Engineering Efficient Specialist Strains for a Synthetic Multi-Species Microbial Consortium

Use of synthetic microbial consortia can help to address some of the limitations of monoculture bioprocessing, including high metabolic burden on the cells and the need to optimize multiple pathways or functions in the same species. Design of synthetic microbial consortia, however, brings the challenge of identifying or engineering strains that can perform optimally within a mixed population and regulating the population composition. Here we present our work on developing methods to optimize microbes for performance in co-culture.

We are working on a synthetic co-culture of the cellulolytic fungus Trichoderma reesei and an Escherichia coli strain that has been designed to produce the drop-in biofuel isobutanol directly from cellulosic substrate in one consolidated bioprocess [1]. The E. coli strain in this system shows suboptimal performance compared to monoculture conditions, demonstrating lower yield and titer, higher byproduct formation, and high plasmid loss. We are developing new ways to generate E. coli strains optimized for co-culture performance. The first is a directed evolution approach involving screening for improved growth with a selection agent in co-culture with T. reesei.  Second, we are taking a systems biology approach to compare the E. coli metabolic state in monoculture and co-culture in order to guide further genetic modification and improvement. Third, we integrate and optimize the copy number of the isobutanol production pathway in the E. coli genome to enable more stable performance.

[1]       Minty JJ, Singer ME, Scholz SA, Bae C-H, Ahn J-H, Foster CE, Liao JC, & Lin XN (2013) Design and characterization of synthetic fungal-bacterial consortia for direct production of isobutanol from cellulosic biomass. Proc Natl Acad Sci USA 110(36): 14592-14597.