ArticleApplied and environmental microbiology2010
Evolutionary dynamics of clustered irregularly interspaced short palindromic repeat systems in the ocean metagenome.
Article in Applied and environmental microbiology, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 21 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.
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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
21 citing papers in PubMed, 55 citations in OpenAlex.
- Clustered Regularly Interspaced Short Palindromic Repeat/CRISPR-Associated Protein and Its Utility All at Sea: Status, Challenges, and Prospects.Microorganisms · 2024Review
- CRISPR-Cas Systems in Gut Microbiome of Children with Autism Spectrum Disorders.Life (Basel, Switzerland) · 2022Article
- Targeted assemblies of cas1 suggest CRISPR-Cas's response to soil warming.The ISME journal · 2020Article
- Natural diversity of CRISPR spacers of Thermus: evidence of local spacer acquisition and global spacer exchange.Philosophical transactions of the Royal Society of London. Series B, Biological sciences · 2019Article
- Aquaculture as a source of empirical evidence for coevolution between CRISPR-Cas and phage.Philosophical transactions of the Royal Society of London. Series B, Biological sciences · 2019Review
- Article
- CRISPRs for Strain Tracking and Their Application to Microbiota Transplantation Data Analysis.The CRISPR journal · 2019Article
- An Enrichment of CRISPR and Other Defense-Related Features in Marine Sponge-Associated Microbial Metagenomes.Frontiers in microbiology · 2016Article
- CRISPR-Cas systems in the marine actinomycete Salinispora: linkages with phage defense, microdiversity and biogeography.BMC genomics · 2014Article
- Article
- Expanding the catalog of cas genes with metagenomes.Nucleic acids research · 2014Article
- Article
- Crass: identification and reconstruction of CRISPR from unassembled metagenomic data.Nucleic acids research · 2013Article
- Holding a grudge: persisting anti-phage CRISPR immunity in multiple human gut microbiomes.RNA biology · 2013Article
- Probabilistic models for CRISPR spacer content evolution.BMC evolutionary biology · 2013Article
- Persisting viral sequences shape microbial CRISPR-based immunity.PLoS computational biology · 2012Article
- CRISPR loci reveal networks of gene exchange in archaea.Biology direct · 2011Article
- CRISPR-based adaptive immune systems.Current opinion in microbiology · 2011Review
- Analysis of streptococcal CRISPRs from human saliva reveals substantial sequence diversity within and between subjects over time.Genome research · 2011Article
- Use of cellular CRISPR (clusters of regularly interspaced short palindromic repeats) spacer-based microarrays for detection of viruses in environmental samples.Applied and environmental microbiology · 2010Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
3 authors at 2 institutions in 1 country.
Funding
Abstract
Clustered regularly interspaced short palindromic repeats (CRISPRs) form a recently characterized type of prokaryotic antiphage defense system. The phage-host interactions involving CRISPRs have been studied in experiments with selected bacterial or archaeal species and, computationally, in completely sequenced genomes. However, these studies do not allow one to take prokaryotic population diversity and phage-host interaction dynamics into account. This gap can be filled by using metagenomic data: in particular, the largest existing data set, generated from the Sorcerer II Global Ocean Sampling expedition. The application of three publicly available CRISPR recognition programs to the Global Ocean metagenome produced a large proportion of false-positive results. To address this problem, a filtering procedure was designed. It resulted in about 200 reliable CRISPR cassettes, which were then studied in detail. The repeat consensuses were clustered into several stable classes that differed from the existing classification. Short fragments of DNA similar to the cassette spacers were more frequently present in the same geographical location than in other locations (P, <0.0001). We developed a catalogue of elementary CRISPR-forming events and reconstructed the likely evolutionary history of cassettes that had common spacers. Metagenomic collections allow for relatively unbiased analysis of phage-host interactions and CRISPR evolution. The results of this study demonstrate that CRISPR cassettes retain the memory of the local virus population at a particular ocean location. CRISPR evolution may be described using a limited vocabulary of elementary events that have a natural biological interpretation.
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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.