Strengths and limitations of 16S rRNA gene amplicon sequencing in revealing temporal microbial community dynamics.
Strengths and limitations of 16S rRNA gene amplicon sequencing in revealing temporal microbial community dynamics.
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16S rRNA基因扩增子测序的优势和局限性在揭示时间微生物群落动力学中。
DOI：
10.1371/journal.pone.0093827
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发表时间：
2014
期刊：
影响因子：
3.7
通讯作者：
Konstantinidis KT
中科院分区：
文献类型：
--
作者：
Poretsky R;Rodriguez-R LM;Luo C;Tsementzi D;Konstantinidis KT
本研究探讨了拉尼尔湖（GA，美国）的短期浮游微生物群落结构和恢复力，同时评估了通过16 S rRNA基因扩增子和宏基因组序列数据识别分类群的技术方面。用454个GS-FLX-Ti对从四个时间上离散的样品产生的16 S rRNA基因扩增子进行测序，从每个样品产生约40，000个rRNA基因序列，并代表约300个观察到的OTU。从相同生物样品获得的重复样品聚集在一起，但观察到与PCR或测序制备步骤相关的几种偏倚。与配套的全群落鸟枪宏基因组数据集相比，每个时间点的OTU估计数量是一致的，但在宏基因组中分别鉴定出1.5倍和1.10倍的门和属。我们的分析表明，16 S rRNA基因捕获了随着时间的推移社区多样性的广泛变化，但与宏基因组数据相比，分辨率有限，灵敏度较低。我们还鉴定了在由扰动分开的四个接近时间点上显示丰度显著变化的OTU，并在宏基因组与16 S rRNA扩增子数据中追踪这些分类群。一个强大的夏季风暴对群落组成的影响小于季节性混合，这揭示了一个独特的生物演替。这项研究提供了深入了解淡水微生物群落和先进的方法来评估社区的多样性和动态原位。
This study explored the short-term planktonic microbial community structure and resilience in Lake Lanier (GA, USA) while simultaneously evaluating the technical aspects of identifying taxa via 16S rRNA gene amplicon and metagenomic sequence data. 16S rRNA gene amplicons generated from four temporally discrete samples were sequenced with 454 GS-FLX-Ti yielding ∼40,000 rRNA gene sequences from each sample and representing ∼300 observed OTUs. Replicates obtained from the same biological sample clustered together but several biases were observed, linked to either the PCR or sequencing-preparation steps. In comparisons with companion whole-community shotgun metagenome datasets, the estimated number of OTUs at each timepoint was concordant, but 1.5 times and ∼10 times as many phyla and genera, respectively, were identified in the metagenomes. Our analyses showed that the 16S rRNA gene captures broad shifts in community diversity over time, but with limited resolution and lower sensitivity compared to metagenomic data. We also identified OTUs that showed marked shifts in abundance over four close timepoints separated by perturbations and tracked these taxa in the metagenome vs. 16S rRNA amplicon data. A strong summer storm had less of an effect on community composition than did seasonal mixing, which revealed a distinct succession of organisms. This study provides insights into freshwater microbial communities and advances the approaches for assessing community diversity and dynamics in situ.
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影响因子：
14.9
作者：
Klindworth A;Pruesse E;Schweer T;Peplies J;Quast C;Horn M;Glöckner FO
通讯作者：
Glöckner FO
影响因子：
3.7
作者：
Gilbert JA;Field D;Swift P;Thomas S;Cummings D;Temperton B;Weynberg K;Huse S;Hughes M;Joint I;Somerfield PJ;Mühling M
通讯作者：
Mühling M
DOI：
10.1038/ismej.2012.8
发表时间：
2012-08
期刊：
The ISME journal
影响因子：
--
作者：
通讯作者：
--
DOI：
10.1098/rstb.2006.1920
发表时间：
2006-11-29
影响因子：
6.3
作者：
Konstantinidis, Konstantinos T.;Ramette, Alban;Tiedje, James M.
通讯作者：
Tiedje, James M.
影响因子：
7
作者：
Li, Ruiqiang;Zhu, Hongmei;Wang, Jun
通讯作者：
Wang, Jun