Controlling metabolic stability of food microbiome for stable indigenous liquor fermentation

Abstract Steering microbial metabolic stability in fermentation is a recurrent goal for developing sustainable and robust microbial food production systems. Indigenous liquor fermentation typically relies on complex microbiome metabolism that makes it difficult to steer fermentation towards consistent high-quality products. Here, we designed a three-step experiment to identify and understand instability factors and to steer fermentation stability accordingly. We found that the metabolic stability of the microbiome fluctuates due to a combination of community assembly responses to fermentation parameters, dynamic benefit allocation between yeasts and Lactobacilli, and functional redundancy of metabolic networks associated with biodiversity. Short-term metabolic stability needs stable allocation of microbial benefits, whereas long-term requires proper functional redundancy. Rationally setting initial parameters and the microbial inoculation ratio is a practical way to optimize metabolic stability for stable solid-state indigenous fermentation. Our study provides insights into the underlying interactions and shows the feasibility of enhancing metabolic functional stability by setting appropriate initial conditions in dynamic microbial ecosystems.