Synthetic Biology and Microbiome Engineering

Cell-free synthetic biology

Cell-free protein expression systems are derived from living cells and contain the necessary machinery needed to efficiently produce new proteins of interest in vitro. Thus, they enable an array of synthetic biology application without the use of living cells. This offers safety benefits by avoiding the potential threat of genetically engineered living cells replicating in the environment. In addition, while living cells essentially have their own agenda and may evolve away from performing an engineered task, cell-free systems offer a simplified context in which all resources can be devoted to the engineered function. Key interests include development of novel gene circuits, artificial cells, cell-free directed evolution, and ‘ruggedized’ cell-free systems for practical applications such as remediation and therapeutics production in the field.

Multicellular scale – Engineering cell populations

Bacterial populations in nature are effectively multicellular organisms. They communicate to coordinate various population level behaviors and are arguably even socially intelligent. In synthetic biology, cell-cell communication can be engineered to program spatial behavior, implement division of labor, and coordinate population level behaviors such as biofilm formation. Synthetic biology offers a powerful tool for developing an understanding of complex natural phenomena such as pattern formation and for exploring the role of molecular level noise on population-level behavior. In addition, cell populations can be engineered for applications such as novel biomaterial fabrication and the implementation of sophisticated biosensors.

Multi species scale — Microbiomes

Microbes inhabit nearly every niche on earth, ranging from thermal vents to arctic permafrost. The advancement of sequencing technologies has driven a rapid expansion in efforts to characterize the microbiomes – the ecological systems of microbes – of a variety of different environments. This, in turn, has led to a deeper appreciation of the roles of the microbiome. For example, the human microbiome plays a strong role in health and performance. The plant microbiome is an important determinant of agricultural productivity and robustness. The microbiome of built environments has been recently explored due to its potential ties to human health as well as material robustness (e.g. potential for corrosion and fouling). Key interests include microbiome characterization, in vitro experiments for revealing mechanistic underpinnings of community structure and, ultimately, microbiome engineering. Microbiome engineering may be accomplished through the targeted addition, removal, and/or genetic manipulation of specific taxa, through the development of designer consortia, or through modification of the host environment (diet, hygeine, building design, etc.). Related efforts involve the development of synthetic biology tools for probing microbiome function as well as for applications in sensing and performance. Finally, microbiota can be mined for new genetic components, novel metabolic pathways, and therapeutic products.