Integrating Microbiomes for Regenerative Food Systems: Recent Insights, Implementations, and Emerging Trends

Microbiomes play a central role in food science by influencing food quality, safety, sustainability, and human health. This review brings together contemporary advancements in the understanding and use of microbiomes in the food system, with a focus on sustainable agriculture, fermentation, food safety, and nutrition. We discuss both traditional approaches (e.g., natural fermentation and soil management) and new high-tech strategies, including precision microbiome engineering, synthetic biology, and machine learning. The major applications under consideration are microbiome-based food preservation, biofertilisers and biopesticides, waste valorisation, and alternative protein production. The socioeconomic context is also being considered, recognizing that while recent advances are more pragmatic in high-income countries, traditional and low-input approaches are still critical in low- and middle-income country (LMIC) settings. The emphasis in this review is laid on food science and food systems, and nutrition and health effects are considered as downstream consequences. The readership includes food scientists, microbiologists, agricultural researchers, and policy decision-makers who care about the integration of microbiome science into resilient and sustainable food systems. By presenting a fair representation of standard and advanced microbiome techniques, this review delineates the prospects and challenges in the application of microbial communities in shaping the future of food.