Choice of bacterial DNA extraction method from fecal material influences community structure as evaluated by metagenomic analysis.
Choice of bacterial DNA extraction method from fecal material influences community structure as evaluated by metagenomic analysis.
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DOI：
10.1186/2049-2618-2-19
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发表时间：
2014
期刊：
影响因子：
15.5
通讯作者：
Licht TR
中科院分区：
文献类型：
--
作者：
Wesolowska-Andersen A;Bahl MI;Carvalho V;Kristiansen K;Sicheritz-Pontén T;Gupta R;Licht TR
近年来，对人体肠道菌群的研究引起了极大的关注。下一代测序技术在细菌基因组学和功能定位中的应用为这一研究领域打开了新的大门。然而，很少有人注意到方法的选择对这些研究结果的影响。在这项研究中，我们对欧洲MetaHIT和美国人类微生物组计划（HMP）这两个主要合作项目所使用的DNA提取方法进行了系统比较。此外，还讨论了浸提前样品浸泡的影响。我们观察到细菌类群的分布取决于方法的显着差异。虽然真核生物DNA是最有效地提取MetaHIT协议，DNA从拟杆菌门内的细菌是最有效地提取HMP协议。虽然令人欣慰的是，个体间的差异明显超过了提取方法选择所导致的差异，但我们的数据突出了比较采用不同方法的研究数据的挑战。
In recent years, studies on the human intestinal microbiota have attracted tremendous attention. Application of next generation sequencing for mapping of bacterial phylogeny and function has opened new doors to this field of research. However, little attention has been given to the effects of choice of methodology on the output resulting from such studies. In this study we conducted a systematic comparison of the DNA extraction methods used by the two major collaborative efforts: The European MetaHIT and the American Human Microbiome Project (HMP). Additionally, effects of homogenizing the samples before extraction were addressed. We observed significant differences in distribution of bacterial taxa depending on the method. While eukaryotic DNA was most efficiently extracted by the MetaHIT protocol, DNA from bacteria within the Bacteroidetes phylum was most efficiently extracted by the HMP protocol. Whereas it is comforting that the inter-individual variation clearly exceeded the variation resulting from choice of extraction method, our data highlight the challenge of comparing data across studies applying different methodologies.
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影响因子：
64.8
作者：
通讯作者：
--
DOI：
10.1093/bioinformatics/bts565
发表时间：
2012-12-01
期刊：
Bioinformatics (Oxford, England)
影响因子：
--
作者：
Fu L;Niu B;Zhu Z;Wu S;Li W
通讯作者：
Li W
影响因子：
64.8
作者：
Arumugam, Manimozhiyan;Raes, Jeroen;Pelletier, Eric;Le Paslier, Denis;Yamada, Takuji;Mende, Daniel R.;Fernandes, Gabriel R.;Tap, Julien;Bruls, Thomas;Batto, Jean-Michel;Bertalan, Marcelo;Borruel, Natalia;Casellas, Francesc;Fernandez, Leyden;Gautier, Laurent;Hansen, Torben;Hattori, Masahira;Hayashi, Tetsuya;Kleerebezem, Michiel;Kurokawa, Ken;Leclerc, Marion;Levenez, Florence;Manichanh, Chaysavanh;Nielsen, H. Bjorn;Nielsen, Trine;Pons, Nicolas;Poulain, Julie;Qin, Junjie;Sicheritz-Ponten, Thomas;Tims, Sebastian;Torrents, David;Ugarte, Edgardo;Zoetendal, Erwin G.;Wang, Jun;Guarner, Francisco;Pedersen, Oluf;de Vos, Willem M.;Brunak, Soren;Dore, Joel;Weissenbach, Jean;Ehrlich, S. Dusko;Bork, Peer
通讯作者：
Bork, Peer
影响因子：
4.4
作者：
Zoetendal, EG;von Wright, A;de Vos, WM
通讯作者：
de Vos, WM
影响因子：
46.9
作者：
Loman, Nicholas J.;Misra, Raju V.;Pallen, Mark J.
通讯作者：
Pallen, Mark J.