A bioinformatics strategy to clarify microbial community structures by analyzing metagenomic sequences on the basis of Batch-Learning Self-Organizing Map

2010 Fiscal Year Final Research Report

• Project/Area Number: 20700273
• Research Category: Grant-in-Aid for Young Scientists (B)
• Allocation Type: Single-year Grants
• Research Field: Bioinformatics/Life informatics
• Research Institution: Nagahama Institute of Bio-Science and Technology
• Principal Investigator: ABE Takashi Nagahama Institute of Bio-Science and Technology, バイオサイエンス学部, 助教 (30390628)
• Project Period (FY): 2008 – 2010
• Keywords: メタゲノム / 塩基組成 / 環境微生物 / 系統推定 / 自己組織化マップ

Research Abstract

Metagenomic approach, which is the genome analysis on a mixture of uncultured microorganisms, has been recently developed to search for novel and industrially useful genes and to study microbial diversity in a wide variety of environments. We have previously developed a Batch-Learning SOM (BLSOM) for genome informatics, which does not depend on the order of data input. Here we used BLSOM as a novel bioinformatics strategy to unveil and visualize microbial community structures and relative abundance of microorganisms within an environmental sample. The present method is also useful for surveys of microorganisms in extremity environment samples and novel pathogenetic microorganisms in clinical samples.

