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dc.contributor.authorYoshitake, Kazutoshi
dc.contributor.authorKimura, Gaku
dc.contributor.authorSakami, Tomoko
dc.contributor.authorWatanabe, Tsuyoshi
dc.contributor.authorTaniuchi, Yukiko
dc.contributor.authorKakehi, Shigeho
dc.contributor.authorKuwata, Akira
dc.contributor.authorYamaguchi, Haruyo
dc.contributor.authorKataoka, Takafumi
dc.contributor.authorKawachi, Masanobu
dc.contributor.authorIkeo, Kazuho
dc.contributor.authorTan, Engkong
dc.contributor.authorIgarashi, Yoji
dc.contributor.authorOhtsubo, Masafumi
dc.contributor.authorWatabe, Shugo
dc.contributor.authorSuzuki, Yutaka
dc.contributor.authorAsakawa, Shuichi
dc.contributor.authorIshino, Sonoko
dc.contributor.authorTashiro, Kosuke
dc.contributor.authorIshino, Yoshizumi
dc.contributor.authorKobayashi, Takanori
dc.contributor.authorMineta, Katsuhiko
dc.contributor.authorGojobori, Takashi
dc.date.accessioned2021-06-14T13:06:14Z
dc.date.available2021-06-14T13:06:14Z
dc.date.issued2021-06-09
dc.date.submitted2020-08-14
dc.identifier.citationYoshitake, K., Kimura, G., Sakami, T., Watanabe, T., Taniuchi, Y., Kakehi, S., … Gojobori, T. (2021). Development of a time-series shotgun metagenomics database for monitoring microbial communities at the Pacific coast of Japan. Scientific Reports, 11(1). doi:10.1038/s41598-021-91615-3
dc.identifier.issn2045-2322
dc.identifier.pmid34108585
dc.identifier.doi10.1038/s41598-021-91615-3
dc.identifier.urihttp://hdl.handle.net/10754/669576
dc.description.abstractAbstractAlthough numerous metagenome, amplicon sequencing-based studies have been conducted to date to characterize marine microbial communities, relatively few have employed full metagenome shotgun sequencing to obtain a broader picture of the functional features of these marine microbial communities. Moreover, most of these studies only performed sporadic sampling, which is insufficient to understand an ecosystem comprehensively. In this study, we regularly conducted seawater sampling along the northeastern Pacific coast of Japan between March 2012 and May 2016. We collected 213 seawater samples and prepared size-based fractions to generate 454 subsets of samples for shotgun metagenome sequencing and analysis. We also determined the sequences of 16S rRNA (n = 111) and 18S rRNA (n = 47) gene amplicons from smaller sample subsets. We thereafter developed the Ocean Monitoring Database for time-series metagenomic data (http://marine-meta.healthscience.sci.waseda.ac.jp/omd/), which provides a three-dimensional bird’s-eye view of the data. This database includes results of digital DNA chip analysis, a novel method for estimating ocean characteristics such as water temperature from metagenomic data. Furthermore, we developed a novel classification method that includes more information about viruses than that acquired using BLAST. We further report the discovery of a large number of previously overlooked (TAG)n repeat sequences in the genomes of marine microbes. We predict that the availability of this time-series database will lead to major discoveries in marine microbiome research.
dc.description.sponsorshipThis work was supported by CREST, the Japanese Science and Technology Agency. Computations were partially performed using the NIG supercomputer at ROIS National Institute of Genetics as well as the computational resources at Computational Bioscience Research Center, King Abdullah University of Science and Technology.
dc.publisherSpringer Science and Business Media LLC
dc.relation.urlhttp://www.nature.com/articles/s41598-021-91615-3
dc.rightsThis article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder.
dc.rights.urihttps://creativecommons.org/licenses/by/4.0
dc.titleDevelopment of a time-series shotgun metagenomics database for monitoring microbial communities at the Pacific coast of Japan
dc.typeArticle
dc.contributor.departmentComputational Bioscience Research Center (CBRC)
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.identifier.journalScientific Reports
dc.eprint.versionPublisher's Version/PDF
dc.identifier.volume11
dc.identifier.issue1
kaust.personMineta, Katsuhiko
kaust.personGojobori, Takashi
dc.date.accepted2021-05-27
refterms.dateFOA2021-06-14T13:07:27Z


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This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder.
Except where otherwise noted, this item's license is described as This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder.