ArticleThe ISME journal2019
Visualization and prediction of CRISPR incidence in microbial trait-space to identify drivers of antiviral immune strategy.
Article in The ISME journal, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 23 papers.
What it found
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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
23 citing papers in PubMed.
- Phage defence-system abundances vary across environments and increase with viral density.Philosophical transactions of the Royal Society of London. Series B, Biological sciences · 2025Article
- Ecological drivers of CRISPR immune systems.mSystems · 2024Article
- Determination of Technological Properties and CRISPR Profiles ofMicroorganisms · 2024Article
- Insight into the natural regulatory mechanisms and clinical applications of the CRISPR-Cas system.Heliyon · 2024Review
- Distribution of specific prokaryotic immune systems correlates with host optimal growth temperature.NAR genomics and bioinformatics · 2024Article
- Article
- Metagenomic clustering links specific metabolic functions to globally relevant ecosystems.mSystems · 2024Article
- Exploring the Frozen Armory: Antiphage Defense Systems in Cold-Adapted Bacteria with a Focus on CRISPR-Cas Systems.Microorganisms · 2024Article
- Genomic basis of environmental adaptation in the widespread poly-extremophilic Exiguobacterium group.The ISME journal · 2024Article
- Escherichia coli CRISPR arrays from early life fecal samples preferentially target prophages.The ISME journal · 2024Article
- Ciprofloxacin-Loaded, pH-Responsive PAMAM-Megamers Functionalized with S-Nitrosylated Hyaluronic Acid Support Infected Wound Healing in Mice without Inducing Antibiotic Resistance.Advanced healthcare materials · 2024Article
- Breaking the Ice: A Review of Phages in Polar Ecosystems.Methods in molecular biology (Clifton, N.J.) · 2024Review
- Analysis of genetic structure and function of clustered regularly interspaced short palindromic repeats loci in 110Frontiers in microbiology · 2023Article
- Extensive diversity and rapid turnover of phage defense repertoires in cheese-associated bacterial communities.Microbiome · 2022Article
- Mucin induces CRISPR-Cas defense in an opportunistic pathogen.Nature communications · 2022Article
- High viral abundance and low diversity are associated with increased CRISPR-Cas prevalence across microbial ecosystems.Current biology : CB · 2022Article
- Global phylogenomic novelty of the Cas1 gene from hot spring microbial communities.Frontiers in microbiology · 2022Article
- Precipitous Increase of Bacterial CRISPR-Cas Abundance at Around 45°C.Frontiers in microbiology · 2022Article
- Immune lag is a major cost of prokaryotic adaptive immunity during viral outbreaks.Proceedings. Biological sciences · 2021Article
- Streamlining CRISPR spacer-based bacterial host predictions to decipher the viral dark matter.Nucleic acids research · 2021Article
Corrections and comments
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Authors and funding
4 authors.
Funding
Abstract
Bacteria and archaea are locked in a near-constant battle with their viral pathogens. Despite previous mechanistic characterization of numerous prokaryotic defense strategies, the underlying ecological drivers of different strategies remain largely unknown and predicting which species will take which strategies remains a challenge. Here, we focus on the CRISPR immune strategy and develop a phylogenetically-corrected machine learning approach to build a predictive model of CRISPR incidence using data on over 100 traits across over 2600 species. We discover a strong but hitherto-unknown negative interaction between CRISPR and aerobicity, which we hypothesize may result from interference between CRISPR-associated proteins and non-homologous end-joining DNA repair due to oxidative stress. Our predictive model also quantitatively confirms previous observations of an association between CRISPR and temperature. Finally, we contrast the environmental associations of different CRISPR system types (I, II, III) and restriction modification systems, all of which act as intracellular immune systems.
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Registered trials
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