Metagenomic Methods: From Seawater to the Database

Md. Shaheed Reza, Atsushi Kobiyama, Jonaira Rashid, Yuichiro Yamada, Yuri Ikeda, Daisuke Ikeda, Nanami Mizusawa, Saki Yanagisawa, Kazuho Ikeo, Shigeru Sato, Takehiko Ogata, Toshiaki Kudo, Shinnosuke Kaga, Shiho Watanabe, Kimiaki Naiki, Yoshimasa Kaga, Satoshi Segawa, Katsuhiko Mineta, Vladimir B. Bajic, Takashi GojoboriShugo Watabe

Research output: Chapter in Book/Report/Conference proceedingChapter

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.
Original languageEnglish (US)
Title of host publicationMarine Metagenomics
PublisherSpringer Singapore
Pages3-16
Number of pages14
ISBN (Print)9789811381331
DOIs
StatePublished - Jul 25 2019

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