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

  • Kaoru Matsumoto
  • Norikazu Kitamura
  • Kazuho IkeoEmail author
Chapter

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.

Keywords

Coastal ocean Bacterioplankton Red tide Seasonality Shotgun metagenomics 

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Copyright information

© Springer Nature Singapore Pte Ltd. 2019

Authors and Affiliations

  • Kaoru Matsumoto
    • 1
  • Norikazu Kitamura
    • 1
  • Kazuho Ikeo
    • 1
    Email author
  1. 1.National Institute of GeneticsShizuokaJapan

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