ArticleScience (New York, N.Y.)2025
Metagenomic editing of commensal bacteria in vivo using CRISPR-associated transposases.
Abstract read
In one paragraph
Article in Science (New York, N.Y.), 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 17 papers.
0numbers the graph read from it
0cells of the map it votes in
17citing papers in PubMed
–field-weighted citation impact
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
17 citing papers in PubMed.
- Engineered bacteria in disease diagnosis and therapy: A synthetic biology perspective.Synthetic and systems biotechnology · 2026Review
- Microbiome ecology and antibiotic treatment failure: resistance spread, microbial competition and community engineering.Microbial genomics · 2026Review
- Systems engineering of engineered live biotherapeutics: A discovery-to-translation framework for streamlining microbiome therapeutic development.Journal of controlled release : official journal of the Controlled Release Society · 2026Review
- Programmable enzymes for targeted gene insertion.Nature reviews. Genetics · 2026Review
- Transferable genetic toolsets for nonmodel gut Clostridia enable in vivo reversible control of metabolite production.Nature biotechnology · 2026Article
- Transposon end recognition and excision mechanisms of type I-F CRISPR-associated transposases.Nature communications · 2026Article
- Maternal and infant gut microbiome.iMeta · 2026Review
- Gut microbiota in health and disease.Molecular biomedicine · 2026Review
- Engineering commensal microbes for host health.Cell host & microbe · 2026Review
- Advances in biocontainment strategies of engineered microbes for use in humans.Current opinion in microbiology · 2026Review
- Gnotobiotic mouse models as tools for dissecting the role of the microbiota in allergy: contributions from the laboratory of gnotobiology in Nový Hrádek.Folia microbiologica · 2026Review
- Engineering the Gut Microbiome: Emerging Genome-Editing Strategies and Therapeutic Applications.Microorganisms · 2026Review
- Structural basis of RNA-guided DNA integration by type I CRISPR-associated transposases.bioRxiv : the preprint server for biology · 2026Article
- Cross-order detection of bacteriophage transduction in microbial communities using RNA barcoding.Nature communications · 2026Article
- Review on Mining Robust Lactic Acid Bacteria for Next-Generation Silage Inoculants via Multi-Omics.Life (Basel, Switzerland) · 2026Review
- Functional genetic signatures of the gut microbiome in cardiometabolic diseases: mechanisms and translational opportunities.Frontiers in microbiomes · 2026Review
- Advances in Molecular Microbiology-From Recent Advances to the Future.Current issues in molecular biology · 2025Article
Corrections and comments
- Commented on by
Authors and funding
13 authors.
Diego Rivera GelsingerDepartment of Systems Biology, Columbia University, New York, NY, USA.ORCID 0000-0002-3786-1205
Carlotta RondaDepartment of Systems Biology, Columbia University, New York, NY, USA.ORCID 0000-0002-7501-914X
Junjie MaDepartment of Microbiology and Immunology, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY, USA.
