Ironing out the wrinkles in the rare biosphere through improved OTU clustering.
Ironing out the wrinkles in the rare biosphere through improved OTU clustering.
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DOI：
10.1111/j.1462-2920.2010.02193.x
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发表时间：
2010-07
影响因子：
5.1
通讯作者：
Sogin ML
中科院分区：
文献类型：
--
作者：
Huse SM;Welch DM;Morrison HG;Sogin ML
PCR 扩增子文库的深度测序有助于在复杂微生物群落的环境 DNA 调查中检测低丰度种群。与此同时，深度测序可能会通过生成低频、容易出错的读数而导致对微生物多样性的高估。即使每个核苷酸位置的测序错误率低于 0.005，通过多重序列比对和完全连锁聚类生成操作分类单元 (OTU) 的常用方法也会显着增加预测的 OTU 数量并夸大丰富度估计值。我们表明，2％的单连锁预聚类方法和基于成对比对的平均连锁聚类可以更准确地预测已知分类组成的单一模板和混合模板制剂中的预期OTU。这种新的聚类方法可以将环境样本中的 OTU 丰富度降低多达 30-60%，但不会减少定义稀有生物圈的长尾等级丰度曲线中 OTU 的比例。
Deep sequencing of PCR amplicon libraries facilitates the detection of low-abundance populations in environmental DNA surveys of complex microbial communities. At the same time, deep sequencing can lead to overestimates of microbial diversity through the generation of low-frequency, error-prone reads. Even with sequencing error rates below 0.005 per nucleotide position, the common method of generating operational taxonomic units (OTUs) by multiple sequence alignment and complete-linkage clustering significantly increases the number of predicted OTUs and inflates richness estimates. We show that a 2% single-linkage preclustering methodology followed by an average-linkage clustering based on pairwise alignments more accurately predicts expected OTUs in both single and pooled template preparations of known taxonomic composition. This new clustering method can reduce the OTU richness in environmental samples by as much as 30–60% but does not reduce the fraction of OTUs in long-tailed rank abundance curves that defines the rare biosphere.
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影响因子：
12.3
作者：
Huse SM;Huber JA;Morrison HG;Sogin ML;Welch DM
通讯作者：
Welch DM
影响因子：
48
作者：
Quince, Christopher;Lanzen, Anders;Sloan, William T.
通讯作者：
Sloan, William T.
影响因子：
4.4
作者：
Schloss, Patrick D.;Westcott, Sarah L.;Weber, Carolyn F.
通讯作者：
Weber, Carolyn F.
影响因子：
56.9
作者：
Huber, Julie A.;Mark Welch, David;Sogin, Mitchell L.
通讯作者：
Sogin, Mitchell L.
影响因子：
5.1
作者：
Gilbert, Jack A.;Field, Dawn;Joint, Ian
通讯作者：
Joint, Ian