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    Metagenomic Methods: From Seawater to the Database

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    Type
    Book Chapter
    Authors
    Reza, Md. Shaheed
    Kobiyama, Atsushi
    Rashid, Jonaira
    Yamada, Yuichiro
    Ikeda, Yuri
    Ikeda, Daisuke
    Mizusawa, Nanami
    Yanagisawa, Saki
    Ikeo, Kazuho
    Sato, Shigeru
    Ogata, Takehiko
    Kudo, Toshiaki
    Kaga, Shinnosuke
    Watanabe, Shiho
    Naiki, Kimiaki
    Kaga, Yoshimasa
    Segawa, Satoshi
    Mineta, Katsuhiko cc
    Bajic, Vladimir B. cc
    Gojobori, Takashi cc
    Watabe, Shugo
    KAUST Department
    Computational Bioscience Research Center (CBRC)
    Applied Mathematics and Computational Science Program
    Computer, Electrical and Mathematical Sciences and Engineering (CEMSE) Division
    Bioscience Program
    Biological and Environmental Sciences and Engineering (BESE) Division
    Date
    2019-07-25
    Online Publication Date
    2019-07-25
    Print Publication Date
    2019
    Embargo End Date
    2020-07-25
    Permanent link to this record
    http://hdl.handle.net/10754/656341
    
    Metadata
    Show full item record
    Abstract
    In this article, methods or techniques of metagenomics including targeted 16S/18S rRNA analyses and shotgun sequencing will be discussed. It is sometimes difficult, especially for beginners, to follow the manufacturer’s recommendation as mentioned in the protocol and to go through different steps from the preparation of starting material (e.g., DNA), library preparation, and so on. We will try to explain all the steps in detail and share our experience here. It all starts with collection of samples and collection of ecological/environmental metadata followed by sample fractionation (optional), extraction of DNA, sequencing, and finally data analyses to interpret results. Sample collection has always been the most important part of a study as it requires proper planning, a good workforce to execute, permission(s) of sampling from appropriate authority, and precaution(s) about endangered species during sampling. Here, we first describe methodology for a shallow river and in the later section methodology for a deep marine bay. In either case, slight modifications can be made to succeed in sampling. Determination of physicochemical parameters as metadata simultaneously is also an important task. These samples are then processed to extract DNA which needs to be representative of all cells present in the sample. Finally, sequencing is done by a next-generation sequencer, and data analyses are completed. Through these methods, scientists are now able to overcome the unculturability problem of more than 99% of environmental microorganisms and uncovered functional gene diversity of environmental microorganisms.
    Citation
    Reza, M. S., Kobiyama, A., Rashid, J., Yamada, Y., Ikeda, Y., Ikeda, D., … Watabe, S. (2019). Metagenomic Methods: From Seawater to the Database. Marine Metagenomics, 3–16. doi:10.1007/978-981-13-8134-8_1
    Publisher
    Springer Nature
    DOI
    10.1007/978-981-13-8134-8_1
    Additional Links
    http://link.springer.com/10.1007/978-981-13-8134-8_1
    ae974a485f413a2113503eed53cd6c53
    10.1007/978-981-13-8134-8_1
    Scopus Count
    Collections
    Biological and Environmental Science and Engineering (BESE) Division; Bioscience Program; Applied Mathematics and Computational Science Program; Computational Bioscience Research Center (CBRC); Book Chapters; Computer, Electrical and Mathematical Science and Engineering (CEMSE) Division

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