Microbiota, fermentation, and metabolite biotransformation: Pathways to functional foods and personalised nutrition

Fermentation is among the oldest biotechnological processes and a modern platform for precision metabolic engineering, enabling the targeted production of health-promoting metabolites. The human gut microbiota, with its complex enzymatic potential, converts dietary substrates into a wide range of bioactive molecules, including short-chain fatty acids, vitamins, neuroactive compounds, and polyphenol-derived metabolites that influence host metabolism, immunity, and neurological functions. Advances in microbial genomics, systems biology, and synthetic biology now allow the design of fermentation processes and engineered microbial strains capable of producing specific metabolites with improved bioavailability and tailored health effects. Precision fermentation integrates traditional microbial fermentation with genome editing, metabolic flux optimisation, and AI-assisted pathway design to achieve predictable yields of vitamins, polyphenols, bioactive peptides, and long-chain polyunsaturated fatty acids. These innovations create opportunities to develop functional foods, nutraceuticals, and personalized nutrition strategies that match metabolite profiles to an individual's microbiome composition. This chapter explores the mechanistic links between microbial metabolism and host health, reviews emerging fermentation technologies for targeted metabolite production, and highlights industrial case studies demonstrating the transition of precision fermentation from research to commercial applications.