From Ancient Fermentation to Modern Functional Foods: Food Microbiology and Biotechnology at the Interface of Tradition and Innovation

Fermentation is one of the oldest food preservation and transformation strategies developed by human societies. Its cultural appropriation predates even the scientific understanding of the role of microorganisms and their metabolic functions. However, significant knowledge gaps remain regarding the mechanisms underlying these effects, as well as safety considerations and regulatory frameworks. This review addresses these gaps through an integrative analysis of the literature, including peer-reviewed studies and systematic reviews focused on food microbiology, microbial dynamics, and health-promoting mechanisms. In particular, yogurt and cheese are addressed as case studies to review the past and present of these ancestral foods in terms of the evolution of fermentation processes, from spontaneous fermentation to controlled and standardized systems, along with the modern biotechnological tools used to characterize and monitor complex microbial communities. Substrates such as stevia, fruits, vegetables, and plant-based milk substitutes are also explored. The scope encompasses enzymatic transformation of raw substrates, biosynthesis of bioactive metabolites, effects on the gut microbiota, and the use of fermented foods as vehicles for “biotic” compounds. Particular attention is paid to safety and regulatory aspects. Fermented foods are culturally important and promising functional platforms, although standardized regulatory frameworks and stronger mechanistic and clinical evidence regarding their health benefits are still needed.