisms (UMs) that shape flavor formation, safety, and health-relevant functions. Recent advances—multi-omics, single-cell genomics, culturomics, and Artificial Intelligence (AI)-driven modeling—are uncovering their metabolic roles and ecological importance. Beyond describing their hidden diversity, UMs open new futures for fermented food innovation: redesigning starters to enhance amino nitrogen while reducing precursors of ethyl carbamate and biogenic amines; developing stable UM-derived postbiotics such as extracellular vesicles for immune modulation; applying AI-guided community design to improve flavor consistency and microbial resilience; and creating personalized synbiotic strategies aligned with consumer microbiomes. Gut-on-chip validation and precision fermentation enable scalable translation, while a metabolite-centered safety framework provides a feasible regulatory path for non-culturable taxa. Framing UMs around deployable functions—rather than cultivability—positions them as key levers for next-generation probiotics, postbiotics, and precision fermented foods.