Enzyme-Based Technologies for the Generation of Emerging Prebiotics and Their Effect on Probiotics

The growing interest in gut health and microbiota modulation has driven significant advances in the development of functional ingredients, particularly prebiotics. While conventional prebiotics like inulin, FOS, and GOS are well-established, there is increasing recognition of emerging prebiotics, including novel oligosaccharides, polyphenolic compounds, and other plant-derived molecules that have great potential in offering a wider scope of health benefits. In this chapter, enzymatic strategies for the synthesis, extraction, and modification of emerging prebiotics are explored, with particular emphasis on their structural diversity. Progress in biocatalysis, including the development of customized enzymes and advanced reactor designs, along with bioprocess optimization, is discussed in the context of improving production efficiency and selectivity. These advances are considered essential for enabling sustainable and scalable approaches to the development of prebiotics. Special attention is given to prebiotics obtained from agrifood byproducts and wastes, in alignment with the principles of the circular economy. Furthermore, the chapter addresses how emerging prebiotics modulate probiotics, including next-generation beneficial microbes, thereby influencing host health beyond classical gut-related effects. The chapter also explores emerging applications focusing on microbiomes of the skin, oral cavity, and vaginal tract, where new prebiotic compounds exhibit promising functional potential. With this comprehensive perspective, the chapter aims to unlock the full potential of emerging prebiotics as versatile health-promoting ingredients for current and future applications.