法国埃利戈公司David Bikard、Xavier Duportet和Jesus Fernandez-Rodriguez课题组合作的研究报道了靶向小鼠肠道细菌的原位定向碱基编辑器。相关论文于2024年7月10日发表在《自然》杂志上。

研究人员设计了一种噬菌体衍生颗粒来递送碱基编辑器并修改小鼠肠道中的大肠杆菌。通过编辑大肠杆菌模型菌株中的β-内酰胺酶基因，单剂量对目标细菌群的中位编辑效率能达到93%。编辑后的细菌可在小鼠肠道中至少稳定存在42天。这通过使用非复制DNA载体实现，从而防止了有效载荷的维持和传播。

然后，研究人员利用这种方法在体外编辑了大肠杆菌和肺炎克雷伯氏菌菌株中与治疗相关的几个基因，并在致病性大肠杆菌菌株中演示了原位编辑一个参与产生卷曲霉素的基因。

该工作证明了直接在肠道中改造细菌的可行性，为研究细菌基因的功能提供了一条新途径，并为设计新的微生物组靶向治疗打开了大门。

据悉，微生物组研究表明越来越多的细菌菌株和基因会影响人类健康。尽管CRISPR衍生工具在编辑人细胞中的致病基因方面取得了巨大成功，但目前还缺乏能在原位对细菌靶点进行编辑的工具。

附：英文原文

Title: In situ targeted base editing of bacteria in the mouse gut

Author: Brdel, Andreas K., Charpenay, Loc H., Galtier, Matthieu, Fuche, Fabien J., Terrasse, Rmi, Poquet, Chlo, Havrnek, Jan, Pignotti, Simone, Krawczyk, Antonina, Arraou, Marion, Prevot, Gautier, Spadoni, Dalila, Yarnall, Matthew T. N., Hessel, Edith M., Fernandez-Rodriguez, Jesus, Duportet, Xavier, Bikard, David

Issue&Volume: 2024-07-10

Abstract: Microbiome research is now demonstrating a growing number of bacterial strains and genes that affect our health1. Although CRISPR-derived tools have shown great success in editing disease-driving genes in human cells2, 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 42days 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.

DOI: 10.1038/s41586-024-07681-w

Source: https://www.nature.com/articles/s41586-024-07681-w