Metagenomic editing of commensal bacteria in vivo using CRISPR-associated transposases

• 成果类型: Article
• 署名作者: Gelsinger, Diego Rivera; Ronda, Carlotta; Ma, Junjie; Kar, Om B.; Edwards, Madeline; Huang, Yiming; Mavros, Chrystal F.; Sun, Yiwei; Perdue, Tyler; Vo, Phuc Leo; Ivanov, Ivaylo I.; Sternberg, Samuel H.; Wang, Harris H.
• 署名单位: Columbia University; Columbia University; Columbia University; Columbia University; Columbia University; Columbia University; Howard Hughes Medical Institute; Columbia University; University of California System; University of California Berkeley; Vertex Pharmaceuticals
• 刊物名称: SCIENCE
• ISSN/ISSBN: 0036-8075; 1095-9203
• DOI: 10.1126/science.adx7604
• 发表日期: 2025-11-13
• 页码: eadx7604
• 关键词: segmented filamentous bacteria; POLYSACCHARIDE UTILIZATION; cells; microbiota; immune; engraftment; resistance; fitness; systems

摘要

Although metagenomic sequencing has revealed a rich microbial biodiversity in the mammalian gut, methods to genetically alter specific species in the microbiome are highly limited. Here, we introduce Metagenomic Editing (MetaEdit) as a platform technology for microbiome engineering that uses optimized CRISPR-associated transposases delivered by a broadly conjugative vector to directly modify diverse native commensal bacteria from mice and humans with new pathways at single-nucleotide genomic resolution. Using MetaEdit, we achieved in vivo genetic capture of native murine Bacteroides by integrating a metabolic payload that enables tunable growth control in the mammalian gut with dietary inulin. We further show in vivo editing of segmented filamentous bacteria, an immunomodulatory small-intestinal microbial species recalcitrant to cultivation. Collectively, this work provides a paradigm to precisely manipulate individual bacteria in native communities across gigabases of their metagenomic repertoire.