Automation and Miniaturization Towards High-Throughput Genome Engineering

Engineering organisms typical requires a three-step design cycle of creating a genetically diverse library, testing that library’s phenotype and finally learning which trait of combinations of modifications contribute towards a desired phenotype.  However, the complexity and non-linearity associated with genome engineering coupled with the low throughput of the design cycles remains a barrier towards thorough and efficient genome engineering.  We describe approaches to improve the rate of library generation and testing through automation and miniaturaztion, respectively. The rate of library generation is improved with a bench-top cell-culture, liquid handling and electroporation system. This allows for the rapid and targeted generation of a diverse library population.  Screening and testing of this diverse population is adapted in a microfluidic setup to improve screening throughput while reducing associated screening costs. These approaches are applied towards olefin and alcohol production in E.coli.