Control of density and composition in an engineered two-member bacterial community

Abstract

As studies continue to demonstrate how our health is related to the status of our various commensal microbiomes, synthetic biologists are developing tools and approaches to control these microbiomes and stabilize healthy states or remediate unhealthy ones. Building on previous work to control bacterial communities, we have constructed a synthetic twomember bacterial consortium engineered to reach population density and composition steady states set by inducer inputs. We detail a screening strategy to search functional parameter space in this high-complexity genetic circuit as well as initial testing of a functional two-member circuit.We demonstrate non-independent changes in total population density and composition steady states with a limited set of varying inducer concentrations. After a dilution to perturb the system from its steady state, density and composition steady states are not regained. Modeling and simulation suggest a need for increased degradation of intercellular signals to improve circuit performance. Future experiments will implement increased signal degradation and investigate the robustness of control of each characteristic to perturbations from steady states.

An automated model reduction tool to guide the design and analysis of synthetic biological circuits

“…Two coupled feedback controllers are designed using various components that control the total population density of the consortium to a desired value and to control the fraction of the two cell types in the consortium. In [30], the theory behind the design of these controllers has been discussed and [31] discusses the details of the implementation of this circuit. In this circuit, each cell in the consortium promotes the production of a toxin that kills itself.…”

“…The description of the model species and the model parameters are given in Appendix B. For more details on the parameter values and description, the reader is referred to [31]. …”

“…Schematic of the composition and population density control synthetic biological circuit of a two-member bacterial community. Figure and caption adapted from[31] with permission. It is a symmetric circuit motif in its two cells to create cis-acting negative feedback loops on each member and trans acting rescues from negative feedback from each member to the other.…”

Embedded control of cell growth using tunable genetic systems

“…A pioneering solution for the self-regulation of population density in single strain microbial populations was proposed in 18 where a quorum sensing based mechanism is used to self-limit the number of the cells. Alternative approaches involve engineering multiple microbial populations to achieve self-regulation of their relative numbers 19–24 and in some cases also regulation of both the consortium size and composition 25,26 . In all previous work, the desired population densities are hard-wired into the design of the synthetic gene regulatory networks.…”

A two-state ribosome and protein model can robustly capture the chemical reaction dynamics of gene expression

“…For model-based design of biological circuits, we need to develop mathematical models that map the system design specifications to the mechanistic details. Commonly used phenomenological models are based on empirical information and their model parameters describe lumped properties of the system that are effective in explaining the observed experimental data [1][2][3][4][5] but have not been readily used for forward engineering of biological circuits. Towards that end, to explore different design possibilities one needs to carefully justify the validity of the underlying assumptions for each model [6].…”