Marine Metagenomic Sequence Counts of Reads Assigned to Taxa Consistently Proportionate to Read Counts Obtained for per g of Seawater Sample

Toshiaki Kudo, Md Shaheed Reza, Atsushi Kobiyama, Jonaira Rashid, Yuichiro Yamada, Yuri Ikeda, Daisuke Ikeda, Nanami Mizusawa, Saki Yanagisawa, Kazuho Ikeo, Shigeru Sato, Takehiko Ogata, Shinnosuke Kaga, Shiho Watanabe, Kimiaki Naiki, Yoshimasa Kaga, Satoshi Segawa, Katsuhiko Mineta, Vladimir Bajic, Takashi GojoboriShugo Watabe

Research output: Chapter in Book/Report/Conference proceedingChapter

1 Citation (Scopus)


Development of high-throughput DNA sequencing technologies has enabled scientists to generate vast amounts of genetic information that may provide a comprehensive understanding of key roles played by environmental microorganisms. Generally the microorganisms inhabit a particular niche and correlate well with environmental changes. It is accepted that the read counts obtained through metagenomic analyses correlate semi-quantitatively with the relative abundance of bacterial species. In our marine metagenomic study conducted on the Ofunato Bay, Iwate Prefecture, Japan, we observed such correlation which exists for bacterioplankton Candidatus Pelagibacter ubique, identified as the dominant bacterial species of the bay. Shotgun metagenomic analyses identified three strains of Ca. Pelagibacter in the bay, viz., dmdA-HTCC1062, dmdAHTCC9022, and O19-dmdA, that showed a dynamic change throughout the year particularly in the 10-m depth zone. Interestingly, the total abundances of those strains that fall in the Ca. Pelagibacter genus were found to correlate well with the read counts per g seawater samples used for analyses. It is assumed that wholegenome sequence (WGS) reads for members of the metagenome would show similar trend provided that proper precautions are taken to ensure collection of representative sample from the environment.

Original languageEnglish
Title of host publicationMarine Metagenomics
Subtitle of host publicationTechnological Aspects and Applications
PublisherSpringer Singapore
Number of pages6
ISBN (Electronic)9789811381348
ISBN (Print)9789811381331
Publication statusPublished - 2019 Jan 1

All Science Journal Classification (ASJC) codes

  • General Medicine
  • General Agricultural and Biological Sciences
  • General Biochemistry,Genetics and Molecular Biology
  • General Environmental Science
  • General Immunology and Microbiology


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