Synthetic Biology Tools for the Gut Microbiota

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Weston Whitaker, Justin Sonnenburg

Stanford University, United States

The gut microbiota is integral to many facets of human biology, including pathogen susceptibility, immune disorders, diabetes and obesity. Gut-resident microbes are highly adapted to perceive and respond to conditions within the gut and can be considered platforms for diagnostic applications, therapeutic production and delivery, and for probing intestinal biology. The gut serves as an interface that is highly evolved and receptive to symbiotic interaction with microbes and represents a promising target for microbially produced therapeutics. Recent microbiota-focused mechanistic studies have elucidated a number of potential avenues for manipulating gut community composition and host response, but require the development of cell-based engineering tools for human-associated microbes. Here we apply synthetic biology principles proven in E. coli to improve the engineering of a model intestinal symbiont Bacteroides thetaiotaomicron (Bt). Our improvements in symbiont engineering include (i) redesigning Bt integration vectors to allow rapid assembly, via Golden Gate (ii) creating and characterizing expression machinery, including promoters stronger than previously available, and (iii) implementing strategies for reduced context dependence of expression machinery to provide reliable control of protein expression in Bt. Synthetic biology offers a powerful approach to study the gut microbiota, providing tools to help bridge the gap between sequencing complex gut microbial communities and defining molecular mechanisms. Applying the principles of synthetic biology to host-associated microbes represents a frontier in biomedicine.