Synthetic microbial consortia: from systematic analysis to construction and applications

Abstract

Synthetic biology is an emerging research field that focuses on using rational engineering strategies to program biological systems, conferring on them new functions and behaviours. By developing genetic parts and devices based on transcriptional, translational, post-translational modules, many genetic circuits and metabolic pathways had been programmed in single cells. Extending engineering capabilities from single-cell behaviours to multicellular microbial consortia represents a new frontier of synthetic biology. Herein, we first reviewed binary interaction modes of microorganisms in microbial consortia and their underlying molecular mechanisms, which lay the foundation of programming cell-cell interactions in synthetic microbial consortia. Systems biology studies on cellular systems enable systematic understanding of diverse physiological processes of cells and their interactions, which in turn offer insights into the optimal design of synthetic consortia. Based on such fundamental understanding, a comprehensive array of synthetic microbial consortia constructed in the last decade were reviewed, including isogenic microbial communities programmed by quorum sensing-based cell-cell communications, sender-receiver microbial communities with one-way communications, and microbial ecosystems wired by two-way (bi-directional) communications. Furthermore, many applications including using synthetic microbial consortia for distributed bio-computations, chemicals and bioenergy production, medicine and human health, and environments were reviewed. Synergistic development of systems and synthetic biology will provide both a thorough understanding of naturally occurring microbial consortia and rational engineering of these complicated consortia for novel applications.

Design of a multicellular feedback control strategy in a synthetic bacterial consortium

“…On the basis of our predictions and of the engineering of microbial communities completed so far [17], [18], [27], [29], we believe that the implementation of a feedback control scheme in a synthetic consortium of living bacteria could provide a useful tool for the realization of robust and versatile embedded cellular controllers. Further in-silico studies tackling the stochasticity of biochemical processes and experimental work towards the implementation of the proposed strategy are currently being carried out and will be reported elsewhere [30].…”

“…Orthogonal quorum sensing systems are being exploited to implement communication across the two populations within the consortium [27]. Moreover, in a realistic scenario the interaction between the inducer molecule acting as the external control reference and the parts within the controller population could be mediated by an intermediate species which in turn affects the production of the regulator forming the complex with the signaling molecule coming from the target cells [28].…”

Engineered biosynthesis of natural products in heterologous hosts

“…Most of the microbial consortium engineering focus on the lignocelluloses bioconversion to produce chemicals and fuels 132, 178 . The progress on the fundamental studies and the applications of artificial consortium was reviewed recently 179 . More recently, engineering of the microbial consortium has been applied to biosynthesis of complex natural products 177 .…”

Engineering Electrode-Attached Microbial Consortia for High-Performance Xylose-Fed Microbial Fuel Cell

“…Rational design of microbial consortia is an efficient engineering strategy to improve system function by the division of overall labor among several species within a microbial community, in which each species in the microbial community is designed to execute what it is expert at. [30][31][32] Herein, a synthetic riboflavin pathway from Bacillus subtilis was introduced into E. coli to facilitate EET of S. oneidensis and improve its initial attachment onto the electrode. Furthermore, a highly hydrophobic S. oneidensis mutant was employed in the consortium to allow the exoelectrogen to better interact with the hydrophobic carbon electrode.…”