Type
Book ChapterAuthors
Reza, Md. ShaheedKobiyama, 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

Bajic, Vladimir B.

Gojobori, Takashi

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
2019-07-25Online Publication Date
2019-07-25Print Publication Date
2019Embargo End Date
2020-07-25Permanent link to this record
http://hdl.handle.net/10754/656341
Metadata
Show full item recordAbstract
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_1Publisher
Springer NatureAdditional Links
http://link.springer.com/10.1007/978-981-13-8134-8_1ae974a485f413a2113503eed53cd6c53
10.1007/978-981-13-8134-8_1