Amplification by PCR artificially reduces the proportion of the rare biosphere in microbial communities.
Amplification by PCR artificially reduces the proportion of the rare biosphere in microbial communities.
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DOI：
10.1371/journal.pone.0029973
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发表时间：
2012
期刊：
影响因子：
3.7
通讯作者：
Mira A
中科院分区：
文献类型：
--
作者：
Gonzalez JM;Portillo MC;Belda-Ferre P;Mira A
微生物世界已被证明具有难以想象的多样性。使用 rRNA 基因和 PCR 扩增来评估微生物群落结构和多样性存在偏差，需要进行分析，以便了解这些估计中涉及的风险。在此，我们表明群落内特定序列目标的 PCR 扩增取决于这些序列占总 DNA 模板的比例。使用定量、实时、多重 PCR 和特定的 Taqman 探针，监测了实验室群落内四种细菌物种的 16S rRNA 基因的扩增。结果表明，每个细菌物种的相对扩增效率是每个类群在群落或多物种 DNA 模板中所代表的分数的非线性函数。因此，在基于 PCR 的调查中，群落中比例较低的类群代表性不足，可能需要处理大量序列才能检测“稀有生物圈”内的一些细菌类群。基于 PCR 的调查得出的微生物群落结构明显偏向于低丰度类群，而低丰度类群是破译自然界微生物多样性完整范围所必需的。
The microbial world has been shown to hold an unimaginable diversity. The use of rRNA genes and PCR amplification to assess microbial community structure and diversity present biases that need to be analyzed in order to understand the risks involved in those estimates. Herein, we show that PCR amplification of specific sequence targets within a community depends on the fractions that those sequences represent to the total DNA template. Using quantitative, real-time, multiplex PCR and specific Taqman probes, the amplification of 16S rRNA genes from four bacterial species within a laboratory community were monitored. Results indicate that the relative amplification efficiency for each bacterial species is a nonlinear function of the fraction that each of those taxa represent within a community or multispecies DNA template. Consequently, the low-proportion taxa in a community are under-represented during PCR-based surveys and a large number of sequences might need to be processed to detect some of the bacterial taxa within the ‘rare biosphere’. The structure of microbial communities from PCR-based surveys is clearly biased against low abundant taxa which are required to decipher the complete extent of microbial diversity in nature.
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影响因子：
5.1
作者：
Gonzalez, JM;Portillo, MC;Saiz-Jimenez, C
通讯作者：
Saiz-Jimenez, C
影响因子：
2.9
作者：
Arezi, B;Xing, WM;Hogrefe, HH
通讯作者：
Hogrefe, HH
影响因子：
4.4
作者：
Ashelford, KE;Chuzhanova, NA;Weightman, AJ
通讯作者：
Weightman, AJ
影响因子：
4.4
作者：
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通讯作者：
Holben, William E.
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影响因子：
6.7
作者：
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通讯作者：
Bushman FD