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Okazaki, Yusuke

Institute for Chemical Research (ICR) Assistant Professor

Okazaki, Yusuke
list
    Last Updated :2022/11/23

    Basic Information

    Affiliated programs (koza)

    • Graduate School of Science, 生物科学専攻 生体分子情報学講座, 助教

    Professional Memberships

    • アメリカ微生物学会(ASM)
    • 国際微生物生態学会(ISME)
    • 日本陸水学会
    • 日本微生物生態学会

    Academic Degree

    • M.Sc(Kyoto University)
    • Ph.D(Kyoto University)

    Academic Resume (Graduate Schools)

    • Kyoto University, 大学院理学研究科生物科学専攻修士課程, 修了
    • Kyoto University, 大学院理学研究科生物科学専攻博士後期課程, 修了

    Academic Resume (Undergraduate School/Majors)

    • Kyoto University, 理学部理学科, 卒業

    Research History

    • From Dec. 2020, To Present
      Kyoto University, Institute for Chemical Research, 助教
    • From Apr. 2018, To Nov. 2020
      日本学術振興会特別研究員(PD)
    • From Apr. 2015, To Mar. 2018
      日本学術振興会特別研究員(DC1)
    • From Apr. 2012, To Mar. 2015
      三菱総合研究所 研究員

    ID,URL

    Website(s) (URL(s))

    researchmap URL

    list
      Last Updated :2022/11/23

      Research

      Research Topics, Overview of the research

      • Research Topics

        Microbial ecology in freshwater lakes

      • Overview of the research

        My research has been focusing on microbial ecology in deep freshwater lakes. Using a combination of field (lake sampling), dry (meta-omics), and wet (cultivation and microscopy)-based approaches, I am trying to challenge broader research topics of microbiology, ecology, and life sciences in general.

      Research Interests

      • ウイルス
      • 細菌
      • メタゲノム
      • 琵琶湖
      • 陸水学
      • 微生物生態学

      Research Areas

      • Life sciences, Genomics
      • Life sciences, Evolutionary biology
      • Life sciences, Ecology and environmental science
      • Life sciences, Marine/Aquatic life sciences

