Development of a time-series shotgun metagenomics database for monitoring microbial communities at the Pacific coast of Japan
Abstract 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 communit...
Guardado en:
| Autores principales: | , , , , , , , , , , , , , , , , , , , , , , |
|---|---|
| Formato: | article |
| Lenguaje: | EN |
| Publicado: |
Nature Portfolio
2021
|
| Materias: | |
| Acceso en línea: | https://doaj.org/article/156306e1f15f4c56b1f3f60e54193e47 |
| Etiquetas: |
Agregar Etiqueta
Sin Etiquetas, Sea el primero en etiquetar este registro!
|
| id |
oai:doaj.org-article:156306e1f15f4c56b1f3f60e54193e47 |
|---|---|
| record_format |
dspace |
| spelling |
oai:doaj.org-article:156306e1f15f4c56b1f3f60e54193e472021-12-02T14:58:24ZDevelopment of a time-series shotgun metagenomics database for monitoring microbial communities at the Pacific coast of Japan10.1038/s41598-021-91615-32045-2322https://doaj.org/article/156306e1f15f4c56b1f3f60e54193e472021-06-01T00:00:00Zhttps://doi.org/10.1038/s41598-021-91615-3https://doaj.org/toc/2045-2322Abstract 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.Kazutoshi YoshitakeGaku KimuraTomoko SakamiTsuyoshi WatanabeYukiko TaniuchiShigeho KakehiAkira KuwataHaruyo YamaguchiTakafumi KataokaMasanobu KawachiKazuho IkeoEngkong TanYoji IgarashiMasafumi OhtsuboShugo WatabeYutaka SuzukiShuichi AsakawaSonoko IshinoKosuke TashiroYoshizumi IshinoTakanori KobayashiKatsuhiko MinetaTakashi GojoboriNature PortfolioarticleMedicineRScienceQENScientific Reports, Vol 11, Iss 1, Pp 1-13 (2021) |
| institution |
DOAJ |
| collection |
DOAJ |
| language |
EN |
| topic |
Medicine R Science Q |
| spellingShingle |
Medicine R Science Q Kazutoshi Yoshitake Gaku Kimura Tomoko Sakami Tsuyoshi Watanabe Yukiko Taniuchi Shigeho Kakehi Akira Kuwata Haruyo Yamaguchi Takafumi Kataoka Masanobu Kawachi Kazuho Ikeo Engkong Tan Yoji Igarashi Masafumi Ohtsubo Shugo Watabe Yutaka Suzuki Shuichi Asakawa Sonoko Ishino Kosuke Tashiro Yoshizumi Ishino Takanori Kobayashi Katsuhiko Mineta Takashi Gojobori Development of a time-series shotgun metagenomics database for monitoring microbial communities at the Pacific coast of Japan |
| description |
Abstract 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 |
article |
| author |
Kazutoshi Yoshitake Gaku Kimura Tomoko Sakami Tsuyoshi Watanabe Yukiko Taniuchi Shigeho Kakehi Akira Kuwata Haruyo Yamaguchi Takafumi Kataoka Masanobu Kawachi Kazuho Ikeo Engkong Tan Yoji Igarashi Masafumi Ohtsubo Shugo Watabe Yutaka Suzuki Shuichi Asakawa Sonoko Ishino Kosuke Tashiro Yoshizumi Ishino Takanori Kobayashi Katsuhiko Mineta Takashi Gojobori |
| author_facet |
Kazutoshi Yoshitake Gaku Kimura Tomoko Sakami Tsuyoshi Watanabe Yukiko Taniuchi Shigeho Kakehi Akira Kuwata Haruyo Yamaguchi Takafumi Kataoka Masanobu Kawachi Kazuho Ikeo Engkong Tan Yoji Igarashi Masafumi Ohtsubo Shugo Watabe Yutaka Suzuki Shuichi Asakawa Sonoko Ishino Kosuke Tashiro Yoshizumi Ishino Takanori Kobayashi Katsuhiko Mineta Takashi Gojobori |
| author_sort |
Kazutoshi Yoshitake |
| title |
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_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_sort |
