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dc.contributor.authorReza, Md. Shaheed
dc.contributor.authorKobiyama, Atsushi
dc.contributor.authorRashid, Jonaira
dc.contributor.authorYamada, Yuichiro
dc.contributor.authorIkeda, Yuri
dc.contributor.authorIkeda, Daisuke
dc.contributor.authorMizusawa, Nanami
dc.contributor.authorYanagisawa, Saki
dc.contributor.authorIkeo, Kazuho
dc.contributor.authorSato, Shigeru
dc.contributor.authorOgata, Takehiko
dc.contributor.authorKudo, Toshiaki
dc.contributor.authorKaga, Shinnosuke
dc.contributor.authorWatanabe, Shiho
dc.contributor.authorNaiki, Kimiaki
dc.contributor.authorKaga, Yoshimasa
dc.contributor.authorSegawa, Satoshi
dc.contributor.authorMineta, Katsuhiko
dc.contributor.authorBajic, Vladimir B.
dc.contributor.authorGojobori, Takashi
dc.contributor.authorWatabe, Shugo
dc.date.accessioned2019-08-05T07:36:08Z
dc.date.available2019-08-05T07:36:08Z
dc.date.issued2019-07-25
dc.identifier.citationReza, 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
dc.identifier.doi10.1007/978-981-13-8134-8_1
dc.identifier.urihttp://hdl.handle.net/10754/656341
dc.description.abstractIn 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.
dc.publisherSpringer Nature
dc.relation.urlhttp://link.springer.com/10.1007/978-981-13-8134-8_1
dc.rightsArchived with thanks to Marine Metagenomics
dc.subjectFree-living microorganisms
dc.subjectParticle-associated microorganisms
dc.subjectShotgun metagenomics
dc.subjectSize fractionation
dc.subjectTargeted metagenomics
dc.titleMetagenomic Methods: From Seawater to the Database
dc.typeBook Chapter
dc.contributor.departmentComputational Bioscience Research Center (CBRC)
dc.contributor.departmentApplied Mathematics and Computational Science Program
dc.contributor.departmentComputer, Electrical and Mathematical Sciences and Engineering (CEMSE) Division
dc.contributor.departmentBioscience Program
dc.contributor.departmentBiological and Environmental Sciences and Engineering (BESE) Division
dc.rights.embargodate2020-07-25
dc.eprint.versionPost-print
dc.contributor.institutionKitasato University School of Marine Biosciences, Sagamihara, Japan
dc.contributor.institutionDepartment of Fisheries Technology, Bangladesh Agricultural University, Mymensingh, Bangladesh
dc.contributor.institutionNational Institute of Genetics, Shizuoka, Japan
dc.contributor.institutionIwate Fisheries Technology Center, Iwate, Japan
dc.contributor.institutionOfunato Fisheries Promotion Center, Iwate Prefectural Government, Iwate, Japan
kaust.personMineta, Katsuhiko
kaust.personBajic, Vladimir B.
kaust.personGojobori, Takashi
dc.date.published-online2019-07-25
dc.date.published-print2019


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