Establishing the feasibility of editing the human gut microbiome

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PROJECT SUMMARY Definitive links between the remarkable inter-individual genotypic variation in the human microbiome and disease are still limited due to the lack of generalizable methods to precisely remove microbial genes from complex microbial communities in situ. Not only would such a technology help transform the microbiome field from a descriptive to a mechanistic discipline, but it would also have immediate clinical applications. The goal of this Focused Technology Research and Development (PAR-19-253) application is to establish a generalizable toolkit to program the endogenous CRISPR-Cas systems in human gut bacteria to knockout genes of interest with unprecedented precision. CRISPR-Cas is a bacterial immune system, composed of RNA-guided nucleases, that protect the cell against bacteriophage and other foreign DNA. Endogenous CRISPR-Cas systems can be programmed to target their own genomic DNA using custom guide RNAs (gRNAs) homologous to a gene of interest. As an initial proof-of-principle we will target a single gut bacterial gene that we discovered is responsible for the inactivation of the cardiac drug digoxin, but if successful this approach could be readily extended to the numerous bacterial species that have now been implicated in host physiology and the predisposition to and treatment of disease. We will pursue the following Specific Aims: (Aim I) the functional validation of a novel CRISPR-Cas system in Eggerthella lenta, a prevalent gut Actinobacterium with multiple links to metabolism and microbial pathogenesis; (Aim II) the isolation and rebooting of bacteriophages that infect human gut bacteria; and (Aim III) the engineering of bacteriophage to program an endogenous gut bacterial CRISPR-Cas system. Our long-term goal is to establish the first modular tools for engineering the gut microbiome to delete one gene, combinations of genes, or even entire metabolic pathways. Importantly, by focusing on endogenous CRISPR-Cas systems, we anticipate that along the way we will uncover basic insights into the diversity, regulation, and function of these systems, with broad implications for our understanding of the complex interactions between bacteriophages, their bacterial hosts, and their shared mammalian habitat. While our early results provide support for feasibility, this high-risk, high- reward technology development plan would have broad implications for the study of microbial communities and host-microbiome interactions while bringing the promise of microbiome-based therapeutics within reach.