Comparison of metagenomic samples using sequence signatures.
Comparison of metagenomic samples using sequence signatures.
复制标题
使用序列特征比较宏基因组样本
DOI：
10.1186/1471-2164-13-730
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发表时间：
2012-12-27
期刊：
影响因子：
4.4
通讯作者：
Zhang X
中科院分区：
文献类型：
--
作者：
Jiang B;Song K;Ren J;Deng M;Sun F;Zhang X
背景序列特征（Sequence signature）是由k-元组（ork-mers，k-gram）的频率定义的，已被广泛用于比较生物个体的基因组序列、鉴定顺式调控模块以及研究调控序列的进化。最近，已经产生了来自各种不同环境的宏基因组样品的许多下一代测序（NGS）读取数据集。这些读段的组装可能是困难的，并且基于将读段映射到基因或途径的分析方法也受到现有数据库的可用性和完整性的限制。然而，基于序列签名的方法不需要完整的基因组或现有的数据库，因此对于使用NGS读取数据比较宏基因组样品可能非常有用。结果我们研究了几种不同的测量方法，包括最近从我们的小组开发的d2，d2* 和d2 S，一种用于从Hao的小组开发的CVTree中的测量方法（以下称为Hao）（Qiet al.，2004），如Willneret等人（2009）中基于相对二核苷酸、三核苷酸和四核苷酸频率的测量，以及频率向量之间的标准测量，用于使用序列签名比较宏基因组样品。我们使用一系列广泛的模拟和三个真实的下一代测序（NGS）宏基因组数据集比较了它们的性能：来自33种哺乳动物宿主物种的39个粪便样本，世界各地的56个海洋样本和来自人类个体的13个粪便样本。结果表明，相异度测量2Scan实现上级性能时，比较宏基因组样本聚类成不同的群体，以及恢复环境梯度影响微生物样品。通过分析获得了对影响宏基因组样品中微生物组成的环境因素的新见解。我们的研究结果表明，哺乳动物肠道的序列签名是密切相关的饮食和肠道生理的哺乳动物，和海洋群落的序列签名是密切相关的位置和temperature.ConclusionsSequence签名可以成功地揭示从NGS读取的宏基因组样本之间的主要群体和梯度关系，而无需比对参考数据库。d2 S相异性度量在所有应用场景中都是一个很好的选择。元组大小的最佳选择取决于测序深度，但在中等测序深度的选择范围内是相当稳健的。
BackgroundSequence signatures, as defined by the frequencies ofk-tuples (ork-mers,k-grams), have been used extensively to compare genomic sequences of individual organisms, to identifycis-regulatory modules, and to study the evolution of regulatory sequences. Recently many next-generation sequencing (NGS) read data sets of metagenomic samples from a variety of different environments have been generated. The assembly of these reads can be difficult and analysis methods based on mapping reads to genes or pathways are also restricted by the availability and completeness of existing databases. Sequence-signature-based methods, however, do not need the complete genomes or existing databases and thus, can potentially be very useful for the comparison of metagenomic samples using NGS read data. Still, the applications of sequence signature methods for the comparison of metagenomic samples have not been well studied.ResultsWe studied several dissimilarity measures, includingd2,d2*andd2Srecently developed from our group, a measure (hereinafter noted asHao) used in CVTree developed from Hao’s group (Qiet al., 2004), measures based on relative di-, tri-, and tetra-nucleotide frequencies as in Willneret al. (2009), as well as standardlpmeasures between the frequency vectors, for the comparison of metagenomic samples using sequence signatures. We compared their performance using a series of extensive simulations and three real next-generation sequencing (NGS) metagenomic datasets: 39 fecal samples from 33 mammalian host species, 56 marine samples across the world, and 13 fecal samples from human individuals. Results showed that the dissimilarity measured2Scan achieve superior performance when comparing metagenomic samples by clustering them into different groups as well as recovering environmental gradients affecting microbial samples. New insights into the environmental factors affecting microbial compositions in metagenomic samples are obtained through the analyses. Our results show that sequence signatures of the mammalian gut are closely associated with diet and gut physiology of the mammals, and that sequence signatures of marine communities are closely related to location and temperature.ConclusionsSequence signatures can successfully reveal major group and gradient relationships among metagenomic samples from NGS reads without alignment to reference databases. Thed2Sdissimilarity measure is a good choice in all application scenarios. The optimal choice of tuple size depends on sequencing depth, but it is quite robust within a range of choices for moderate sequencing depths.
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DOI：
10.1126/science.1198719
发表时间：
2011-05-20
期刊：
Science (New York, N.Y.)
影响因子：
--
作者：
Muegge BD;Kuczynski J;Knights D;Clemente JC;González A;Fontana L;Henrissat B;Knight R;Gordon JI
通讯作者：
Gordon JI
DOI：
10.1073/pnas.83.14.5155
发表时间：
1986-07-01
影响因子：
11.1
作者：
BLAISDELL, BE
通讯作者：
BLAISDELL, BE
DOI：
10.1073/pnas.0807920105
发表时间：
2008-11-18
影响因子：
11.1
作者：
Fierer, Noah;Hamady, Micah;Knight, Rob
通讯作者：
Knight, Rob
影响因子：
48
作者：
Mavromatis, Konstantinos;Ivanova, Natalia;Kyrpides, Nikos C.
通讯作者：
Kyrpides, Nikos C.
影响因子：
56.9
作者：
Gill, Steven R.;Pop, Mihai;Nelson, Karen E.
通讯作者：
Nelson, Karen E.