Comparative analysis of CRISPR cassettes from the human gut metagenomic contigs.
Comparative analysis of CRISPR cassettes from the human gut metagenomic contigs.
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DOI：
10.1186/1471-2164-15-202
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发表时间：
2014-03-17
期刊：
影响因子：
4.4
通讯作者：
Artamonova II
中科院分区：
文献类型：
--
作者：
Gogleva AA;Gelfand MS;Artamonova II
CRISPR（重复的规则间隔短回文重复序列）是一种原核适应性防御系统，可提供对外来复制子（如病毒和质粒）的抗性。CRISPR盒中的间隔区赋予针对病毒和含有与间隔区互补的区域的质粒的免疫力，因此它们在个体菌株和生态系统中保留原核生物与其病毒之间相互作用的足迹。人类肠道是众多微生物的丰富栖息地，但其中很大一部分是不可培养的，并且对它们以及它们的CRISPR系统知之甚少。我们使用了来自三个开放项目的人类肠道宏基因组数据，以表征人类相关微生物群中CRISPR盒的组成和动力学。将现有的CRISPR识别算法和先前设计的过滤程序应用于组装的人类肠道宏基因组重叠群，我们发现了388个CRISPR盒，其中373个具有先前在完整基因组或其他数据集中未观察到的重复序列。3,545个鉴定的间隔区中只有171个与来自人类肠道宏基因组重叠群的原型间隔区偶联。与GenBank序列匹配的数量可以忽略不计，为26个间隔区提供了原型间隔区。CRISPR盒的重建使我们能够跟踪间隔区内容的动态。与其他已发表的观察结果一致，我们表明不同盒（因此可能是较旧的盒）共享的间隔区倾向于尾部末端，而宏基因组中匹配的间隔区在盒中分布不均匀，表明倾向于形成靠近CRISPR盒活性末端的簇，邻近前导序列，因此表明原核生物和病毒之间在人类肠道中的动态相互作用。值得注意的是，间隔区与同一个体的宏基因组中的原型间隔区匹配的频率与随机对照相当，但可能与来自其他个体的宏基因组的原型间隔区匹配。对组装的重叠群的分析是对基于原始读段分析的方法的补充，因此提供了关于CRISPR盒的组成和进化的额外数据，揭示了宏基因组中CRISPR-噬菌体相互作用的动力学。本文的在线版本（doi：10.1186/1471-2164-15-202）包含补充材料，可供授权用户使用。
CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) is a prokaryotic adaptive defence system that provides resistance against alien replicons such as viruses and plasmids. Spacers in a CRISPR cassette confer immunity against viruses and plasmids containing regions complementary to the spacers and hence they retain a footprint of interactions between prokaryotes and their viruses in individual strains and ecosystems. The human gut is a rich habitat populated by numerous microorganisms, but a large fraction of these are unculturable and little is known about them in general and their CRISPR systems in particular. We used human gut metagenomic data from three open projects in order to characterize the composition and dynamics of CRISPR cassettes in the human-associated microbiota. Applying available CRISPR-identification algorithms and a previously designed filtering procedure to the assembled human gut metagenomic contigs, we found 388 CRISPR cassettes, 373 of which had repeats not observed previously in complete genomes or other datasets. Only 171 of 3,545 identified spacers were coupled with protospacers from the human gut metagenomic contigs. The number of matches to GenBank sequences was negligible, providing protospacers for 26 spacers. Reconstruction of CRISPR cassettes allowed us to track the dynamics of spacer content. In agreement with other published observations we show that spacers shared by different cassettes (and hence likely older ones) tend to the trailer ends, whereas spacers with matches in the metagenomes are distributed unevenly across cassettes, demonstrating a preference to form clusters closer to the active end of a CRISPR cassette, adjacent to the leader, and hence suggesting dynamical interactions between prokaryotes and viruses in the human gut. Remarkably, spacers match protospacers in the metagenome of the same individual with frequency comparable to a random control, but may match protospacers from metagenomes of other individuals. The analysis of assembled contigs is complementary to the approach based on the analysis of original reads and hence provides additional data about composition and evolution of CRISPR cassettes, revealing the dynamics of CRISPR-phage interactions in metagenomes. The online version of this article (doi:10.1186/1471-2164-15-202) contains supplementary material, which is available to authorized users.
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