Research Products

• [Journal Article] Prediction of directional changes of influenza A virus genome sequences with emphasis on pandemic H1N1/09 as a model case. (2011)
  • Author(s): Yuki Iwasaki, Takashi Abe, Kennosuke Wada, Mastic Itoh, Toshimichi Ikemura (equal contributions).
  • Journal Title: DNA Research 18 Pages: 125-136
• [Journal Article] A novel bioinformatics strategy for searching industrially useful genome resources from metagenomic sequence libraries. (2011)
  • Author(s): Hiroshi Uehara, Yuki Iwasaki, Chieko Wada, Toshimichi Ikemura, Takashi Abe
  • Journal Title: Genes & Genetic Systems 86 Pages: 53-66
• [Journal Article] tRNADB-CE 2011 : tRNA gene database curated manually by experts. (2011)
  • Author(s): Takashi Abe, Toshimichi Ikemura, Junichi Sugahara, Akio Kanai, Yasuo Ohara, Hiroshi Uehara, Makoto Kinouchi, Shigehiko Kanaya, Yuko Yamada, Akira Muto, Hachiro Inokuchi
  • Journal Title: Nucleic Acids Research 39 Pages: D210-D213
• [Journal Article] Approaches to understanding adaptations of skin color variation by detecting gene-environment interactions. (2010)
  • Author(s): Sumiko Anno, Kazuhiko Ohshima, Takashi Abe
  • Journal Title: Expert Review ofMolecular Diagnosis 10 Pages: 987-991
• [Journal Article] Preliminary Evaluation of Batch-Learning Self-Organizing Map Algorithm on a Graphic Processor. (2010)
  • Author(s): Akihiro Shitara, Yuri Nishikawa, Masato Yoshimi, Takashi Abe Toshimichi Ikemura, Hideharu Amano.
  • Journal Title: Proceedings ofParallel and Distributed Computing and Networks Pages: 676-089
• [Journal Article] Novel bioinformatics for inter- and intraspecies comparison of genome signatures in plant genomes. (2009)
  • Author(s): Takashi Abe, Kennosuke Wada, Yuki Iwasaki, Toshimichi Ikemura
  • Journal Title: Plant Biotechnology 26 Pages: 469-477
• [Journal Article] A novel bioinfonmatics strategy for function prediction of poorly-characterized protein genes obtained from metagenome analyses (2009)
  • Author(s): Takashi Abe, Shigehiko Kanaya, Hiroshi Uehara, Toshimichi Ikemura
  • Journal Title: DNA Research 16 Pages: 287-298
• [Journal Article] tRNADB-CE: tRNA gene database curated manually by experts. (2009)
  • Author(s): Takashi Abe, Toshimichi Ikemura, Yasuo Ohara, Hiroshi Uehara, Makoto Kinouchi, Shigehiko Kanaya, Yuko Yamada, Akira Mum, Hachiro Inokuchi
  • Journal Title: Nucleic Acids Research 37 Pages: D163-D168
• [Journal Article] Relationships between replication timing and GC content of cancer-related genes on human chromosomes 11q and 21q. (2009)
  • Author(s): Yoshihisa Watanabe, Takashi Abe, Toshimichi Ikemura, Masato Maekawa
  • Journal Title: Gene 433 Pages: 26-31
• [Journal Article] Batch-Learning Self-Organizing Map for Predicting Functions of Poorly-Characterized Proteins Massively Accumulated. (2009)
  • Author(s): Takashi Abe, Shigehiko Kanaya, Toshimichi Ikemura
  • Journal Title: WSOM 2009 (J.C.Principe and R.Miikkulainen (Eds.)), LNCS 5629 Pages: 1-9
• [Journal Article] A Large-Scale Genomics Studies Conducted with Batch-Learning SOM Utilizing High-Performance Supercomputers. (2009)
  • Author(s): Takashi Abe, Yuta Hamano, Shigehiko Kanaya, Kennosuke Wada, Toshimichi Ikemura
  • Journal Title: IWANN 2009 Part I (J.Cabestany et al.(Eds.)), LNCS 5517 Pages: 829-836
• [Journal Article] Intra-Species Diversity between Seven Bifidobacterium adolescentis Strains Identified by Genome-Wide Tiling Array Analysis. (2009)
  • Author(s): Kazumasa Yasui, Mototsugu Tabata, Satoki Yamada, Takashi Abe, Toshimichi Ikemura, Ro Osawa, Tohru Suzuki
  • Journal Title: Biosci.Biotechnol.Biochem 73 Pages: 1422-1424
• [Journal Article] The genome of Pelotomaculum thermopropionicum reveals niche-associated evolution in anaerobic microbiota. (2008)
  • Author(s): Tomoyuki Kosaka, Souichiro Kato, Takefumi Shimoyama, Shunichi Ishii, Takashi Abe, Kazuya Watanabe
  • Journal Title: Genome Research 18(13) Pages: 442-448
• [Journal Article] Interactions between SNP Alleles at Multiple Loci Contribute to Skin Color Differences between Caucasoid and Mongoloid Subjects. (2008)
  • Author(s): Sumiko Anno, Takashi Abe, Takushi Yamamoto
  • Journal Title: International Journal of Biological Sciences 4 Pages: 81-86
• [Journal Article] Metagenomic analysis of 0.2-μm-passable microorganisms in deep-sea hydrothermal fluid.
