ArticleNature microbiology2022
Species- and site-specific genome editing in complex bacterial communities.
Article in Nature microbiology, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 156 papers.
What it found
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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.
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Who cites it
156 citing papers in PubMed, 272 citations in OpenAlex.
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- Phylogeny-agnostic strain-level prediction of phage-host interactions from genomes using machine learning.Nature microbiology · 2026Article
- Programmable enzymes for targeted gene insertion.Nature reviews. Genetics · 2026Review
- Genome-wide fitness profiling reveals flagellar rotation as an energetic liability during anaerobic maintenance inbioRxiv : the preprint server for biology · 2026Article
- Transposon end recognition and excision mechanisms of type I-F CRISPR-associated transposases.Nature communications · 2026Article
- Describing the persistence landscape for introducing microbes into complex communities.Applied and environmental microbiology · 2026Review
- Phage host range: determinants, dynamics and applications.Nature reviews. Microbiology · 2026Review
- Altering our (soils') future.EMBO reports · 2026Article
- Engineering commensal microbes for host health.Cell host & microbe · 2026Review
- Cross-family and phage-specific gene requirements for Klebsiella infection revealed by scalable RB-TnSeq genetic screens.PLoS genetics · 2026Article
- Structure of the Type I-F3 CAST holo integration complex reveals licensing mechanisms during RNA-guided DNA integration.bioRxiv : the preprint server for biology · 2026Article
- The Gut Microbiome Dependency Continuum in Drug Discovery: A Unified Pharmacology Framework Linking Clinical Drugs, Natural Products, and Engineered Microbial Therapeutics.Biotech (Basel (Switzerland)) · 2026Review
- Base Editors for Engineering Industrial Microorganisms: Types, Applications, and Future Perspectives.Biotechnology journal · 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
- Article
- Extensive spontaneous genome reduction in Paraburkholderia sabiae.Scientific reports · 2026Article
- Article
96 more citing papers are in PubMed but not listed here.
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Authors and funding
21 authors at 6 institutions in 2 countries.
Funding
Abstract
Understanding microbial gene functions relies on the application of experimental genetics in cultured microorganisms. However, the vast majority of bacteria and archaea remain uncultured, precluding the application of traditional genetic methods to these organisms and their interactions. Here, we characterize and validate a generalizable strategy for editing the genomes of specific organisms in microbial communities. We apply environmental transformation sequencing (ET-seq), in which nontargeted transposon insertions are mapped and quantified following delivery to a microbial community, to identify genetically tractable constituents. Next, DNA-editing all-in-one RNA-guided CRISPR-Cas transposase (DART) systems for targeted DNA insertion into organisms identified as tractable by ET-seq are used to enable organism- and locus-specific genetic manipulation in a community context. Using a combination of ET-seq and DART in soil and infant gut microbiota, we conduct species- and site-specific edits in several bacteria, measure gene fitness in a nonmodel bacterium and enrich targeted species. These tools enable editing of microbial communities for understanding and control.
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What OpenQuestion holds
Registered trials
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.