著者
Miho Hirai Shinro Nishi Miwako Tsuda Michinari Sunamura Yoshihiro Takaki Takuro Nunoura
出版者
Japanese Society of Microbial Ecology / Japanese Society of Soil Microbiology / Taiwan Society of Microbial Ecology / Japanese Society of Plant Microbe Interactions / Japanese Society for Extremophiles
雑誌
Microbes and Environments (ISSN:13426311)
巻号頁・発行日
vol.32, no.4, pp.336-343, 2017 (Released:2017-12-27)
参考文献数
34
被引用文献数
3 11

Shotgun metagenomics is a low biased technology for assessing environmental microbial diversity and function. However, the requirement for a sufficient amount of DNA and the contamination of inhibitors in environmental DNA leads to difficulties in constructing a shotgun metagenomic library. We herein examined metagenomic library construction from subnanogram amounts of input environmental DNA from subarctic surface water and deep-sea sediments using two library construction kits: the KAPA Hyper Prep Kit and Nextera XT DNA Library Preparation Kit, with several modifications. The influence of chemical contaminants associated with these environmental DNA samples on library construction was also investigated. Overall, shotgun metagenomic libraries were constructed from 1 pg to 1 ng of input DNA using both kits without harsh library microbial contamination. However, the libraries constructed from 1 pg of input DNA exhibited larger biases in GC contents, k-mers, or small subunit (SSU) rRNA gene compositions than those constructed from 10 pg to 1 ng DNA. The lower limit of input DNA for low biased library construction in this study was 10 pg. Moreover, we revealed that technology-dependent biases (physical fragmentation and linker ligation vs. tagmentation) were larger than those due to the amount of input DNA.

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外部データベース (DOI)

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いよいよ、もうすぐ環境サンプルにも手を出すということで、昨日教えてもらったHirai et al. 2017(https://t.co/6cHdCDL2fV)の、 超微量環境DNAサンプルをつかったサンプル調整、シーケンスバイアスに関する論文読む
編集長の絶大な権力を持ってすれば一つの号に関係する研究者の3つの論文を掲載することも可能なのである(笑)。っていうか現実は、頑張って皆に投稿を呼びかけているだけであるが。そしてオルトメトリックス向上活動(笑)… https://t.co/Rg46wo1uKk

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