Global patterns of 16S rRNA diversity at a depth of millions of sequences per sample
Global patterns of 16S rRNA diversity at a depth of millions of sequences per sample
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DOI：
10.1073/pnas.1000080107
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发表时间：
2011-03-15
影响因子：
11.1
通讯作者：
Knight, Rob
中科院分区：
文献类型：
--
作者：
Caporaso, J. Gregory;Lauber, Christian L.;Knight, Rob
正在进行的高通量测序革命继续使小规模研究人员绘制生物圈微生物组成图的能力民主化。特别是，新的测序平台和新的软件工具的共同进化允许以前所未有的规模进行数据采集和分析。在这里，我们报告了这场共同进化军备竞赛的下一阶段，使用Illumina GAIIx平台对25个环境样本和三个已知的“模拟社区”进行测序，每个样本平均有310万个读数。我们表现出良好的一致性，在分类恢复和夺回多样性模式，以前报道的基础上荟萃分析的许多研究文献（特别是，盐水/非盐水分裂环境样品和主机相关和自由生活的社区之间的分裂）。我们还证明，2，000个Illumina单端读数足以重新捕获我们在完整数据集中观察到的样本之间的相同关系。因此，这些结果开辟了进行大规模研究的可能性，同时分析数千个样本，以前所未有的空间和时间分辨率调查微生物群落。
The ongoing revolution in high-throughput sequencing continues to democratize the ability of small groups of investigators to map the microbial component of the biosphere. In particular, the coevolution of new sequencing platforms and new software tools allows data acquisition and analysis on an unprecedented scale. Here we report the next stage in this coevolutionary arms race, using the Illumina GAIIx platform to sequence a diverse array of 25 environmental samples and three known "mock communities" at a depth averaging 3.1 million reads per sample. We demonstrate excellent consistency in taxonomic recovery and recapture diversity patterns that were previously reported on the basis of meta-analysis of many studies from the literature (notably, the saline/nonsaline split in environmental samples and the split between host-associated and free-living communities). We also demonstrate that 2,000 Illumina single-end reads are sufficient to recapture the same relationships among samples that we observe with the full dataset. The results thus open up the possibility of conducting large-scale studies analyzing thousands of samples simultaneously to survey microbial communities at an unprecedented spatial and temporal resolution.