ArticleNature microbiology2021
Roles of bacteriophages, plasmids and CRISPR immunity in microbial community dynamics revealed using time-series integrated meta-omics.
Article in Nature microbiology, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 39 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
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.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
39 citing papers in PubMed, 78 citations in OpenAlex.
- Hi-C sequencing deciphers phage and plasmid host networks in wastewater biofilms.Environmental science and ecotechnology · 2026Article
- Identification and comparative genomic analysis of prophage sequences and CRISPR‒Cas immunity in Methylococcus genomes: insights into industrial methane bioconversion.Biotechnology for biofuels and bioproducts · 2026Article
- Co-occurrence of diverse defense systems shapes complex microbe-virus relationships in deep-sea cold seeps.Nature communications · 2026Article
- Discarded diversity: novel megaphages, auxiliary metabolic genes, and virally encoded CRISPR-Cas systems in landfills.Virology journal · 2025Article
- Gut Microbiome and Intestinal Colonization with Multidrug-Resistant Strains of Enterobacterales: An Interplay Between Microbial Communities.Antibiotics (Basel, Switzerland) · 2025Review
- The virulence regulator CovR boosts CRISPR-Cas9 immunity in Group B Streptococcus.Nature communications · 2025Article
- Metaproteomics in the One Health framework for unraveling microbial effectors in microbiomes.Microbiome · 2025Review
- Unveiling plasmid diversity and functionality in pristine groundwater.Environmental microbiome · 2025Article
- Global analysis of the metaplasmidome: ecological drivers and spread of antibiotic resistance genes across ecosystems.Microbiome · 2025Article
- Long-term metagenomic insights into the roles of antiviral defense systems in stabilizing activated sludge bacterial communities.The ISME journal · 2025Article
- Mobile genetic elements: the hidden puppet masters underlying infant gut microbiome assembly?Microbiome research reports · 2025Article
- High-throughput single-cell sequencing of activated sludge microbiome.Environmental science and ecotechnology · 2025Article
- SpacerPlacer: ancestral reconstruction of CRISPR arrays reveals the evolutionary dynamics of spacer deletions.Nucleic acids research · 2024Article
- Selection and horizontal gene transfer underlie microdiversity-level heterogeneity in resistance gene fate during wastewater treatment.Nature communications · 2024Article
- Characteristics and immune functions of the endogenous CRISPR-Cas systems in myxobacteria.mSystems · 2024Article
- Dynamics of CRISPR-mediated virus-host interactions in the human gut microbiome.The ISME journal · 2024Article
- Forecasting the dynamics of a complex microbial community using integrated meta-omics.Nature ecology & evolution · 2024Article
- NCRD: A non-redundant comprehensive database for detecting antibiotic resistance genes.iScience · 2023Article
- Characterization and diversity of CRISPR/Cas systems in Klebsiella oxytoca.Molecular genetics and genomics : MGG · 2023Article
- Long-Read Sequencing Reveals Extensive DNA Methylations in Human Gut Phagenome Contributed by Prevalently Phage-Encoded Methyltransferases.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2023Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
23 authors at 9 institutions in 4 countries.
Funding
Abstract
Viruses and plasmids (invasive mobile genetic elements (iMGEs)) have important roles in shaping microbial communities, but their dynamic interactions with CRISPR-based immunity remain unresolved. We analysed generation-resolved iMGE-host dynamics spanning one and a half years in a microbial consortium from a biological wastewater treatment plant using integrated meta-omics. We identified 31 bacterial metagenome-assembled genomes encoding complete CRISPR-Cas systems and their corresponding iMGEs. CRISPR-targeted plasmids outnumbered their bacteriophage counterparts by at least fivefold, highlighting the importance of CRISPR-mediated defence against plasmids. Linear modelling of our time-series data revealed that the variation in plasmid abundance over time explained more of the observed community dynamics than phages. Community-scale CRISPR-based plasmid-host and phage-host interaction networks revealed an increase in CRISPR-mediated interactions coinciding with a decrease in the dominant 'Candidatus Microthrix parvicella' population. Protospacers were enriched in sequences targeting genes involved in the transmission of iMGEs. Understanding the factors shaping the fitness of specific populations is necessary to devise control strategies for undesirable species and to predict or explain community-wide phenotypes.
Indexed as
Identifiers
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.