In situ targeted base editing of gut bacteria in mice

Microbiome research is revealing a growing number of bacterial strains and genes that impact our health. While 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 E. coli colonizing the mouse gut. The editing of a beta-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 at least 42 days after 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 K. pneumoniae strains in vitro, and demonstrate in situ editing of a gene involved in the production of curli in a pathogenic E. coli strain. By enabling the modification of bacteria directly in the gut, our approach offers a new avenue to investigate the function of bacterial genes and presents an opportunity for the development of novel microbiome-targeted therapies.