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Chronic diseases are a severe problem affecting the modern world's population, and these diseases are highly correlated with the dysbiosis of the gut microbiome. It is essential to propose new ingredients that can regulate the gut microbiome and meet the industrial and technological requirements for application in food. Due to their proteolytic activity during fermentation processes, yeast cells are known to contribute to the generation of bioactive peptides with multiple functionalities. Although most studies show the contribution of Saccharomyces cerevisiae in producing metabolites with biological activities, the possible role of other yeast species/strains should not be unnoticed. Yarrowia lipolytica is an unconventional oleaginous yeast with GRAS (Generally Recognized as Safety) status acknowledged for its ability to utilize a wide range of hydrophobic compounds as a substrate, producing several valuable metabolites, such as proteins, peptides, and amino acids. Solid-state fermentation (SSF) can be highlighted among the options for yeast cultivation and bioproduction of high-added-value metabolites. In SSF, the support used for producing metabolites through yeast can be replaced by agro-industrial by-products. In this context, the Brazilian Amazon biome has one of the greatest diversities in the world, with fruits that can be used in the food industry. The cupuassu (Theobroma grandiflorum) stands out for having seeds used to extract fat. The cupuassu cake generated after fat extraction still has a high residual content of lipids (21.3%), proteins (14.9%), and carbohydrates (22%) in its composition, which makes it an ideal substrate for biotechnological applications such as the production of probioactive (postbiotics and paraprobiotics) compounds. Probioactives represent a new category of biological response modifiers. Yeast-derived peptides produced during fermentation can exhibit different bioactivities, such as antioxidant, antimicrobial, antihypertensive, hypocholesterolemic, and antidiabetic. From a practical point of view, probioactive compounds are more stable and safer for industrial uses. Preserving the biological properties of produced metabolites under different conditions and during digestion is a great challenge for their employment in the formulation of functional food. In this context, to inactivate the culture of Y. lipolytica, high-intensity ultrasound fits as an emerging non-thermal technology that minimizes the effects caused by heat on the technological, nutritional, and sensory qualities of food products. For probioactive compounds to be released in a controlled/directed manner within the human body and to be protected against unfavorable processing and storage conditions, microencapsulation is a possible technique to formulate a probioactive ingredient that is stable in terms of physicochemical and bioactivities and will be subject to less variation in packaging, storage, and transport steps. Probioactive compounds could reduce inflammation, help maintain colon and gut homeostasis, and could be the next wave of supplements to promote better gut health. Finally, the maintenance of the in vitro biological activities of the probioactive compounds under controlled gastrointestinal conditions and their influence on the modulation of the gut microbiome must be evaluated.
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