4.5 Article

Roles of bacteriophages, plasmids and CRISPR immunity in microbial community dynamics revealed using time-series integrated meta-omics

期刊

NATURE MICROBIOLOGY
卷 6, 期 1, 页码 123-+

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NATURE PORTFOLIO
DOI: 10.1038/s41564-020-00794-8

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资金

  1. Luxembourg National Research Fund (FNR)
  2. PRIDE doctoral training unit grant [PRIDE15/10907093]
  3. CORE grants [CORE/15/BM/10404093, CORE/17/SM/11689322]
  4. European Union ERASysAPP grant [INTER/SYSAPP/14/05]
  5. proof-of-concept grant [PoC/13/02]
  6. European Union Joint Programming in Neurodegenerative Diseases grant [INTER/JPND/12/01]
  7. ATTRACT grant [A09/03]
  8. AFR Ph.D. grant [PHD-2014-1/7934898]
  9. CORE Junior grant [C15/SR/10404839]
  10. Integrated Biobank of Luxembourg
  11. Luxembourg Ministry of Higher Education and Research
  12. `Plan Technologies de la Sante du Gouvernement du Grand-Duche de Luxembourg' through the Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg

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The study found that CRISPR plays a more important role in defense against plasmids than phages, and the variability in plasmid abundance over time has a greater impact on community dynamics than phages. In addition, the enrichment of protospacers targeting genes involved in the transmission of iMGEs helps understand population fitness and devise control strategies.
CRISPR-based immunity and microbial community dynamics in a wastewater treatment plant over one and a half years. 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.

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