Om B KarDepartment of Systems Biology, Columbia University, New York, NY, USA.ORCID 0009-0005-8056-9436
Madeline EdwardsDepartment of Microbiology and Immunology, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY, USA.ORCID 0000-0003-0134-2806
Yiming HuangDepartment of Systems Biology, Columbia University, New York, NY, USA.ORCID 0000-0003-1932-2803
Chrystal F MavrosDepartment of Systems Biology, Columbia University, New York, NY, USA.ORCID 0000-0003-3914-7512
Yiwei SunDepartment of Systems Biology, Columbia University, New York, NY, USA.ORCID 0000-0002-5974-6232
Tyler PerdueDepartment of Systems Biology, Columbia University, New York, NY, USA.ORCID 0009-0004-3023-0883
Phuc Leo VoDepartment of Molecular Pharmacology and Therapeutics, Columbia University, New York, NY, USA.ORCID 0000-0002-3719-7770
Ivaylo I IvanovDepartment of Microbiology and Immunology, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY, USA.ORCID 0000-0001-5337-3386
Samuel H SternbergDepartment of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, USA.ORCID 0000-0001-8240-9114
Harris H WangDepartment of Systems Biology, Columbia University, New York, NY, USA.ORCID 0000-0003-2164-4318
Funding
Center for Genomic Editing and Recording: Development and Application of Next-Generation Genome and Epigenome Editing Methods to Advance the Study and Treatment of Human DiseaseRM1HG009490 · NHGRI · WHITEHEAD INSTITUTE FOR BIOMEDICAL RES · PI Brittany S. Adamson, Martin Joseph Ankrah Aryee · 2017 to 2026
$22.7MThe Organoid and Cell Culture CoreP30DK132710 · NIDDK · COLUMBIA UNIVERSITY HEALTH SCIENCES · PI Robert F. Schwabe · 2022 to 2026
$7.2MRole of intestinal commensal-induced Th17 cells and mucosal immunity in metabolic diseaseR01DK098378 · NIDDK · COLUMBIA UNIVERSITY HEALTH SCIENCES · PI Ivaylo Ivanov Ivanov · 2013 to 2026
$6.5MePACE: automation platforms for adaptable and scalable continuous evolution of biomolecules with therapeutic potentialR01EB027793 · NIBIB · BROAD INSTITUTE, INC. · PI Ahmad Samir Khalil, DAVID R LIU · 2019 to 2026
$6.1MMicron-scale Spatial Metagenomic Mapping of Microbial Biogeography in the Gastrointestinal TractR01AI132403 · NIAID · COLUMBIA UNIVERSITY HEALTH SCIENCES · PI Harris H Wang · 2017 to 2026
$6.0MThe Role of Secondary Bile Acids in Gastro-Esophageal NeoplasiaR01CA272898 · NCI · COLUMBIA UNIVERSITY HEALTH SCIENCES · PI Julian Abrams, Michael Quante · 2022 to 2026
$4.1MEcological dynamics and metabolic interactions in thegut microbiome across space and timeR01DK118044 · NIDDK · COLUMBIA UNIVERSITY HEALTH SCIENCES · PI VITKUP, DENNIS, WANG, HARRIS H · 2018 to 2022
$3.4MA high-performance and versatile technology for precision microbiome engineeringR01EB031935 · NIBIB · COLUMBIA UNIVERSITY HEALTH SCIENCES · PI Samuel Henry Sternberg, Harris H Wang · 2021 to 2026
$3.3MMaintenance of mucosal homeostasis by commensal Th17 cellsU01AI163069 · NIAID · COLUMBIA UNIVERSITY HEALTH SCIENCES · PI Ivaylo Ivanov Ivanov · 2021 to 2026
$2.8MNon-redundant functions of type 3 innate lymphoid cells in mucosal immunityR01AI144808 · NIAID · COLUMBIA UNIVERSITY HEALTH SCIENCES · PI IVANOV, IVAYLO IVANOV · 2019 to 2022
$1.9MNew mechanism of commensal bacteria interaction with host immunityR21AI126305 · NIAID · COLUMBIA UNIVERSITY HEALTH SCIENCES · PI IVANOV, IVAYLO IVANOV · 2017 to 2018
$440kDiscovery of immunomodulatory gut microbes with MAGICR21AI146817 · NIAID · COLUMBIA UNIVERSITY HEALTH SCIENCES · PI IVANOV, IVAYLO IVANOV · 2019 to 2020
$437kHoward Hughes Medical InstituteNCI NIH HHS R01 CA272898NHGRI NIH HHS RM1 HG009490NIAID NIH HHS R01 AI132403NIAID NIH HHS R01 AI144808NIAID NIH HHS R21 AI126305NIAID NIH HHS R21 AI146817NIAID NIH HHS U01 AI163069NIBIB NIH HHS R01 EB027793NIBIB NIH HHS R01 EB031935NIDDK NIH HHS P30 DK132710NIDDK NIH HHS R01 DK098378NIDDK NIH HHS R01 DK118044
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
Indexed as
BacteroidesCRISPR-Cas SystemsGastrointestinal MicrobiomeGene EditingAnimalsClustered Regularly Interspaced Short Palindromic RepeatsHumansMetagenomeMetagenomicsMiceMice, Inbred C57BLSymbiosis
Identifiers
What OpenQuestion holds
Textmetadata
LicenceCC BY
Read underepoch 390
Registered trials
None linked
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.