ArticleThe ISME journal2016
Metagenomic reconstructions of bacterial CRISPR loci constrain population histories.
Article in The ISME journal, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 38 papers.
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Who cites it
38 citing papers in PubMed, 79 citations in OpenAlex.
- Co-occurrence of diverse defense systems shapes complex microbe-virus relationships in deep-sea cold seeps.Nature communications · 2026Article
- Predicting inter-microbial host specificity in oral biofilms using a lightweight relation-aware knowledge graph model.Frontiers in cellular and infection microbiology · 2026Article
- Host Competitive Asymmetries Accelerate Viral Evolution in a Microbe-Virus Coevolutionary System.Ecology letters · 2025Article
- SpacerPlacer: ancestral reconstruction of CRISPR arrays reveals the evolutionary dynamics of spacer deletions.Nucleic acids research · 2024Article
- Comprehensive analysis of the CRISPR-Cas systems in Streptococcus thermophilus strains isolated from traditional yogurts.Antonie van Leeuwenhoek · 2024Article
- Dynamics of CRISPR-mediated virus-host interactions in the human gut microbiome.The ISME journal · 2024Article
- Hi-C metagenome sequencing reveals soil phage-host interactions.Nature communications · 2023Article
- Lysogenic bacteriophages encoding arsenic resistance determinants promote bacterial community adaptation to arsenic toxicity.The ISME journal · 2023Article
- CRISPR-Cas effector specificity and cleavage site determine phage escape outcomes.PLoS biology · 2023Article
- Molecular Relationships in Biofilm Formation and the Biosynthesis of Exoproducts in Pseudoalteromonas spp.Marine biotechnology (New York, N.Y.) · 2022Review
- Immune lag is a major cost of prokaryotic adaptive immunity during viral outbreaks.Proceedings. Biological sciences · 2021Article
- Long-run bacteria-phage coexistence dynamics under natural habitat conditions in an environmental biotechnology system.The ISME journal · 2021Article
- Evaluation of CRISPR Diversity in the Human Skin Microbiome for Personal Identification.mSystems · 2021Article
- Identification of Natural CRISPR Systems and Targets in the Human Microbiome.Cell host & microbe · 2021Article
- Pruning and Tending Immune Memories: Spacer Dynamics in the CRISPR Array.Frontiers in microbiology · 2021Review
- Roles of bacteriophages, plasmids and CRISPR immunity in microbial community dynamics revealed using time-series integrated meta-omics.Nature microbiology · 2021Article
- The size of the immune repertoire of bacteria.Proceedings of the National Academy of Sciences of the United States of America · 2020Article
- Atypical organizations and epistatic interactions of CRISPRs and cas clusters in genomes and their mobile genetic elements.Nucleic acids research · 2020Article
- Diversified local CRISPR-Cas immunity to viruses of Sulfolobus islandicus.Philosophical transactions of the Royal Society of London. Series B, Biological sciences · 2019Article
- CRISPR-Cas immunity leads to a coevolutionary arms race between Streptococcus thermophilus and lytic phage.Philosophical transactions of the Royal Society of London. Series B, Biological sciences · 2019Article
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Authors and funding
4 authors at 3 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Bacterial CRISPR-Cas systems provide insight into recent population history because they rapidly incorporate, in a unidirectional manner, short fragments (spacers) from coexisting infective virus populations into host chromosomes. Immunity is achieved by sequence identity between transcripts of spacers and their targets. Here, we used metagenomics to study the stability and dynamics of the type I-E CRISPR-Cas locus of Leptospirillum group II bacteria in biofilms sampled over 5 years from an acid mine drainage (AMD) system. Despite recovery of 452,686 spacers from CRISPR amplicons and metagenomic data, rarefaction curves of spacers show no saturation. The vast repertoire of spacers is attributed to phage/plasmid population diversity and retention of old spacers, despite rapid evolution of the targeted phage/plasmid genome regions (proto-spacers). The oldest spacers (spacers found at the trailer end) are conserved for at least 5 years, and 12% of these retain perfect or near-perfect matches to proto-spacer targets. The majority of proto-spacer regions contain an AAG proto-spacer adjacent motif (PAM). Spacers throughout the locus target the same phage population (AMDV1), but there are blocks of consecutive spacers without AMDV1 target sequences. Results suggest long-term coexistence of Leptospirillum with AMDV1 and periods when AMDV1 was less dominant. Metagenomics can be applied to millions of cells in a single sample to provide an extremely large spacer inventory, allow identification of phage/plasmids and enable analysis of previous phage/plasmid exposure. Thus, this approach can provide insights into prior bacterial environment and genetic interplay between hosts and their viruses.
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