      Papers

      • Long-Read-Resolved, Ecosystem-Wide Exploration of Nucleotide and Structural Microdiversity of Lake Bacterioplankton Genomes
        Yusuke Okazaki; Shin-ichi Nakano; Atsushi Toyoda; Hideyuki Tamaki
        mSystems, 08 Aug. 2022, Peer-reviewed, Lead author, Corresponding author
      • Ecogenomics sheds light on diverse lifestyle strategies in freshwater CPR.
        Maria-Cecilia Chiriac; Paul-Adrian Bulzu; Adrian-Stefan Andrei; Yusuke Okazaki; Shin-Ichi Nakano; Markus Haber; Vinicius Silva Kavagutti; Paul Layoun; Rohit Ghai; Michaela M Salcher
        Microbiome, 04 Jun. 2022, Peer-reviewed
      • Microdiversity and phylogeographic diversification of bacterioplankton in pelagic freshwater systems revealed through long-read amplicon sequencing
        Yusuke Okazaki; Shohei Fujinaga; Michaela M. Salcher; Cristiana Callieri; Atsushi Tanaka; Ayato Kohzu; Hideo Oyagi; Hideyuki Tamaki; Shin-ichi Nakano
        Microbiome, Jan. 2021, Peer-reviewed, Lead author, Corresponding author
      • Long-read metagenomics using PromethION uncovers oral bacteriophages and their interaction with host bacteria
        Koji Yahara; Masato Suzuki; Aki Hirabayashi; Wataru Suda; Masahira Hattori; Yutaka Suzuki; Yusuke Okazaki
        Nature Communications, Jan. 2021, Peer-reviewed, Last author
      • Describing macroecological patterns in microbes: Approaches for comparative analyses of operational taxonomic unit read number distribution with a case study of global oceanic bacteria
        Ryosuke Nakadai; Yusuke Okazaki; Shunsuke Matsuoka
        Environmental DNA, Oct. 2020, Peer-reviewed
      • Genome‐resolved viral and cellular metagenomes revealed potential key virus‐host interactions in a deep freshwater lake
        Yusuke Okazaki; Yosuke Nishimura; Takashi Yoshida; Hiroyuki Ogata; Shin‐ichi Nakano
        Environmental Microbiology, Dec. 2019, Peer-reviewed, Lead author, Corresponding author
      • Metaepigenomic analysis reveals the unexplored diversity of DNA methylation in an environmental prokaryotic community.
        Satoshi Hiraoka; Yusuke Okazaki; Mizue Anda; Atsushi Toyoda; Shin-Ichi Nakano; Wataru Iwasaki
        Nature communications, 11 Jan. 2019, Peer-reviewed
      • Widespread Dominance of Kinetoplastids and Unexpected Presence of Diplonemids in Deep Freshwater Lakes.
        Mukherjee I; Hodoki Y; Okazaki Y; Fujinaga S; Ohbayashi K; Nakano SI
        Frontiers in microbiology, 2019, Peer-reviewed
      • The Broad Habitat Spectrum of the CL500-11 Lineage (Phylum Chloroflexi), a Dominant Bacterioplankton in Oxygenated Hypolimnia of Deep Freshwater Lakes
        Yusuke Okazaki; Michaela M. Salcher; Cristiana Callieri; Shin-ichi Nakano
        Frontiers in Microbiology, 27 Nov. 2018, Peer-reviewed, Lead author, Corresponding author
      • Hidden in plain sight-highly abundant and diverse planktonic freshwater Chloroflexi.
        Mehrshad M; Salcher MM; Okazaki Y; Nakano SI; Šimek K; Andrei AS; Ghai R
        Microbiome, Oct. 2018, Peer-reviewed
      • Distributions and geochemical behaviors of oxyanion-forming trace elements and uranium in the Hövsgöl–Baikal–Yenisei water system of Mongolia and Russia
        Akihito Mochizuki; Takahiro Murata; Ko Hosoda; Toshiya Katano; Yuji Tanaka; Tetsuro Mimura; Osamu Mitamura; Shin ichi Nakano; Yusuke Okazaki; Yuko Sugiyama; Yasuhiro Satoh; Yasunori Watanabe; Ayuriin Dulmaa; Chananbaatar Ayushsuren; Darmaa Ganchimeg; Valentin V. Drucker; Vladimir A. Fialkov; Masahito Sugiyama
        Journal of Geochemical Exploration, May 2018, Peer-reviewed
      • Ubiquity and quantitative significance of bacterioplankton lineages inhabiting the oxygenated hypolimnion of deep freshwater lakes
        Yusuke Okazaki; Shohei Fujinaga; Atsushi Tanaka; Ayato Kohzu; Hideo Oyagi; Shin-ichi Nakano
        ISME JOURNAL, Oct. 2017, Peer-reviewed, Lead author, Corresponding author
      • Vertical partitioning of freshwater bacterioplankton community in a deep mesotrophic lake with a fully oxygenated hypolimnion (Lake Biwa, Japan)
        Yusuke Okazaki; Shin-Ichi Nakano
        ENVIRONMENTAL MICROBIOLOGY REPORTS, Oct. 2016, Peer-reviewed, Lead author, Corresponding author
      • A novel alphaproteobacterial ectosymbiont promotes the growth of the hydrocarbon-rich green alga Botryococcus braunii
        Yuuhiko Tanabe; Yusuke Okazaki; Masaki Yoshida; Hiroshi Matsuura; Atsushi Kai; Takashi Shiratori; Ken-ichiro Ishida; Shin-ichi Nakano; Makoto M. Watanabe
        SCIENTIFIC REPORTS, Jul. 2015, Peer-reviewed
      • Seasonal dominance of CL500-11 bacterioplankton (phylum Chloroflexi) in the oxygenated hypolimnion of Lake Biwa, Japan
        Yusuke Okazaki; Yoshikuni Hodoki; Shin-ichi Nakano
        FEMS MICROBIOLOGY ECOLOGY, Jan. 2013, Peer-reviewed, Lead author

      Misc.

