Bacterial-fungal cross-kingdom interactions in synthetic consortia: boosting secondary metabolites and sustainable food fermentation

Bacterial-fungal consortia (BFC) consistently outperform aseptic or single-species cultures in producing high-value secondary metabolites, yet the underlying cross-kingdom interaction mechanisms remain poorly understood. In food fermentations, BFCs enhance process robustness, substrate turnover, and bioactive profiles for sustainable functional foods. In these consortia, bacteria and fungi engage in complex cooperative and competitive interactions, involving signaling molecules, genetic regulation, and metabolic flux redistribution to enhance secondary metabolite yields. Based on the ecological compatibility and molecular communication mechanisms, a synthetic microbiology framework for constructing high-yield BFCs was proposed. This systematic approach included selecting appropriate coculture partners, setting up the BFC, and optimizing cultivation conditions. Functional BFCs can be effectively applied to: food fermentation, improving fermentation efficiency, nutritional value, flavor complexity, and food safety. The review provides an overview of BFCs for secondary metabolite production, with emphasis on their cross-kingdom communication mechanisms. It explores the construction and optimization of BFCs and their applications in food fermentation, identifying future directions for enhancing secondary metabolite yields.