Development of a time-series shotgun metagenomics database for monitoring microbial communities at the Pacific coast of Japan

Kazutoshi Yoshitake,Yoji Igarashi,Akira Kuwata,Kazuho Ikeo,Masanobu Kawachi,Takafumi Kataoka,Masafumi Ohtsubo,Shigeho Kakehi,Engkong Tan,Katsuhiko Mineta,Sonoko Ishino,Shuichi Asakawa,Haruyo Yamaguchi,Yukiko Taniuchi,Yutaka Suzuki,Yuji Ishino ,Gaku Kimura,Takanori Kobayashi,Kosuke Tashiro,Tomoko Sakami,Tsuyoshi Watanabe,Shugo Watabe,Takashi Gojobori

doi:10.1038/s41598-021-91615-3

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.

Highlights

With the advent of next-generation DNA sequencing, advanced metagenomic studies have been conducted worldwide, starting with the first shotgun metagenomic sequence analysis of the waters of the Sargasso Sea by Venter et al.[1]
We developed the Ocean Monitoring Database to display the time-series shotgun metagenomic data
Between March 2012 and May 2016, seawater samples were collected from five different locations around Sendai Bay, Ofunato Bay, and A-line

Summary

Introduction

With the advent of next-generation DNA sequencing, advanced metagenomic studies have been conducted worldwide, starting with the first shotgun metagenomic sequence analysis of the waters of the Sargasso Sea by Venter et al.[1]. Shotgun metagenome sequencing is advantageous because it comprehensively detects organisms without PCR bias while targeting all sequences, including those of novel genes[3] This approach is expensive and requires complex data analysis and assembly, which likely explains the fewer number of studies available on shotgun-sequenced metagenomes than those based on amplicon sequencing. To help filling the current gap in our knowledge of the structure and function of marine microbiomes, we routinely collected samples in the northeastern Pacific coastal region of Japan (Sendai Bay, Ofunato Bay, and Akkeshi off Hokkaido [A-line]) between 2012 and 2016. This region is rich in nutrients, such as nitrogen and phosphorus, vital for the growth of phytoplankton.

Methods

Results

Conclusion