development of a time-series shotgun metagenomics database for monitoring microbial communities at the pacific coast of japan |
| publisher |
Nature Portfolio |
| publishDate |
2021 |
| url |
https://doaj.org/article/156306e1f15f4c56b1f3f60e54193e47 |
| work_keys_str_mv |
AT kazutoshiyoshitake developmentofatimeseriesshotgunmetagenomicsdatabaseformonitoringmicrobialcommunitiesatthepacificcoastofjapan AT gakukimura developmentofatimeseriesshotgunmetagenomicsdatabaseformonitoringmicrobialcommunitiesatthepacificcoastofjapan AT tomokosakami developmentofatimeseriesshotgunmetagenomicsdatabaseformonitoringmicrobialcommunitiesatthepacificcoastofjapan AT tsuyoshiwatanabe developmentofatimeseriesshotgunmetagenomicsdatabaseformonitoringmicrobialcommunitiesatthepacificcoastofjapan AT yukikotaniuchi developmentofatimeseriesshotgunmetagenomicsdatabaseformonitoringmicrobialcommunitiesatthepacificcoastofjapan AT shigehokakehi developmentofatimeseriesshotgunmetagenomicsdatabaseformonitoringmicrobialcommunitiesatthepacificcoastofjapan AT akirakuwata developmentofatimeseriesshotgunmetagenomicsdatabaseformonitoringmicrobialcommunitiesatthepacificcoastofjapan AT haruyoyamaguchi developmentofatimeseriesshotgunmetagenomicsdatabaseformonitoringmicrobialcommunitiesatthepacificcoastofjapan AT takafumikataoka developmentofatimeseriesshotgunmetagenomicsdatabaseformonitoringmicrobialcommunitiesatthepacificcoastofjapan AT masanobukawachi developmentofatimeseriesshotgunmetagenomicsdatabaseformonitoringmicrobialcommunitiesatthepacificcoastofjapan AT kazuhoikeo developmentofatimeseriesshotgunmetagenomicsdatabaseformonitoringmicrobialcommunitiesatthepacificcoastofjapan AT engkongtan developmentofatimeseriesshotgunmetagenomicsdatabaseformonitoringmicrobialcommunitiesatthepacificcoastofjapan AT yojiigarashi developmentofatimeseriesshotgunmetagenomicsdatabaseformonitoringmicrobialcommunitiesatthepacificcoastofjapan AT masafumiohtsubo developmentofatimeseriesshotgunmetagenomicsdatabaseformonitoringmicrobialcommunitiesatthepacificcoastofjapan AT shugowatabe developmentofatimeseriesshotgunmetagenomicsdatabaseformonitoringmicrobialcommunitiesatthepacificcoastofjapan AT yutakasuzuki developmentofatimeseriesshotgunmetagenomicsdatabaseformonitoringmicrobialcommunitiesatthepacificcoastofjapan AT shuichiasakawa developmentofatimeseriesshotgunmetagenomicsdatabaseformonitoringmicrobialcommunitiesatthepacificcoastofjapan AT sonokoishino developmentofatimeseriesshotgunmetagenomicsdatabaseformonitoringmicrobialcommunitiesatthepacificcoastofjapan AT kosuketashiro developmentofatimeseriesshotgunmetagenomicsdatabaseformonitoringmicrobialcommunitiesatthepacificcoastofjapan AT yoshizumiishino developmentofatimeseriesshotgunmetagenomicsdatabaseformonitoringmicrobialcommunitiesatthepacificcoastofjapan AT takanorikobayashi developmentofatimeseriesshotgunmetagenomicsdatabaseformonitoringmicrobialcommunitiesatthepacificcoastofjapan AT katsuhikomineta developmentofatimeseriesshotgunmetagenomicsdatabaseformonitoringmicrobialcommunitiesatthepacificcoastofjapan AT takashigojobori developmentofatimeseriesshotgunmetagenomicsdatabaseformonitoringmicrobialcommunitiesatthepacificcoastofjapan |
| _version_ |
1718389246911315968 |