Engineering Next-Generation Microbial Consortia for Therapeutic Applications

Control of microbiota composition and function is a key challenge faced by synthetic biologists who seek to reprogram microorganisms for therapeutic applications. The field currently lacks tools that can i) facilitate the programmed introduction of engineered microbes into the human gastrointestinal environment, ii) control their behavior in a spatiotemporal manner, and iii) trigger their subsequent removal and biocontainment. To this end, genetic circuits for non-model organisms need to be developed so that advanced biological programs can be implemented in therapeutically relevant chassis beyond the classic E. coli Nissle (EcN) and Lactococcus probiotics. Transcriptional programming (T-Pro) using synthetic transcription factors (TFs) and promoters allows for the creation of complex, low-resource genetic circuits based on a universal framework. Here, we used T-Pro to develop a toolkit for programming gene expression (endogenous and heterologous) in the Bacteroides genus for the development of living therapeutic bacteria. These genetic circuits can interface with CRISPRi for multiplexed control of community fitness, as well as optimized secretion systems for the delivery of therapeutic payloads in situ. This platform technology was leveraged for the creation of a synthetic microbial consortium that provides combination therapy in a murine disease model for ulcerative colitis. We further paired this technology with an engineered EcN strain that is able to communicate with our Bacteroides consortium via programmed information exchange. These cellular control platforms will facilitate the design of next-generation therapeutic consortia for the treatment of myriad diseases.