Eligo Bioscience, Paris, France.
Institut Pasteur, Université Paris Cité, Synthetic Biology, Paris, France.
Nature. 2024 Aug;632(8026):877-884. doi: 10.1038/s41586-024-07681-w. Epub 2024 Jul 10.
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.
微生物组研究现在表明，越来越多的细菌菌株和基因会影响我们的健康。虽然基于 CRISPR 的工具在编辑人类细胞中致病基因方面已经取得了巨大成功，但我们目前缺乏在原位实现细菌靶标可比成功的工具。在这里，我们设计了一种噬菌体衍生的颗粒来递送碱基编辑器，并修饰定植于小鼠肠道的大肠杆菌。对模型大肠杆菌菌株中β-内酰胺酶基因的编辑导致目标细菌群体的中位编辑效率为 93%，单次剂量即可达到。在治疗后至少 42 天内，编辑后的细菌在小鼠肠道中稳定维持。这是通过使用非复制性 DNA 载体实现的，从而防止了有效载荷的维持和传播。然后，我们利用这种方法在体外编辑大肠杆菌和肺炎克雷伯菌菌株中几个具有治疗意义的基因，并在一种致病性大肠杆菌菌株中展示了与卷曲菌产生相关的基因的原位编辑。我们的工作证明了在肠道中直接修饰细菌的可行性，为研究细菌基因的功能开辟了新途径，并为设计新的针对微生物组的治疗方法打开了大门。
