Metagenomic sequencing of an in vitro-simulated microbial community.
Metagenomic sequencing of an in vitro-simulated microbial community.
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DOI：
10.1371/journal.pone.0010209
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发表时间：
2010-04-16
期刊：
影响因子：
3.7
通讯作者：
Eisen JA
中科院分区：
文献类型：
--
作者：
Morgan JL;Darling AE;Eisen JA
微生物在地球上占主导地位，但许多物种很难甚至不可能在实验室条件下进行研究。直接从环境中对DNA进行测序，一种通常被称为宏基因组学的技术，是对微生物生命进行编目的重要工具。这种不依赖培养的方法包括收集含有微生物的样本，从样本中提取DNA，并对DNA进行测序。一个样品可能含有许多不同的微生物、大型生物，甚至是自由漂浮的环境DNA。宏基因组学的一个基本挑战是根据通过DNA测序产生的reads中观察到的生物体DNA的频率来估计样品中生物体的丰度。我们创造了十种微生物的混合物，它们的基因组序列是已知的。每种混合物含有相同数量的每种细胞。然后，我们从混合物中提取DNA，对DNA进行测序，并测量在测序DNA中观察到每种生物基因组区域的频率。我们发现，观察到的每一种生物的reads映射频率并没有反映出每种混合物中已知的细胞数量相等。相对生物体丰度变化显著取决于DNA提取和测序方案所使用的。我们描述了一种新的数据资源，用于测量宏基因组分组方法的准确性，通过体外模拟宏基因组社区创建。我们的体外模拟可以用来补充以前的硅基准研究。在构建一个合成群落并对其宏基因组进行测序的过程中，我们遇到了几个可能影响迄今为止大多数宏基因组实验的观察偏倚来源，并为比较宏基因组研究提出了挑战。DNA制备方法在我们的研究中具有特别深远的影响，这意味着不同方案制备的样品不适合用于比较宏基因组学。
Microbial life dominates the earth, but many species are difficult or even impossible to study under laboratory conditions. Sequencing DNA directly from the environment, a technique commonly referred to as metagenomics, is an important tool for cataloging microbial life. This culture-independent approach involves collecting samples that include microbes in them, extracting DNA from the samples, and sequencing the DNA. A sample may contain many different microorganisms, macroorganisms, and even free-floating environmental DNA. A fundamental challenge in metagenomics has been estimating the abundance of organisms in a sample based on the frequency with which the organism's DNA was observed in reads generated via DNA sequencing. We created mixtures of ten microbial species for which genome sequences are known. Each mixture contained an equal number of cells of each species. We then extracted DNA from the mixtures, sequenced the DNA, and measured the frequency with which genomic regions from each organism was observed in the sequenced DNA. We found that the observed frequency of reads mapping to each organism did not reflect the equal numbers of cells that were known to be included in each mixture. The relative organism abundances varied significantly depending on the DNA extraction and sequencing protocol utilized. We describe a new data resource for measuring the accuracy of metagenomic binning methods, created by in vitro-simulation of a metagenomic community. Our in vitro simulation can be used to complement previous in silico benchmark studies. In constructing a synthetic community and sequencing its metagenome, we encountered several sources of observation bias that likely affect most metagenomic experiments to date and present challenges for comparative metagenomic studies. DNA preparation methods have a particularly profound effect in our study, implying that samples prepared with different protocols are not suitable for comparative metagenomics.
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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
嗜盐古菌中受调控的多倍体。
影响因子：
3.7
作者：
Breuert S;Allers T;Spohn G;Soppa J
通讯作者：
Soppa J
DOI：
10.1073/pnas.0608309103
发表时间：
2006-11-14
影响因子：
11.1
作者：
Kugelberg, Elisabeth;Kofoid, Eric;Roth, John R.
通讯作者：
Roth, John R.
影响因子：
5
作者：
Carrigg, Cora;Rice, Olivia;O'Flaherty, Vincent
通讯作者：
O'Flaherty, Vincent
影响因子：
7
作者：
Barabote, Ravi D.;Xie, Gary;Berry, Alison M.
通讯作者：
Berry, Alison M.