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利用时间序列整合宏基因组学揭示噬菌体、质粒和 CRISPR 免疫在微生物群落动态中的作用。

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

机构信息

Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg.

Megeno S.A., Esch-sur-Alzette, Luxembourg.

出版信息

Nat Microbiol. 2021 Jan;6(1):123-135. doi: 10.1038/s41564-020-00794-8. Epub 2020 Nov 2.

DOI:10.1038/s41564-020-00794-8
PMID:33139880
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC7752763/
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.

摘要

病毒和质粒（侵袭性移动遗传元件（iMGE））在塑造微生物群落方面发挥着重要作用，但它们与基于 CRISPR 的免疫的动态相互作用仍未得到解决。我们使用整合的宏基因组学分析了来自生物污水处理厂的微生物联合体中跨越一年半的一代 resolved 型 iMGE-宿主动态。我们鉴定了 31 个细菌宏基因组组装基因组，这些基因组编码完整的 CRISPR-Cas 系统及其相应的 iMGE。CRISPR 靶向的质粒数量比噬菌体至少多五倍，突出了 CRISPR 介导的防御质粒的重要性。我们的时间序列数据分析的线性模型表明，随着时间的推移，质粒丰度的变化解释了更多观察到的群落动态，而不是噬菌体。基于社区规模的 CRISPR 质粒-宿主和噬菌体-宿主相互作用网络揭示了与优势“Candidatus Microthrix parvicella”种群减少相对应的 CRISPR 介导相互作用的增加。原间隔区序列富含靶向 iMGE 传播相关基因的序列。了解塑造特定种群适应性的因素对于设计针对不良物种的控制策略以及预测或解释全社区表型是必要的。

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2
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3
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4
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5
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