The rational exploration of microbial diversity
The rational exploration of microbial diversity
复制标题
DOI：
10.1038/ismej.2008.69
复制
发表时间：
2008-10-01
期刊：
影响因子：
11
通讯作者：
Sloan, William T.
中科院分区：
文献类型：
--
作者：
Quince, Christopher;Curtis, Thomas P.;Sloan, William T.
对微生物世界的探索是一系列令人兴奋的意外发现，尽管我们对所面临的任务的大小基本上没有进行合理的估计。然而，从长远来看，可以通过估计微生物群落的多样性和描述它们所需的努力来实现更结构化的调查。在非常大的样本中发现新的微生物类群的速度表明，在土壤和海洋中仍有更多的类群有待发现。我们应用一个强大的统计方法，从这些环境中的大型基因序列库，以估计多样性和测序的努力，以获得一个给定的分数的多样性。在上层海洋，我们预测大约有1400个基因组类型，而鸟枪读数的仅仅五倍增加就可以产生90%的宏基因组，也就是说，所有分类群的所有基因。然而，在深海，热液喷口和土壤中的生物多样性可能要大两个数量级，仅根据16S rDNA中3%的差异获得90%的分类多样性就需要数百倍于目前数量的样本。获得90%的宏基因组将需要数万倍于目前的测序工作。尽管对高度多样性的环境进行明确的测序尚不可能，但我们可以利用类群丰度分布，开始规划和开发所需的方法和策略。这将开启探索微生物世界的新阶段。
The exploration of the microbial world has been an exciting series of unanticipated discoveries despite being largely uninformed by rational estimates of the magnitude of task confronting us. However, in the long term, more structured surveys can be achieved by estimating the diversity of microbial communities and the effort required to describe them. The rates of recovery of new microbial taxa in very large samples suggest that many more taxa remain to be discovered in soils and the oceans. We apply a robust statistical method to large gene sequence libraries from these environments to estimate both diversity and the sequencing effort required to obtain a given fraction of that diversity. In the upper ocean, we predict some 1400 phylotypes, and a mere fivefold increase in shotgun reads could yield 90% of the metagenome, that is, all genes from all taxa. However, at deep ocean, hydrothermal vents and diversities in soils can be up to two orders of magnitude larger, and hundreds of times the current number of samples will be required just to obtain 90% of the taxonomic diversity based on 3% difference in 16S rDNA. Obtaining 90% of the metagenome will require tens of thousands of times the current sequencing effort. Although the definitive sequencing of hyperdiverse environments is not yet possible, we can, using taxa-abundance distributions, begin to plan and develop the required methods and strategies. This would initiate a new phase in the exploration of the microbial world.