Marine Metagenomic Sequence Counts of Reads Assigned to Taxa Consistently Proportionate to Read Counts Obtained for per g of Seawater Sample
Type
Book ChapterAuthors
Kudo, ToshiakiReza, Md. Shaheed
Kobiyama, Atsushi
Rashid, Jonaira
Yamada, Yuichiro
Ikeda, Yuri
Ikeda, Daisuke
Mizusawa, Nanami
Yanagisawa, Saki
Ikeo, Kazuho
Sato, Shigeru
Ogata, Takehiko
Kaga, Shinnosuke
Watanabe, Shiho
Naiki, Kimiaki
Kaga, Yoshimasa
Segawa, Satoshi
Mineta, Katsuhiko

Bajic, Vladimir B.

Gojobori, Takashi

Watabe, Shugo
KAUST Department
Computational Bioscience Research Center (CBRC)Applied Mathematics and Computational Science Program
Computer, Electrical and Mathematical Sciences and Engineering (CEMSE) Division
Bioscience Program
Biological and Environmental Sciences and Engineering (BESE) Division
Date
2019-07-25Online Publication Date
2019-07-25Print Publication Date
2019Embargo End Date
2020-07-25Permanent link to this record
http://hdl.handle.net/10754/656340
Metadata
Show full item recordAbstract
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, dmdA-HTCC9022, 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 whole-genome 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.Citation
Kudo, T., Reza, M. S., Kobiyama, A., Rashid, J., Yamada, Y., Ikeda, Y., … Watabe, S. (2019). Marine Metagenomic Sequence Counts of Reads Assigned to Taxa Consistently Proportionate to Read Counts Obtained for per g of Seawater Sample. Marine Metagenomics, 183–188. doi:10.1007/978-981-13-8134-8_12Publisher
Springer NatureAdditional Links
http://link.springer.com/10.1007/978-981-13-8134-8_12ae974a485f413a2113503eed53cd6c53
10.1007/978-981-13-8134-8_12