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Development of a time-series shotgun metagenomics database for monitoring microbial communities at the Pacific coast of Japan
Although 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. More...
Autores principales: | , , , , , , , , , , , , , , , , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Nature Publishing Group UK
2021
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8190148/ https://www.ncbi.nlm.nih.gov/pubmed/34108585 http://dx.doi.org/10.1038/s41598-021-91615-3 |
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author | Yoshitake, Kazutoshi Kimura, Gaku Sakami, Tomoko Watanabe, Tsuyoshi Taniuchi, Yukiko Kakehi, Shigeho Kuwata, Akira Yamaguchi, Haruyo Kataoka, Takafumi Kawachi, Masanobu Ikeo, Kazuho Tan, Engkong Igarashi, Yoji Ohtsubo, Masafumi Watabe, Shugo Suzuki, Yutaka Asakawa, Shuichi Ishino, Sonoko Tashiro, Kosuke Ishino, Yoshizumi Kobayashi, Takanori Mineta, Katsuhiko Gojobori, Takashi |
author_facet | Yoshitake, Kazutoshi Kimura, Gaku Sakami, Tomoko Watanabe, Tsuyoshi Taniuchi, Yukiko Kakehi, Shigeho Kuwata, Akira Yamaguchi, Haruyo Kataoka, Takafumi Kawachi, Masanobu Ikeo, Kazuho Tan, Engkong Igarashi, Yoji Ohtsubo, Masafumi Watabe, Shugo Suzuki, Yutaka Asakawa, Shuichi Ishino, Sonoko Tashiro, Kosuke Ishino, Yoshizumi Kobayashi, Takanori Mineta, Katsuhiko Gojobori, Takashi |
author_sort | Yoshitake, Kazutoshi |
collection | PubMed |
description | Although 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. |
format | Online Article Text |
id | pubmed-8190148 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2021 |
publisher | Nature Publishing Group UK |
record_format | MEDLINE/PubMed |
spelling | pubmed-81901482021-06-10 Development of a time-series shotgun metagenomics database for monitoring microbial communities at the Pacific coast of Japan Yoshitake, Kazutoshi Kimura, Gaku Sakami, Tomoko Watanabe, Tsuyoshi Taniuchi, Yukiko Kakehi, Shigeho Kuwata, Akira Yamaguchi, Haruyo Kataoka, Takafumi Kawachi, Masanobu Ikeo, Kazuho Tan, Engkong Igarashi, Yoji Ohtsubo, Masafumi Watabe, Shugo Suzuki, Yutaka Asakawa, Shuichi Ishino, Sonoko Tashiro, Kosuke Ishino, Yoshizumi Kobayashi, Takanori Mineta, Katsuhiko Gojobori, Takashi Sci Rep Article Although 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. Nature Publishing Group UK 2021-06-09 /pmc/articles/PMC8190148/ /pubmed/34108585 http://dx.doi.org/10.1038/s41598-021-91615-3 Text en © The Author(s) 2021 https://creativecommons.org/licenses/by/4.0/Open Access 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. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/ (https://creativecommons.org/licenses/by/4.0/) . |
spellingShingle | Article Yoshitake, Kazutoshi Kimura, Gaku Sakami, Tomoko Watanabe, Tsuyoshi Taniuchi, Yukiko Kakehi, Shigeho Kuwata, Akira Yamaguchi, Haruyo Kataoka, Takafumi Kawachi, Masanobu Ikeo, Kazuho Tan, Engkong Igarashi, Yoji Ohtsubo, Masafumi Watabe, Shugo Suzuki, Yutaka Asakawa, Shuichi Ishino, Sonoko Tashiro, Kosuke Ishino, Yoshizumi Kobayashi, Takanori Mineta, Katsuhiko Gojobori, Takashi Development of a time-series shotgun metagenomics database for monitoring microbial communities at the Pacific coast of Japan |
title | Development of a time-series shotgun metagenomics database for monitoring microbial communities at the Pacific coast of Japan |
title_full | Development of a time-series shotgun metagenomics database for monitoring microbial communities at the Pacific coast of Japan |
title_fullStr | Development of a time-series shotgun metagenomics database for monitoring microbial communities at the Pacific coast of Japan |
title_full_unstemmed | Development of a time-series shotgun metagenomics database for monitoring microbial communities at the Pacific coast of Japan |
title_short | Development of a time-series shotgun metagenomics database for monitoring microbial communities at the Pacific coast of Japan |
title_sort | development of a time-series shotgun metagenomics database for monitoring microbial communities at the pacific coast of japan |
topic | Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8190148/ https://www.ncbi.nlm.nih.gov/pubmed/34108585 http://dx.doi.org/10.1038/s41598-021-91615-3 |
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