Quenching corrinoid-based interactions in a model bacterial coculture.

Abstract

Microbial community structure is driven, in part, by the metabolic interdependencies of resident microbes. Thus, manipulating specific metabolic interactions represents one attractive way to both understand how microbial communities perform complex functions and alter them for therapeutic or environmental effects. However, it is not yet possible to control the availability of those metabolites produced by some members of the community that are required by others. Here, we report the development of a metabolite quenching strategy that disrupts a specific metabolic interaction involving corrinoids, the vitamin B12 family of cofactors, by applying a high-affinity corrinoid-binding protein, BtuG, to bacteria engaged corrinoid cross-feeding. Using a model coculture composed of Sinorhizobium meliloti, a bacterium that produces a corrinoid (cobalamin), and an Escherichia coli strain engineered to be corrinoid-dependent, we demonstrate corrinoid quenching by sequestration of extracellular corrinoid and show that BtuG specifically blocks corrinoid-dependent growth. We use this tool to calculate the amount of cobalamin released by S. meliloti cells and find that the cobalamin release rate is dependent on the growth phase of the producer, increasing to a maximum of approximately 40 cobalamin molecules per minute per cell in late exponential phase. This work establishes a strategy to selectively block microbial interactions that may be more broadly applied to dissecting community structure and function. We expect that applying high-affinity molecular sponges to quench nutrient sharing will allow for the identification of key nutrients that structure microbial communities and empower precision microbiome manipulation strategies.