      • 大水深淡水湖のユニークな微生物生態系
        岡崎友輔
        海洋化学研究, Apr. 2022, Lead author
      • 湖沼の微生物生態系が教えてくれること
        岡﨑 友輔
        日本微生物生態学会誌, 2021
      • 一杯の湖水に秘められた難題
        岡崎友輔
        生物工学会誌, Nov. 2020, Lead author
      • ネオウイルス学に出会うまで
        岡崎友輔
        ネオウイルス学ニュースレター, Nov. 2019, Lead author
      • 琵琶湖堆積物からの過去100年のウイルス叢復元の試み
        本庄三恵; 槻木玲美; 加三千宣; 岡崎友輔; 木村成子; 吉田天士; 左子芳彦; 工藤洋
        日本生態学会大会講演要旨(Web), 2019
      • メタゲノム解析でひも解く淡水湖のファージの多様性と生態
        岡崎友輔; 西村陽介; 吉田天士; 緒方博之; 中野伸一
        日本微生物生態学会大会(Web), 2019
      • Comment from award winner at 8th JSPS IKUSHI PRIZE
        岡崎 友輔
        陸水学雑誌 = Japanese journal of limnology, May 2018
      • Metagenomics of prokaryotes and viruses in pelagic Lake Biwa
        岡崎 友輔
        京都大学化学研究所スーパーコンピュータシステム研究成果報告書, 2017
      • P-19 Effects of surface planktonic production on bacterial abundance, composition and activity in hypolimnion of Lake Biwa(Poster Session)
        OKAZAKI YUSUKE; NAKANO SHIN-ICHI
        日本微生物生態学会講演要旨集, 2010

      Presentations

      • “湖の微生物生態系”を対象としたゲノム・多型・遺伝子発現の網羅的比較解析
        岡崎友輔; 中野 伸一; 豊田 敦; 玉木 秀幸
        日本微生物生態学会第35回大会, 01 Nov. 2022
      • 湖沼深⽔層の細菌の⽣態学
        岡崎友輔; 中野伸一
        日本陸水学会第86回大会, Sep. 2022
      • Long-read-resolved, ecosystem-wide exploration of nucleotide and structural microdiversity of lake bacterioplankton genomes
        Yusuke Okazaki; Shin-ichi Nakano; Atsushi Toyoda; Hideyuki Tamaki
        18th International Symposium on Microbial Ecology, Aug. 2022
      • Long- and short-read-resolved microdiversity of lake bacterioplankton genomes
        Yusuke Okazaki
        METAGENOMICS FORUM, Apr. 2022, Invited
      • ロングリード解析で拓くメタゲノムビニングの限界と環境細菌ゲノムの微小多様性
        岡崎友輔; 中野伸一; 豊田敦; 玉木秀幸
        微生物生態学会第34回大会, Oct. 2021
      • ロングリードメタゲノム解析で拓く環境微生物の多様性
        岡崎友輔
        大隅基礎科学創成財団 微生物コンソーシアム, Oct. 2021, Invited
      • 湖内および湖間の細菌のゲノム多様性の解明
        岡崎友輔; 藤永承平; 田中敦; 高津文人; 大八木英夫; 中野伸一
        日本陸水学会第85回大会, Sep. 2021
      • Ecogenomics of bacteria and viruses in the water column of Lake Biwa
        Yusuke Okazaki
        35th Congress of the International Society of Limnology, Aug. 2021
      • 大水深淡水湖のユニークな微生物生態系
        岡崎友輔
        京都化学者クラブ 第374 回例会, Aug. 2021, Invited
      • ロングリードアンプリコンシーケンスで紐解く湖沼細菌の系統内多様性
        岡崎友輔
        2021 PacBio Japan Virtual User Group Meeting, May 2021, Invited

      Awards

      • 18 Sep. 2022
        日本陸水学会 二〇二二年度 吉村賞
      • Mar. 2018
        JSPS, Ikushi Prize

