Principles for designing synthetic microbial communities

Abstract

Advances in synthetic biology to build microbes with defined and controllable properties are enabling new approaches to design and program multispecies communities. This emerging field of synthetic ecology will be important for many areas of biotechnology, bioenergy and bioremediation. This endeavor draws upon knowledge from synthetic biology, systems biology, microbial ecology and evolution. Fully realizing the potential of this discipline requires the development of new strategies to control the intercellular interactions, spatiotemporal coordination, robustness, stability and biocontainment of synthetic microbial communities. Here, we review recent experimental, analytical and computational advances to study and build multispecies microbial communities with defined functions and behavior for various applications. We also highlight outstanding challenges and future directions to advance this field.

Multiplex transcriptional characterizations across diverse bacterial species using cell‐free systems

“…Lastly, we developed multiple hybrid lysates and characterized their gene expression properties, demonstrating tunable species selectivity of regulatory sequences based on mixing ratios. We anticipate that future applications of hybrid lysates that take advantage of the combined metabolic properties of multiple microbes will enable production of useful biomolecules (Yi et al , ), and may aid in the development of artificial minimal cells with properties of multiple species (Noireaux et al , ; Johns et al , ).…”

Harnessed viruses in the age of metagenomics and synthetic biology: an update on infectious clone assembly and biotechnologies of plant viruses

“…Notwithstanding, a major goal of synthetic biology is to build engineered organisms with improved or new functions and applications that can solve real-world needs (Liu and Stewart, 2015). Advanced biocontainment systems have been designed to control microorganism escapees (Johns et al, 2016;Lee et al, 2018).…”

“…Plant viruses can exist as populations, and mixtures of different species are common in nature (Elena et al, 2014; Pag an and Garc ıa-Arenal, 2018). The use of synthetic multispecies Cross-protection Delivery of mild virus strains to prevent infections by their severe relatives Ziebell and Carr (2010) Weed biocontrol Viruses triggering lethal systemic necrosis as bioherbicides Harding and Raizada (2015) Pest biocontrol Enhanced toxin and pesticide delivery for insect and nematode control communities is an emerging trend to augment microbiome systems for industrial and environmental biotechnology (Johns et al, 2016). Simultaneous delivery of viruses with specialized tasks can additively give rise to population functions that are simply more efficient or could be difficult or impossible to achieve otherwise (Figure 3).…”

Microbial mutualism dynamics governed by dose-dependent toxicity of cross-fed nutrients

“…Cocultures preserve core aspects of natural systems while offering greater practical experimental control (Shou et al, 2007;Hillesland and Stahl, 2010;Summers et al, 2010;Harcombe, 2010;Momeni et al, 2011;Hom and Murray, 2014;Mee et al, 2014). They are also more amenable to modeling than are natural systems and facilitate the development, experimental testing and refining of models for predicting community behavior (Zomorrodi and Segrè, 2015;Johns et al, 2016;Lindemann et al, 2016;Widder et al, 2016). As such, cocultures are very useful for defining the principles that underlie the stability and performance of microbial communities.…”