Ronda Carlotta, Perdue Tyler, Schwanz Logan, Rivera Gelsinger Diego, Brockmann Leonie, Kaufman Andrew, Huang Yiming, Sternberg Samuel H, Wang Harris H
Department of System Biology, Columbia University, New York, NY, USA.
Innovative Genomics Institute, University California Berkeley, Berkeley, CA, USA.
Nat Biomed Eng. 2025 Jul 18. doi: 10.1038/s41551-025-01453-1.
Targeted gene manipulation in a complex microbial community is an enabling technology for precise microbiome editing. Here we introduce BACTRINS, an in situ microbiome engineering platform designed for efficient and precise genomic insertion of a desired payload and simultaneous knockout of target genes. This system leverages conjugation-mediated delivery of CRISPR-associated transposases to achieve RNA-guided genomic integration, allowing precise insertion of a therapeutic payload while neutralizing pathogen virulence without causing cell death. When applied against an Enterobacteriaceae Shiga toxin-producing pathogen in the gut, this system delivers a CRISPR-associated transposase by bacterial conjugation for site-specific inactivation of the Shiga toxin gene and integration of a nanobody therapeutic payload to disrupt pathogen attachment. A single dose of this therapy results in high-efficiency Shiga gene inactivation and improved survival in a murine infection model of Shiga-producing pathogen. This work establishes a new type of live bacterial therapeutic capable of reducing gut infections by transforming toxigenic pathogens into commensal protectors.
在复杂的微生物群落中进行靶向基因操作是精确编辑微生物组的一项赋能技术。在此，我们介绍BACTRINS，这是一个原位微生物组工程平台，旨在高效、精确地将所需的有效载荷插入基因组，并同时敲除靶基因。该系统利用接合介导的CRISPR相关转座酶递送，以实现RNA引导的基因组整合，从而在不导致细胞死亡的情况下精确插入治疗性有效载荷，同时中和病原体的毒力。当应用于肠道中产生志贺毒素的肠杆菌科病原体时，该系统通过细菌接合递送CRISPR相关转座酶，用于志贺毒素基因的位点特异性失活以及纳米抗体治疗性有效载荷的整合，以破坏病原体的附着。在产生志贺毒素的病原体的小鼠感染模型中，单剂量这种疗法可实现高效的志贺基因失活并提高存活率。这项工作建立了一种新型的活菌疗法，能够通过将产毒病原体转化为共生保护者来减少肠道感染。
