Computational Design of Synthetic Microbial Communities Incorporating Competitive and Cooperative Interactions

The human microbiota consists of a large number of interacting species, which enables stable coexistence and community function. Manipulating microbial composition, and the resultant metabolic output, offers a novel solution to treating inflammatory diseases such as Crohn’s disease and ulcerative colitis. As a step towards this, we aim to engineer synthetic communities in vitro, allowing us to understand the fundamental components required to form stable microbial communities.

The existence and maintenance of microbial consortia is dependent upon interactions between the community members. Here, we demonstrate a modelling framework for simulating microbial consortia existing in a chemostat environment, interacting via quorum sensing and microcin expression, combined with crossfeeding of essential nutrients. Using this framework, we have been able to predict system configurations that give the highest probability for stable steady state community establishment, and infer the necessary design principles. This model informed approach allows us to focus our experimental efforts on the most probable candidate systems, with the potential to drastically reduce the time and resources required to build stable microbial communities.