Enhancing Probiotic Performance in Food Matrices: From Strain Selection to Bioengineering

Probiotics are central to functional food innovation, but their application is limited by viability loss during processing, storage, and gastrointestinal (GI) transit. A key insight is that viability and functionality are distinct attributes; maintaining high cell counts does not guarantee that probiotics retain their beneficial properties. Despite extensive literature on individual probiotic delivery strategies, no prior review has integrated strain selection, matrix design, protective technologies, and bioengineering into a single end‐to‐end framework. This review examines strategies to enhance probiotic performance across food matrices, emphasizing that effective delivery requires preserving both viability and functionality. Strain selection based on stress tolerance and adaptation via sublethal exposure are key approaches to improve robustness. Dairy matrices provide inherent protection to probiotics, whereas nondairy systems, including fruits, cereals, meat, and chocolate, require complementary technologies to enhance probiotic survival. Microencapsulation methods, including spray drying, extrusion, emulsification, and electrospraying, enhance probiotic stability and enable targeted GI release. Furthermore, prebiotic co‐encapsulation and synbiotic formulations improve survival and functionality through synergistic effects. Advances in genetic engineering, including CRISPR‐based tools, enable the development of next‐generation probiotics with improved stress tolerance and metabolic capabilities, although regulatory challenges remain. We conclude that effective probiotic delivery depends on integrating strain selection, matrix design, protective technologies, and bioengineering tailored to specific applications while preserving functionality throughout shelf life.