RT Journal Article SR Electronic T1 In situ targeted mutagenesis of gut bacteria JF bioRxiv FD Cold Spring Harbor Laboratory SP 2022.09.30.509847 DO 10.1101/2022.09.30.509847 A1 Brödel, Andreas K A1 Charpenay, Loïc A1 Galtier, Matthieu A1 Fuche, Fabien J A1 Terrasse, Rémi A1 Poquet, Chloé A1 Arraou, Marion A1 Prevot, Gautier A1 Spadoni, Dalila A1 Hessel, Edith M A1 Fernandez-Rodriguez, Jesus A1 Duportet, Xavier A1 Bikard, David YR 2022 UL http://biorxiv.org/content/early/2022/09/30/2022.09.30.509847.abstract AB Microbiome research is revealing a growing number of bacterial 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. Here we engineer a phage-derived particle to deliver a base editor and modify E. coli colonizing the mouse gut. This was achieved using a non-replicative DNA payload, preventing maintenance and dissemination of the payload, while allowing for an editing efficiency of up to 99.7% of the target bacterial population. The editing of a β-lactamase gene resulted in the stable maintenance of edited bacteria in the mouse gut at least 42 days after treatment. By enabling the in situ modification of bacteria directly in the gut, our approach offers a novel avenue to investigate the function of bacterial genes and provides an opportunity to develop novel microbiome-targeted therapies.Competing Interest StatementAll authors are current employees or paid advisors of Eligo Bioscience. Eligo Bioscience owns US patents #11,224,621 and #11,376,286, and international patent application WO2021/204967 relating to certain research described in this article.