Microbial consortia exhibit spatial patterning across diverse environments. Since probing the self-organization of natural microbial communities is limited by their inherent complexity, synthetic models have emerged as attractive alternatives. In this study, we develop novel frameworks of bacterial communication and explore the emergent spatiotemporal organization of microbes. Specifically, we built quorum sensing-mediated models of microbial growth that are utilized to characterize the dynamics of communities from arbitrary initial configurations and establish the effectiveness of our communication strategies in coupling the growth rates of microbes. Our simulations indicate that the behavior of quorum sensing-coupled consortia can be most effectively modulated by the rates of secretion of acyl homoserine lactones. Such a mechanism of control enables the construction of desired relative populations of constituent species in spatially organized populations. Our models accurately recapitulate previous experiments that have investigated pattern formation in synthetic multi-cellular systems. Additionally, our software tool enables the easy implementation and analysis of our frameworks for a variety of initial configurations and simplifies the development of sophisticated gene circuits facilitating distributed computing. Overall, we demonstrate the potential of spatial organization as a tunable parameter in synthetic biology by introducing a communication paradigm based on the location and strength of coupling of microbial strains.
Microbial consortia exhibit spatial patterning in several environments. However, the study of such patterning is limited by the inherent complexity of natural systems. An attractive alternative to study such systems involves the use of model synthetic microbial communities, which are convenient frameworks that allow the reuse of circuit components by eliminating cross-talk through compartmentalization of modules in genetic circuits. Computational models facilitate the understanding of how spatial organization can be harnessed as a tunable parameter in 2D cultures. We propose a Quorum Sensing-Mediated Model to engineer communication between strains in a consortium. This is implemented using a cellular automaton. We further analyze the properties of this model and compare them with those of the traditionally used Metabolite Mediated Model. Our studies indicate that modulating the rate of secretion of quorum sensing molecules is the most effective means of regulating community behavior. The models and codes are available from https://github.com/RamanLab/picCASO.
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