Towards a Genetically Engineered Gut Microbiome
The gut microbiome influences long-term health. The balance of microbial populations shifts with age to become more harmful, certainly more inflammatory. While it is possible to produce sizable benefits to health via rejuvenation of the aged gut microbiome with simple approaches, such as fecal microbiota transplantation using a young donor, the future will clearly involve more of the application of biotechnology to the problem. If one can produce lasting change in the composition of the gut microbiome by delivering microbes in sufficient quantity, then why not deliver engineered versions of existing gut microbes that are altered to produce less inflammatory signaling or more beneficial metabolites?
Microbiome research is now demonstrating a growing number of bacterial strains and genes that affect our health. Although CRISPR-derived tools have shown great success in editing disease-driving genes in human cells, we currently lack the tools to achieve comparable success for bacterial targets in situ. Here we engineer a phage-derived particle to deliver a base editor and modify Escherichia coli colonizing the mouse gut. Editing of a β-lactamase gene in a model E. coli strain resulted in a median editing efficiency of 93% of the target bacterial population with a single dose. Edited bacteria were stably maintained in the mouse gut for at least 42 days following treatment.
This was achieved using a non-replicative DNA vector, preventing maintenance and dissemination of the payload. We then leveraged this approach to edit several genes of therapeutic relevance in E. coli and Klebsiella pneumoniae strains in vitro and demonstrate in situ editing of a gene involved in the production of curli in a pathogenic E. coli strain. Our work demonstrates the feasibility of modifying bacteria directly in the gut, offering a new avenue to investigate the function of bacterial genes and opening the door to the design of new microbiome-targeted therapies.