VITCOMIC2: visualization tool for the phylogenetic composition of microbial communities based on 16S rRNA gene amplicons and metagenomic shotgun sequencing.
VITCOMIC2: visualization tool for the phylogenetic composition of microbial communities based on 16S rRNA gene amplicons and metagenomic shotgun sequencing.
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DOI：
10.1186/s12918-018-0545-2
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发表时间：
2018-03-19
影响因子：
--
通讯作者：
Kurokawa K
中科院分区：
文献类型：
--
作者：
Mori H;Maruyama T;Yano M;Yamada T;Kurokawa K
基于 16S rRNA 基因的扩增子测序分析广泛用于确定微生物群落的分类组成。一旦获得每个群落的分类组成，就可以通过系统发育树推断类群之间的进化关系。因此，分类单元之间的分类组成和系统发育关系的组合表示是理解微生物群落结构的有力方法。然而，应用基于系统发育树的表示法以及每个群落中数千个或更多类群的丰度信息是一项艰巨的任务。为此，我们之前开发了工具 VITCOMIC（微生物群落分类组成的可视化工具），该工具基于基因组测序的微生物的系统发育信息。在这里，我们介绍 VITCOMIC2，它对 VITCOMIC 进行了实质性改进，这对于解决与基于 16S rRNA 基因的微生物群落分析相关的几个问题是必要的。我们开发了 VITCOMIC2 来提供（i）针对广泛参考类群（包括未培养类群）的序列同一性搜索； (ii) 类群之间 16S rRNA 基因拷贝数差异的标准化； (iii)通过应用基于图形处理单元的序列同一性搜索工具CLAST进行快速序列同一性搜索； (iv) 准确的分类组成推断和近全长的 16S rRNA 基因序列重建，用于宏基因组鸟枪测序； (v) 交互式用户界面，用于同时表示微生物群落的分类组成和类群之间的系统发育关系。我们通过使用来自模拟微生物群落的宏基因组鸟枪法测序数据验证了过程 (ii) 和 (iv) 的准确性。 VITCOMIC2 中的改进使用户能够根据从宏基因组鸟枪法和扩增子测序获得的 16S rRNA 基因序列数据，直观地了解微生物群落的组成。本文的在线版本 (10.1186/s12918-018-0545-2) 包含补充材料，可供授权用户使用。
The 16S rRNA gene-based amplicon sequencing analysis is widely used to determine the taxonomic composition of microbial communities. Once the taxonomic composition of each community is obtained, evolutionary relationships among taxa are inferred by a phylogenetic tree. Thus, the combined representation of taxonomic composition and phylogenetic relationships among taxa is a powerful method for understanding microbial community structure; however, applying phylogenetic tree-based representation with information on the abundance of thousands or more taxa in each community is a difficult task. For this purpose, we previously developed the tool VITCOMIC (VIsualization tool for Taxonomic COmpositions of MIcrobial Community), which is based on the genome-sequenced microbes’ phylogenetic information. Here, we introduce VITCOMIC2, which incorporates substantive improvements over VITCOMIC that were necessary to address several issues associated with 16S rRNA gene-based analysis of microbial communities. We developed VITCOMIC2 to provide (i) sequence identity searches against broad reference taxa including uncultured taxa; (ii) normalization of 16S rRNA gene copy number differences among taxa; (iii) rapid sequence identity searches by applying the graphics processing unit-based sequence identity search tool CLAST; (iv) accurate taxonomic composition inference and nearly full-length 16S rRNA gene sequence reconstructions for metagenomic shotgun sequencing; and (v) an interactive user interface for simultaneous representation of the taxonomic composition of microbial communities and phylogenetic relationships among taxa. We validated the accuracy of processes (ii) and (iv) by using metagenomic shotgun sequencing data from a mock microbial community. The improvements incorporated into VITCOMIC2 enable users to acquire an intuitive understanding of microbial community composition based on the 16S rRNA gene sequence data obtained from both metagenomic shotgun and amplicon sequencing. The online version of this article (10.1186/s12918-018-0545-2) contains supplementary material, which is available to authorized users.
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