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Shotgun Metagenome Analyses: Seasonality Monitoring in Sendai Bay and Search for Red Tide Marker Sequences

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Marine Metagenomics

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Abstract

Along with the advancement of sequencing technology, shotgun metagenomics has been applied for microbial community study. Shotgun metagenomics enables to examine not only taxonomic structure but also functional profile based on the gene repertory. It also allows broad comparative analysis including unknown sequences without annotation. Here we first mention about overview of shotgun metagenomics for microbial community study and then introduce two examples of study that applied different approaches. One is seasonality monitoring based on taxonomic and functional gene composition. This is monthly-bimonthly monitoring of surface water in Sendai Bay, Japan, for about a year. We observed typical seasonality in the taxonomic composition and also found seasonality in the overall functional gene composition. The other is search for red tide marker sequences that applied broad comparative analysis. This search is for sequences that showed different abundance between red tide samples and control samples in Buzen Sea, Japan, using the assembled contigs as the reference. As the candidate of the red tide marker sequences, we obtained 1220 contigs including those without taxonomic annotation. As in these examples, shotgun metagenomic studies provide insights to help understanding marine microbial community.

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Author information

Authors and Affiliations

  1. National Institute of Genetics, Shizuoka, Japan

    Kaoru Matsumoto, Norikazu Kitamura & Kazuho Ikeo

Authors
  1. Kaoru Matsumoto
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  2. Norikazu Kitamura
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  3. Kazuho Ikeo
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Corresponding author

Correspondence to Kazuho Ikeo .

Editor information

Editors and Affiliations

  1. Computational Bioscience Research Center, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia

    Takashi Gojobori

  2. Japan Fisheries Research and Education Agency (Retired), Yokohama, Japan

    Tokio Wada

  3. Kitasato University School of Marine Biosciences, Sagamihara, Japan

    Takanori Kobayashi

  4. Computational Bioscience Research Center, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia

    Katsuhiko Mineta

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© 2019 Springer Nature Singapore Pte Ltd.

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Matsumoto, K., Kitamura, N., Ikeo, K. (2019). Shotgun Metagenome Analyses: Seasonality Monitoring in Sendai Bay and Search for Red Tide Marker Sequences. In: Gojobori, T., Wada, T., Kobayashi, T., Mineta, K. (eds) Marine Metagenomics. Springer, Singapore. https://doi.org/10.1007/978-981-13-8134-8_10

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