Accurate taxonomy assignments from 16S rRNA sequences produced by highly parallel pyrosequencers.
Accurate taxonomy assignments from 16S rRNA sequences produced by highly parallel pyrosequencers.
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高度平行的焦索测序者产生的16S rRNA序列的准确分类学分配。
DOI：
10.1093/nar/gkn491
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发表时间：
2008-10
影响因子：
14.9
通讯作者：
Knight R
中科院分区：
文献类型：
--
作者：
Liu Z;DeSantis TZ;Andersen GL;Knight R
最近推出的大规模平行焦磷酸测序仪能够利用16S核糖体RNA（rRNA）序列对微生物群落组成进行快速、低成本的分析。然而，一个主要的挑战是设计一种工作流程，以便能够准确、快速地将分类学信息分配到每个读段，从而使每个群落的组成能够与每个物种、属、科或门的成员可能扮演的生态角色联系起来。在此，我们使用三个大型的16S rRNA数据集来测试基于全长序列的分类学信息是否能够被模拟焦磷酸测序仪输出的短读段重新获取。我们发现不同的分类学归类方法在重新获取全长16S rRNA序列中的分类学信息的能力上有很大差异：大多数方法对用于测序的16S rRNA基因区域敏感，但许多方法和rRNA区域的组合能产生一致且准确的结果。为了处理从各种微生物群落调查（包括来自人体栖息地的那些）中获得的大量部分16S rRNA序列数据集，我们建议使用Greengenes或RDP分类器，片段至少250个碱基，从引物R357、R534、R798、F343或F517中的一个开始。
The recent introduction of massively parallel pyrosequencers allows rapid, inexpensive analysis of microbial community composition using 16S ribosomal RNA (rRNA) sequences. However, a major challenge is to design a workflow so that taxonomic information can be accurately and rapidly assigned to each read, so that the composition of each community can be linked back to likely ecological roles played by members of each species, genus, family or phylum. Here, we use three large 16S rRNA datasets to test whether taxonomic information based on the full-length sequences can be recaptured by short reads that simulate the pyrosequencer outputs. We find that different taxonomic assignment methods vary radically in their ability to recapture the taxonomic information in full-length 16S rRNA sequences: most methods are sensitive to the region of the 16S rRNA gene that is targeted for sequencing, but many combinations of methods and rRNA regions produce consistent and accurate results. To process large datasets of partial 16S rRNA sequences obtained from surveys of various microbial communities, including those from human body habitats, we recommend the use of Greengenes or RDP classifier with fragments of at least 250 bases, starting from one of the primers R357, R534, R798, F343 or F517.
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影响因子：
12.3
作者：
Knight R;Maxwell P;Birmingham A;Carnes J;Caporaso JG;Easton BC;Eaton M;Hamady M;Lindsay H;Liu Z;Lozupone C;McDonald D;Robeson M;Sammut R;Smit S;Wakefield MJ;Widmann J;Wikman S;Wilson S;Ying H;Huttley GA
通讯作者：
Huttley GA
影响因子：
14.9
作者：
Ludwig, W;Strunk, O;Schleifer, KH
通讯作者：
Schleifer, KH
DOI：
10.1073/pnas.0504978102
发表时间：
2005-08-02
影响因子：
11.1
作者：
Ley, RE;Bäckhed, F;Gordon, JI
通讯作者：
Gordon, JI
影响因子：
14.9
作者：
Liu Z;Lozupone C;Hamady M;Bushman FD;Knight R
通讯作者：
Knight R
DOI：
10.2307/2412448
发表时间：
1970-01-01
期刊：
SYSTEMATIC ZOOLOGY
影响因子：
--
作者：
FITCH, WM
通讯作者：
FITCH, WM