Dynamic cybergenetic control of bacterial co-culture composition via optogenetic feedback

Abstract

Communities of microbes play important roles in natural environments and hold great potential for deploying division-of-labor strategies in synthetic biology and bioproduction. However, the difficulty of controlling the composition of microbial consortia over time hinders their optimal use in many applications. Here, we present a fully automated, high-throughput platform that combines real-time measurements and computer-controlled optogenetic modulation of bacterial growth to implement precise and robust compositional control of a two-strain E. coli community. Additionally, we develop a general framework for dynamic modeling of synthetic genetic circuits in the physiological context of E. coli and use a host-aware model to determine the optimal control parameters of our closed-loop compositional control system. Our platform succeeds in stabilizing the strain ratio of multiple parallel co-cultures at arbitrary levels and in changing these targets over time, opening the door for the implementation of dynamic compositional programs in synthetic bacterial communities.

Ratiometric control of cell phenotypes in monostrain microbial consortia

“…For example, in [ 21 ], the authors considered a microbial consortium already comprising two different cell strains, adjusting the dilution rate in a chemostat to regulate the relative numbers of the populations in the consortium, while the platform developed in [ 27 ], although powerful, relies on delivering a different control input to each cell and, in addition, all controlled cells are cultured in spatially distinct environments. Moreover, in [ 28 ], a non-reversible, efficient differentiation control mechanism has been proposed for the creation and maintenance of cellular sub-populations in single-strain microbial consortia, while a computer-controlled optogenetic platform for the regulation of the ratio of a two-strain Escherichia coli community has been recently presented in [ 29 ].…”