Directed evolution of microbial co-cultures for improved production of costly metabolites

Adaptive laboratory evolution (ALE) has been successfully used to obtain cells with improved characteristics for biotechnological applications, like increased stress tolerance. However, the range of ALE applications has been limited to traits directly linked to cell growth. Here, we propose the use of synthetic obligatory mutualistic microbial communities for the increased production of fitness-costly metabolites. The metabolic cross-feeding relationship between the species couples the production of a target metabolite to the survival and proliferation of the community, resulting in improved fitness, despite of the potential production cost. We successfully evolved communities consisting of natural vitamin secreting lactic acid bacteria and engineered Saccharomyces cerevisiae, for the improved production of two different B group vitamins (riboflavin and folate). Our findings demonstrate a method to increase the precision of laboratory evolution, leading to the selective production of fitness-costly metabolites, creating strains for biotechnological applications, especially when the use of genetically engineered strains is restricted. For example, the overproducing bacterial strains of this study can be readily used for the production of food with increased nutritional value.