      External funds: Kakenhi

      • Who is the host of uncultivated viruses? Linking viral and bacterial genomes in the environment
        Grant-in-Aid for Early-Career Scientists
        Basic Section 45040:Ecology and environment-related
        Kyoto University
        岡崎 友輔
        From 01 Apr. 2022, To 31 Mar. 2025, Granted
        メタゲノム;琵琶湖;微生物生態学
      • Elucidating the molecular heterogeneity of dissolved organic matter that governs its long-term persistence
        Grant-in-Aid for Scientific Research (B)
        Basic Section 63010:Environmental dynamic analysis-related
        Kobe University
        木田 森丸
        From 01 Apr. 2022, To 31 Mar. 2025, Granted
        溶存有機物;長期残存性;微生物;分子多様性;低分子
      • Molecular ecological mechanism of bloom disintegration by viral infection
        Grant-in-Aid for Scientific Research (A)
        Medium-sized Section 40:Forestry and forest products science, applied aquatic science, and related fields
        Kochi University
        長崎 慶三
        From 01 Apr. 2022, To 31 Mar. 2027, Granted
        赤潮;ウイルス;長鎖反復アミノ酸長鎖配列;糖鎖;宿主特異性
      • Ecology of giant viruses inhabiting the aphotic zone of the sea
        Grant-in-Aid for Scientific Research (A)
        Medium-sized Section 40:Forestry and forest products science, applied aquatic science, and related fields
        Kyoto University
        緒方 博之
        From 01 Apr. 2022, To 31 Mar. 2026, Granted
        巨大ウイルス;無光層;生態
      • Unveiling the organic matter dynamics functioning in lake hypolimnion
        Grant-in-Aid for Scientific Research (A)
        Medium-sized Section 40:Forestry and forest products science, applied aquatic science, and related fields
        Kyoto University
        中野 伸一
        From 01 Apr. 2022, To 31 Mar. 2026, Granted
        湖沼深水層;有機物動態;高分子溶存有機物;沈降粒子;微生物ループ
      • Microbial Nitrogen Pump: Bacterial semi-labile dissolved organic nitrogen as a nutrient transport pathway in aquatic systems
        Grant-in-Aid for Scientific Research (B)
        Basic Section 63010:Environmental dynamic analysis-related
        Lake Biwa Environmental Research Institute
        山口 保彦
        From 01 Apr. 2021, To 31 Mar. 2024, Granted
        溶存有機物;窒素循環;アミノ酸;細菌;窒素同位体
      • Research on microbial loop unique to lake hypolimnion
        Grant-in-Aid for Challenging Research (Exploratory)
        Kyoto University
        Shin-ichi Nakano
        From 30 Jun. 2017, To 31 Mar. 2019, Project Closed
        湖沼;深水層;微生物ループ;CL500-11細菌;キネトプラスチド鞭毛虫;ピコ植物プランクトン;微生物群集組成;細菌;原生生物;鞭毛虫;湖沼深水層;群集ゲノム解析;食物連鎖

      External funds: others

      • 先端的環境ゲノム解析で迫る原核生物の種内ゲノム多様化の謎
        京都大学教育研究振興財団 令和3年度 研究活動推進助成
        From 01 Jul. 2021, To 31 Mar. 2022
        岡崎友輔
      • 環境微生物・ウイルスのドライな謎にウェットに迫る
        京都大学創立 125 周年記念ファンド【くすのき・125】
        From 13 Sep. 2021, To 31 Mar. 2025
        岡崎友輔
      list
        Last Updated :2022/11/23

        Education

        Teaching subject(s)

