Genetic Engineering of Resident Bacteria in the Gut Microbiome

Abstract

Techniques by which to genetically manipulate members of the microbiota enable both the evaluation of host-microbe interactions and an avenue by which to monitor and modulate human physiology. Genetic engineering applications have traditionally focused on model gut residents, such as Escherichia coli and lactic acid bacteria. However, emerging efforts by which to develop synthetic biology toolsets for "nonmodel" resident gut microbes could provide an improved foundation for microbiome engineering. As genome engineering tools come online, so too have novel applications for engineered gut microbes. Engineered resident gut bacteria facilitate investigations of the roles of microbes and their metabolites on host health and allow for potential live microbial biotherapeutics. Due to the rapid pace of discovery in this burgeoning field, this minireview highlights advancements in the genetic engineering of all resident gut microbes.

Keywords: CRISPR-Cas; metabolic engineering; microbiome; nonmodel organisms; synthetic biology.

FIG 1

Increasing microbiome knowledge enables the engineering of novel bacterial species. An increased number of (A) correlational studies have linked shifts from a healthy gut to various disease states to corresponding changes in the gut microbiota. Recently developed experimental and predictive methods that explore this correlational information can be used to understand factors pertaining to healthy microbiota states and to generate (B) genetic tools with which novel bacterial chassis in the microbiome can be tamed. These tools include, but are not limited to, plasmids and genome integration strategies for the transfer and maintenance of genetic material as well as parts from synthetic biology toolkits to control gene expression, such as promoters and ribosome binding sites (RBS).

FIG 2

Genetic editing schemes enable functional perturbations while maintaining microbiota composition. Using engineering strategies, the molecular metabolism of endogenous bacteria can be manipulated by adding or removing genes that encode beneficial or deleterious phenotypes.

FIG 3

Engineered sentinel microbes as resident therapeutic factories. Microbes acting as sentinels can be engineered to continuously probe the intestinal environment to sense the disease state, transduce these signals to activate engineered pathways, and produce therapeutic compounds in response to the detected disease.