Metagenomic editing of commensal bacteria in vivo using CRISPR-associated transposases
Year: 2025
Type: article
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.
Source: Science
Institutions: Columbia University, Howard Hughes Medical Institute
Language: English
Subfield: Molecular Biology
Domain: Life Sciences
Open Access status: hybrid
Funders: National Science Foundation, Howard Hughes Medical Institute, Burroughs Wellcome Fund, Irma T. Hirschl Trust, Wellcome Trust, Simons Society of Fellows, Emerson Collective, National Institutes of Health, Irving Medical Center, Columbia University, Office of Naval Research, National Human Genome Research Institute, National Cancer Institute, National Institute of Allergy and Infectious Diseases, National Institute of Diabetes and Digestive and Kidney Diseases, National Institute of Biomedical Imaging and Bioengineering, Air Force Research Laboratory, Kalispel Charitable Fund
Awards: New mechanism of commensal bacteria interaction with host immunity, G1939380420, G2023952753, G2448318396, G2878457584, G3009497520, G3286784856, Maintenance of mucosal homeostasis by commensal Th17 cells, CAREER: Functional and evolutionary analysis of transposon-encoded, RNA-guided nucleases across the three domains, G3909092490, Ecological dynamics and metabolic interactions in thegut microbiome across space and time, G4428141482, G4504108201, G4650627052, G4697950702, G4823669508, G4988360024, G5052434461, G5439864067, G5811817018, G601860838, MTM 2: The rules of microbiota colonization of the mammalian gut, G6188540885, A high-performance and versatile technology for precision microbiome engineering, G6606343224, G6671297155, G6741691291, Discovery of immunomodulatory gut microbes with MAGIC, G7907826354, G8876996369, G9000214573, G9000228654, ePACE: automation platforms for adaptable and scalable continuous evolution of biomolecules with therapeutic potential, Role of intestinal commensal-induced Th17 cells and mucosal immunity in metabolic disease, The Columbia University Digestive and Liver Disease Research Center
OpenAlex ID: W4416180253