Ecological perspectives on synthetic biology: insights from microbial population biology

Abstract

The metabolic capabilities of microbes are the basis for many major biotechnological advances, exploiting microbial diversity by selection or engineering of single strains. However, there are limits to the advances that can be achieved with single strains, and attention has turned toward the metabolic potential of consortia and the field of synthetic ecology. The main challenge for the synthetic ecology is that consortia are frequently unstable, largely because evolution by constituent members affects their interactions, which are the basis of collective metabolic functionality. Current practices in modeling consortia largely consider interactions as fixed circuits of chemical reactions, which greatly increases their tractability. This simplification comes at the cost of essential biological realism, stripping out the ecological context in which the metabolic actions occur and the potential for evolutionary change. In other words, evolutionary stability is not engineered into the system. This realization highlights the necessity to better identify the key components that influence the stable coexistence of microorganisms. Inclusion of ecological and evolutionary principles, in addition to biophysical variables and stoichiometric modeling of metabolism, is critical for microbial consortia design. This review aims to bring ecological and evolutionary concepts to the discussion on the stability of microbial consortia. In particular, we focus on the combined effect of spatial structure (connectivity of molecules and cells within the system) and ecological interactions (reciprocal and non-reciprocal) on the persistence of microbial consortia. We discuss exemplary cases to illustrate these ideas from published studies in evolutionary biology and biotechnology. We conclude by making clear the relevance of incorporating evolutionary and ecological principles to the design of microbial consortia, as a way of achieving evolutionarily stable and sustainable systems.

Diabetes Enhances IL-17 Expression and Alters the Oral Microbiome to Increase Its Pathogenicity

“…We found that diabetes led to reduced oral microbial diversity, consistent with reports that diabetic patients and animal models exhibit decreased bacterial diversity in other sites (Hartstra et al, 2015; Patterson et al, 2015; Ussar et al, 2016). The reduced diversity could potentially enhance susceptibility to the formation of a pathogenic microbiome as a highly diverse ecosystems is generally more stable and healthier than communities dominated by fewer taxa (Escalante et al, 2015). …”

Synthetic Ecology of Microbes: Mathematical Models and Applications

“…Many existing consortia design strategies rely on the assumption that interactions among community members are fixed. However, patterns of inter-species interactions can be significantly modulated by environmental changes, and can change during the course of evolutionary adaptation 233 . Thus, understanding processes that may guarantee stability and resilience in presence of these changes would require taking explicitly into account the volatility and context-dependence of interactions.…”

Modeling population dynamics in a microbial consortium under control of a synthetic pheromone‐mediated communication system

“…Despite the well‐documented success of pure cultures, this strategy is challenged by the increasing complexity of biotechnological processes, for example, bioconversion of low‐cost substrates into high‐value products. In this context, pure cultures may be outperformed by consortia . Compared with pure cultures, consortia have several important benefits.…”