ArticleNature communications2020
Recording mobile DNA in the gut microbiota using an Escherichia coli CRISPR-Cas spacer acquisition platform.
Article in Nature communications, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 47 papers.
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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
47 citing papers in PubMed, 79 citations in OpenAlex.
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- A yeast synthetic biotic platform for delivery of therapeutic nanobodies to ameliorate gastrointestinal inflammation.Disease models & mechanisms · 2026Article
- Information storage across a microbial community using universal RNA barcoding.Nature biotechnology · 2026Article
- Synthetic Biology of Plants and Microbes for Agriculture, Environment, and Future Applications.Chemical reviews · 2026Review
- CRISPR-based genetic tools for the study of host-microbe interactions.Infection and immunity · 2025Review
- Therapeutic engineering of the gut microbiome using synthetic biology and metabolic tools: a comprehensive review with E. coli Nissle 1917 as a model case study.Archives of microbiology · 2025Review
- Deep mutational scanning identifies Cas1 and Cas2 variants that enhance type II-A CRISPR-Cas spacer acquisition.Nature communications · 2025Article
- Commercial utilization of bacteriocins: tackling challenges and exploring their potential as alternatives to antibiotics.Future microbiology · 2025Review
- Article
- Design and regulation of engineered bacteria for environmental release.Nature microbiology · 2025Review
- Probing and manipulating the gut microbiome with chemistry and chemical tools.Gut microbiome (Cambridge, England) · 2025Review
- Genetically engineered bacteria as inflammatory bowel disease therapeutics.Engineering microbiology · 2024Review
- Toward DNA-Based Recording of Biological Processes.International journal of molecular sciences · 2024Review
- Assessing spacer acquisition rates inFrontiers in microbiology · 2024Article
- Comprehensive Analysis of CRISPR-Cas Systems and Their Influence on Antibiotic Resistance inBioinformatics and biology insights · 2024Article
- Current examining methods and mathematical models of horizontal transfer of antibiotic resistance genes in the environment.Frontiers in microbiology · 2024Review
- Engineering E. coli strains using antibiotic-resistance-gene-free plasmids.Cell reports methods · 2023Article
- Clinically relevant antibiotic resistance genes are linked to a limited set of taxa within gut microbiome worldwide.Nature communications · 2023Article
- Global transmission of broad-host-range plasmids derived from the human gut microbiome.Nucleic acids research · 2023Article
- Highly active CRISPR-adaptation proteins revealed by a robust enrichment technology.Nucleic acids research · 2023Article
Corrections and comments
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Authors and funding
4 authors at 1 institution in 1 country.
Funding
Abstract
The flow of genetic material between bacteria is central to the adaptation and evolution of bacterial genomes. However, our knowledge about DNA transfer within complex microbiomes is lacking, with most studies of horizontal gene transfer (HGT) relying on bioinformatic analyses of genetic elements maintained on evolutionary timescales or experimental measurements of phenotypically trackable markers. Here, we utilize the CRISPR-Cas spacer acquisition process to detect DNA acquisition events from complex microbiota in real-time and at nucleotide resolution. In this system, an E. coli recording strain is exposed to a microbial sample and spacers are acquired from transferred plasmids and permanently stored in genomic CRISPR arrays. Sequencing and analysis of acquired spacers enables identification of the transferred plasmids. This approach allowed us to identify individual mobile elements without relying on phenotypic markers or post-transfer replication. We found that HGT into the recording strain in human clinical fecal samples can be extensive and is driven by different plasmid types, with the IncX type being the most actively transferred.
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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.