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This study aimed to develop innovative microencapsulated formulations of Pichia kluyveri CCMA 0615 and Saccharomyces cerevisiae CCMA 0732, strains known for their probiotic potential. The yeasts (8 log CFU/mL) were microencapsulated using the spray drying technique with whey powder (WP at 15%, 20%, and 30%) and sodium alginate (ALG at 1%). Scanning electron microscopy was initially performed to confirm microcapsule integrity and provide ultrastructural characterization. The viability of the cells was evaluated immediately after drying and over two months of storage at 4 ºC and 25 ºC. Selected formulations were subsequently applied in functional beverage fermentation, and their viability and survival under simulated gastrointestinal tract (GIT) conditions were assessed. The viability of spray-dried microencapsulated yeasts was shown to be dependent on both the strain and encapsulating matrix, ranging from 84% to 99%. Notably, P. kluyveri microcapsules required refrigeration for optimal stability. Microencapsulated yeasts maintained consistent fermentative profiles during functional beverage fermentation, demonstrating carbohydrate consumption, lactic acid production (0.30–1.10 g/L), alcohol production (0.2–1.61 g/L), and high viability during storage. Furthermore, microencapsulation of P. kluyveri with 15% WP and 1% ALG maintained high viability under GIT conditions, with survival rates exceeding 84% when isolated and over 94% when incorporated into a food matrix. This study demonstrates that innovative microencapsulation techniques can enhance the viability of probiotic yeasts, thereby improving their biotechnological application and facilitating the efficient delivery of probiotics to the host.
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