Multidimensional metrics for estimating phage abundance, distribution, gene density, and sequence coverage in metagenomes.
Multidimensional metrics for estimating phage abundance, distribution, gene density, and sequence coverage in metagenomes.
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DOI：
10.3389/fmicb.2015.00381
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发表时间：
2015
影响因子：
5.2
通讯作者：
Edwards RA
中科院分区：
文献类型：
--
作者：
Aziz RK;Dwivedi B;Akhter S;Breitbart M;Edwards RA
噬菌体是地球上最丰富的生物实体，发挥着重要的生态作用，但目前测序的噬菌体基因组并不能充分代表它们的多样性，而且对这些测序基因组在自然界中的丰度和分布知之甚少。虽然噬菌体生态学的研究从宏基因组测序的出现中受益匪浅，但仍然缺乏对各种生态系统中噬菌体基因和基因组的系统调查，有关噬菌体生物学，生活方式和生态学的基本问题仍然没有答案。为了解决这些问题，并改善不同宏基因组中的ESTs的比较分析，我们使用网络工具噬菌体Eco-ESTs筛选了一组公开可用的宏基因组样本的核心序列，以获得与完全测序的ESTs相关的序列。然后，我们采用并部署了一系列数学和统计指标，用于对各种生态系统中噬菌体基因和基因组的丰度和分布进行多维估计。单独使用这些指标的实验表明，它们在强调环境宏基因组中已知噬菌体序列的普遍但不均匀的分布方面是有用的。结合使用这些指标，使我们能够将噬菌体基因组分解为与其基因型和分类类别以及其生态特性相关的簇。我们建议将这组指标添加到当前的元病毒分析管道中，在那里它们可以提供有关噬菌体镶嵌，栖息地特异性和进化的见解。
Phages are the most abundant biological entities on Earth and play major ecological roles, yet the current sequenced phage genomes do not adequately represent their diversity, and little is known about the abundance and distribution of these sequenced genomes in nature. Although the study of phage ecology has benefited tremendously from the emergence of metagenomic sequencing, a systematic survey of phage genes and genomes in various ecosystems is still lacking, and fundamental questions about phage biology, lifestyle, and ecology remain unanswered. To address these questions and improve comparative analysis of phages in different metagenomes, we screened a core set of publicly available metagenomic samples for sequences related to completely sequenced phages using the web tool, Phage Eco-Locator. We then adopted and deployed an array of mathematical and statistical metrics for a multidimensional estimation of the abundance and distribution of phage genes and genomes in various ecosystems. Experiments using those metrics individually showed their usefulness in emphasizing the pervasive, yet uneven, distribution of known phage sequences in environmental metagenomes. Using these metrics in combination allowed us to resolve phage genomes into clusters that correlated with their genotypes and taxonomic classes as well as their ecological properties. We propose adding this set of metrics to current metaviromic analysis pipelines, where they can provide insight regarding phage mosaicism, habitat specificity, and evolution.