Estimating bacterial diversity for ecological studies: methods, metrics, and assumptions.
Estimating bacterial diversity for ecological studies: methods, metrics, and assumptions.
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DOI：
10.1371/journal.pone.0125356
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发表时间：
2015
期刊：
影响因子：
3.7
通讯作者：
Matthews B
中科院分区：
文献类型：
--
作者：
Birtel J;Walser JC;Pichon S;Bürgmann H;Matthews B
为了了解自然环境中微生物的分布和多样性，估计微生物多样性的方法已经迅速发展。对于细菌群落，16S rRNA 基因是首选的系统发育标记基因，但大多数研究仅选择 16S rRNA 的特定区域来估计细菌多样性。尽管源自 DNA 提取、引物选择和 PCR 扩增的偏差已得到充分记录，但我们在这里讨论可变区的选择如何影响广泛的标准生态指标，例如物种丰富度、系统发育多样性、β 多样性和等级丰度分布。我们使用 Illumina 双端测序来估计瑞士 20 个天然湖泊的细菌多样性，这些湖泊源自三个修剪过的可变 16S rRNA 区域（V3、V4、V5）。 16S rRNA 区域之间的物种丰富度、系统发育多样性、群落组成、β 多样性和等级丰度分布存在显着差异。总体而言，V3 和 V5 区域量化的多样性模式比 V4 区域评估的多样性模式更相似。当分析序列聚类过程中使用的不同序列相似性阈值的数据集以及对来自 Greengenes 数据库的序列参考数据集使用相同的分析时，获得了类似的结果。此外，我们还使用 ARISA 指纹图谱测量了同一湖泊样本的物种丰富度，但没有发现 Illumina 和 ARISA 估计的物种丰富度之间存在很强的关系。我们的结论是，16S rRNA 区域的选择显着影响细菌多样性和物种分布的估计，并且在比较不同可变区域的数据以及使用不同测序技术时需要谨慎。
Methods to estimate microbial diversity have developed rapidly in an effort to understand the distribution and diversity of microorganisms in natural environments. For bacterial communities, the 16S rRNA gene is the phylogenetic marker gene of choice, but most studies select only a specific region of the 16S rRNA to estimate bacterial diversity. Whereas biases derived from from DNA extraction, primer choice and PCR amplification are well documented, we here address how the choice of variable region can influence a wide range of standard ecological metrics, such as species richness, phylogenetic diversity, β-diversity and rank-abundance distributions. We have used Illumina paired-end sequencing to estimate the bacterial diversity of 20 natural lakes across Switzerland derived from three trimmed variable 16S rRNA regions (V3, V4, V5). Species richness, phylogenetic diversity, community composition, β-diversity, and rank-abundance distributions differed significantly between 16S rRNA regions. Overall, patterns of diversity quantified by the V3 and V5 regions were more similar to one another than those assessed by the V4 region. Similar results were obtained when analyzing the datasets with different sequence similarity thresholds used during sequences clustering and when the same analysis was used on a reference dataset of sequences from the Greengenes database. In addition we also measured species richness from the same lake samples using ARISA Fingerprinting, but did not find a strong relationship between species richness estimated by Illumina and ARISA. We conclude that the selection of 16S rRNA region significantly influences the estimation of bacterial diversity and species distributions and that caution is warranted when comparing data from different variable regions as well as when using different sequencing techniques.
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影响因子：
5.9
作者：
FAITH, DP
通讯作者：
FAITH, DP
DOI：
10.1073/pnas.1101591108
发表时间：
2011-08-23
影响因子：
11.1
作者：
Burke, Catherine;Steinberg, Peter;Thomas, Torsten
通讯作者：
Thomas, Torsten
影响因子：
11
作者：
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通讯作者：
Matthews, Blake
DOI：
10.1073/pnas.0805962105
发表时间：
2008-11-04
影响因子：
11.1
作者：
Cadotte, Marc W.;Cardinale, Bradley J.;Oakley, Todd H.
通讯作者：
Oakley, Todd H.
影响因子：
8.8
作者：
Anderson, Marti J.;Crist, Thomas O.;Swenson, Nathan G.
通讯作者：
Swenson, Nathan G.