{"doi":"10.1126/science.adx7604","title":"Metagenomic editing of commensal bacteria in vivo using CRISPR-associated transposases","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.","journal":"Science","year":2025,"id":509952,"datarank":0.0,"base_score":0.0,"endowment":0.0,"self_citation_contribution":0.0,"citation_network_contribution":0.0,"self_endowment_contribution":0.0,"citer_contribution":0.0,"corpus_percentile":null,"corpus_rank":null,"citation_count":25,"citer_count":0,"citers_with_citation_signal":0,"citers_with_endowment":0,"datacite_reuse_total":0,"is_dataset":false,"is_dataset_confidence":0.949,"is_data_producer":false,"deposit_databanks":null,"is_oa":true,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":"2025-01-01","fair_score":null,"fair_percentile":null,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":561675,"name":"Carlotta Ronda","orcid":"0000-0002-7501-914X","position":1,"is_corresponding":false},{"id":414600,"name":"Junjie Ma","orcid":"0000-0001-5751-887X","position":2,"is_corresponding":false},{"id":1365172,"name":"Om B. Kar","orcid":"0009-0005-8056-9436","position":3,"is_corresponding":false},{"id":1020109,"name":"Madeline Edwards","orcid":"0000-0003-0134-2806","position":4,"is_corresponding":false},{"id":628109,"name":"Yiming Huang","orcid":"0000-0003-1932-2803","position":5,"is_corresponding":false},{"id":1254601,"name":"Chrystal F. Mavros","orcid":"0000-0003-3914-7512","position":6,"is_corresponding":false},{"id":884434,"name":"Yiwei Sun","orcid":"0000-0002-5974-6232","position":7,"is_corresponding":false},{"id":1365173,"name":"Tyler Perdue","orcid":"0009-0004-3023-0883","position":8,"is_corresponding":false},{"id":561674,"name":"Phuc Leo H. Vo","orcid":"0000-0002-3719-7770","position":9,"is_corresponding":false},{"id":483517,"name":"Ivaylo I. Ivanov","orcid":"0000-0001-5337-3386","position":10,"is_corresponding":false},{"id":561678,"name":"Samuel H. Sternberg","orcid":"0000-0001-8240-9114","position":11,"is_corresponding":false},{"id":288479,"name":"Harris H. Wang","orcid":"0000-0003-2164-4318","position":12,"is_corresponding":false},{"id":289818,"name":"Diego R. Gelsinger","orcid":"0000-0002-3786-1205","position":0,"is_corresponding":true}],"reference_count":87,"raw_metadata":null,"created_at":"2026-07-19T02:47:30.942539Z","pmid":"41231980","pmcid":null,"fwci":null,"citation_percentile":null,"influential_citations":0,"oa_status":null,"license":null,"views":0,"total_file_size_bytes":0,"version_count":0,"fair_f":null,"fair_a":null,"fair_i":null,"fair_r":null,"fair_zscore":null,"fair_rationale":null,"fair_model":null,"fair_agent_version":null,"fair_fulltext_source":null,"fair_has_llm":null,"fair_computed_at":null,"clinical_trials":[],"software_tools":[],"db_accessions":[],"linked_datasets":[],"topics":[]}