Engineering the microbiome for form and function

Microbial communities hold great potential for a range of biotechnological applications where dividing labor between multiple organisms can enable increased productivity, novel functions or combinations of functions, or simplified process optimization and flexibility by treating the different organisms as modules that can easily be swapped and recombined. An ongoing challenge remains the development of strategies and toos for controlling community composition, feedback between the organisms, and how to optimally divide labor between multiple species. We have developed new set regulatory components and systems that can be used to turn gene expression on or off in response to a cell-cell communication signal, and enable interspecies communication between representative Gram-negative (Escherichia coli) and Gram-positive (Bacillus megaterium) organisms. We are also employing new strategies to control the growth and coexistence of species in co-cultures by manipulating ecological interactions; a key challenge for applications with microbial consortia. We will describe the use of synthetic ecology approaches, where both the environment and cells are manipulated, to control community composition in batch, fed-batch and continuous culture. Finally, we will describe our recent efforts to distribute functions between these microbes in a model bioprocess and our broader efforts to understand the links between form and function in natural and engineered microbial communities.