Metagenomic editing of commensal bacteria in vivo using CRISPR-associated transposases
Diego R. Gelsinger, Carlotta Ronda, Junjie Ma, Om B. Kar, Madeline Edwards, Yiming Huang, Chrystal F. Mavros, Yiwei Sun, Tyler Perdue, Phuc Leo H. Vo, Ivaylo I. Ivanov, Samuel H. Sternberg, Harris H. Wang
Abstract
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.