        • From 01 Apr. 2022, To 31 Mar. 2023
          Seminar on Critical Reading of Scientific Papers A
          8404, Year-long, Graduate School of Pharmaceutical Sciences, 2
        • From 01 Apr. 2022, To 31 Mar. 2023
          Seminar on Bioinformatics IB
          9062, Fall, Graduate School of Science, 1
        • From 01 Apr. 2022, To 31 Mar. 2023
          Skill Development for Bioinformatics
          5001, Year-long, Graduate School of Pharmaceutical Sciences, 4
        • From 01 Apr. 2022, To 31 Mar. 2023
          Advanced Course on Biological Science B
          9012, Fall, Graduate School of Science, 2
        • From 01 Apr. 2022, To 31 Mar. 2023
          Pharmaceutical Laboratory Coaching Practice A
          8301, Year-long, Graduate School of Pharmaceutical Sciences, 1
        • From 01 Apr. 2022, To 31 Mar. 2023
          Seminar on Bioinformatics IC
          9063, Spring, Graduate School of Science, 1
        • From 01 Apr. 2022, To 31 Mar. 2023
          Seminar on Bioinformatics IIB
          9066, Fall, Graduate School of Science, 1
        • From 01 Apr. 2022, To 31 Mar. 2023
          Seminar on Bioinformatics IIA
          9065, Spring, Graduate School of Science, 1
        • From 01 Apr. 2022, To 31 Mar. 2023
          Bioinformatics
          3768, Spring, Faculty of Science, 2
        • From 01 Apr. 2022, To 31 Mar. 2023
          Seminar on Bioinformatics IA
          9061, Spring, Graduate School of Science, 1
        • From 01 Apr. 2022, To 31 Mar. 2023
          Seminar on Bioinformatics IID
          9068, Fall, Graduate School of Science, 1
        • From 01 Apr. 2022, To 31 Mar. 2023
          Seminar on Bioinformatics IIC
          9067, Spring, Graduate School of Science, 1
        • From 01 Apr. 2022, To 31 Mar. 2023
          Research Proposal Writing Practice A
          8402, Year-long, Graduate School of Pharmaceutical Sciences, 1
        • From 01 Apr. 2022, To 31 Mar. 2023
          Medical Frontier Science Research A
          8406, Year-long, Graduate School of Pharmaceutical Sciences, 4
        • From 01 Apr. 2022, To 31 Mar. 2023
          Bioinformatics
          9136, Spring, Graduate School of Science, 2
        • From 01 Apr. 2022, To 31 Mar. 2023
          Seminar on Bioinformatics ID
          9064, Fall, Graduate School of Science, 1
        • From Apr. 2021, To Mar. 2022
          Bioinformatics
          Spring, 理学研究科
        • From Apr. 2021, To Mar. 2022
          Bioinformatics
          Spring, 理学部
        • From Apr. 2021, To Mar. 2022
          Seminar on Bioinformatics IA
          Spring, 理学研究科
        • From Apr. 2021, To Mar. 2022
          Seminar on Bioinformatics IB
          Fall, 理学研究科
        • From Apr. 2021, To Mar. 2022
          Seminar on Bioinformatics IC
          Spring, 理学研究科
        • From Apr. 2021, To Mar. 2022
          Seminar on Bioinformatics ID
          Fall, 理学研究科
        • From Apr. 2021, To Mar. 2022
          Seminar on Bioinformatics IIA
          Spring, 理学研究科
        • From Apr. 2021, To Mar. 2022
          Seminar on Bioinformatics IIB
          Fall, 理学研究科
        • From Apr. 2021, To Mar. 2022
          Seminar on Bioinformatics IIC
          Spring, 理学研究科
        • From Apr. 2021, To Mar. 2022
          Seminar on Bioinformatics IID
          Fall, 理学研究科
        • From Apr. 2021, To Mar. 2022
          Skill Development for Bioinformatics
          Year-long, 薬学研究科
        • From Apr. 2021, To Mar. 2022
          Bioinformatics :Advanced Course
          Fall, 理学研究科
        • From Apr. 2021, To Mar. 2022
          Bioinformatics I: Target Discovery
          Fall, 薬学研究科

        Part-time lecturer

        • From 01 Apr. 2022, To 30 Sep. 2022
          バイオインフォマティクス
          期間内120時間, 理学部
        list
          Last Updated :2022/11/23

          Administration

          Faculty management (title, position)

          • From 01 Apr. 2021, To 31 Mar. 2022
            化学研究所広報委員会委員
          list
            Last Updated :2022/11/23

            Academic, Social Contribution

            Committee Memberships

            • From Feb. 2022, To Dec. 2023
              企画委員, 日本陸水学会

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