  • Author(s): Ryosuke Nakai, Takashi Abe, Haruko Takeyama, Takeshi Naganuma
  • Journal Title: Marine Biotechnology in press
• [Presentation] Visualization ofgenome signatures and its application to virus and eukaryote genomes (2010)
  • Author(s): Takashi Abe, Yuki Iwasaki, Hiroshi Uehara, Kennosuke Wada, Toshimichi Ikemura
  • Organizer: An International Meeting honouring Jacques Monod on the 100th Anniversary of his birth and the 40th Anniversary ofhis book
  • Place of Presentation: Ravello, Italy(oral)
  • Year and Date: 20101020-20101023
• [Presentation] tRNADB-CE : Trna gene database curated manually by experts. (2010)
  • Author(s): Takashi Abe, Toshimichi Ikemura, yasuo Ohara, Hiroshi Uehara, Makoto Kinouchi, Junichi Sugahara, Akio Kanai, Shigehiko Kanaya, Yuko Yamada, Akira Muto, Hachiro Inokuchi
  • Organizer: 23rd Trna workshop
  • Place of Presentation: Aveiro, Portugal(oral)
  • Year and Date: 20100128-20100202
• [Presentation] 一括学習型自己組織化マップ法によるメタゲノム配列解析を対象にした環境微生物群集構造の解明 (2010)
  • Author(s): 阿部貴志, 大井学, 伊藤輝二, 岡田和典, 岩崎裕貴, 和田健之介, 金谷重彦, 池村淑道
  • Organizer: 第33回日本分子生物学会年会
  • Place of Presentation: 神戸(口頭/ポスタ)
  • Year and Date: 2010-12-08
• [Presentation] tRNADB-CEを用いたメタゲノム配列データに対する新規分子系統マーカーとしてのtRNA遺伝子の利用 (2010)
  • Author(s): 阿部貴志, 井口八郎, 上原啓史, 山田優子,武藤〓, 池村淑道
  • Organizer: 日本進化学会第12回東京大会
  • Place of Presentation: 東京(口頭)
  • Year and Date: 2010-08-02
• [Presentation] Unveiling microbial diversity of uncultured environmental microbe mixtures and functions of metagenome sequences using Batch Learning Self-Organizing Map (BLSOM). (2009)
  • Author(s): Takashi Abe,Shigehiko Kanaya, Toshimichi Ikemura.
  • Organizer: International Symposium on Marine Genomics 2009 Oral
  • Place of Presentation: Okinawa, Japan
  • Year and Date: 20091215-20091218
• [Presentation] tRNADB-CE:エキスパートがキーユレートしたtRNA遺伝子データベース (2009)
  • Author(s): 阿部貴志, 池村淑道, 小原康雄, 上原啓史, 平野晋也, 木ノ内誠, 金谷重彦, 菅原潤一, 金井明夫, 山田優子, 武藤〓, 井口八郎
  • Organizer: RNA学会第11回大会
  • URL: 〓
  • Place of Presentation: 新潟(口頭)
  • Year and Date: 20090727-20090729
• [Presentation] 一括学習型自己組織化地図法による全ゲノム・全タンパク質配列を対象にした大規模ポストゲノム解析 (2009)
  • Author(s): 阿部貴志、金谷重彦、池村淑道
  • Organizer: 第3回微生物ゲノム学会
  • Place of Presentation: 東京(口頭)
  • Year and Date: 20090300
• [Presentation] エキスパートがキュレートしたtRNA遺伝子データベース (2009)
  • Author(s): 阿部貴志、小原康雄、上原啓史、中泉友紀、平野晋也、木ノ内誠、金谷重彦、山田優子、武藤〓、井口八郎、池村淑道
  • Organizer: 第3回微生物ゲノム学会
  • Place of Presentation: 東京(口頭)
  • Year and Date: 20090300
• [Presentation] 学部生シニア世代の共同作業としての「高精度・高機能な遺伝子データベース」の構築とその利用 (2009)
  • Author(s): 阿部貴志、小原康雄、上原啓史、平野晋也、木ノ内誠、金谷重彦、菅原潤一、金井明夫、山田優子、武藤〓、井口八郎、池村淑道
  • Organizer: 日本遺伝学会第81回大会
  • Place of Presentation: 長野(口頭)
  • Year and Date: 2009-09-16
• [Presentation] 一括学習型自己組織化地図法(Batch-LearningSelf-Organizing Map:BLSOM)による環境生物ゲノム由来断片配列からの知識発見 (2008)
  • Author(s): 阿部貴志、金谷重彦、池村淑道
  • Organizer: 第31回日本分子生物学会年会・第81回日本生化学会大会合同大会
  • Place of Presentation: 神戸(ポスタ・口頭)
  • Year and Date: 20081200
• [Presentation] エキスパートがキュレートしたtRNAデータベース (2008)
  • Author(s): 阿部貴志、池村淑道、小原康雄、武藤あきら、山田優子、上原啓史、木ノ内誠、金谷重彦、井口八郎
  • Organizer: 日本遺伝学会第80回大会
  • Place of Presentation: 名古屋(口頭)
  • Year and Date: 20080900
• [Presentation] 一括学習型自己組織化地図法(Batch Learning Self-Organizing Map:SOM)による環境微生物ゲノム群集の解明 (2008)
  • Author(s): 阿部貴志、金谷重彦、池村淑道
  • Organizer: 日本遺伝学会第80回大会
  • Place of Presentation: 名古屋(口頭)
  • Year and Date: 20080900
• [Presentation] 学部教育におけるDDBJの活用について (2008)
  • Author(s): 阿部貴志
  • Organizer: DDBJing講習会
  • Place of Presentation: 三島(講師)
  • Year and Date: 20080600
• [Presentation] オリゴペプタイド情報を用いた-括学習型の自己組織化マップ法による機能未知のタンパク質類の機能推定法の開発 (2008)
  • Author(s): 阿部貴志、金谷重彦、池村淑道
  • Organizer: 第2回日本微生物学会年会
  • Place of Presentation: 大阪(口頭)
  • Year and Date: 20080300
• [Presentation] Phylogenetic characterization of non-rRNA sequences from uncultured environmental microbe mixtures on the basis of Batch Learning Self-Organizing Map (BLSOM). (2008)
  • Author(s): Takashi Abe, Hideaki Sugawara, Shigehiko Kanaya, Toshimichi Ikemura.
  • Organizer: XXXI Symposium on Polar Biology (Oral)
  • Place of Presentation: Tokyo, Japan
  • Year and Date: 2008-12-03
• [Presentation] A novel bioinformatics strategy for prediction of functions of a massive amount of poorly-characterized protein genes btained by metagenome studies. (2008)
  • Author(s): Takashi Abe, Shigehiko Kanaya, Hiroshi Uehara, Toshimichi Ikemura.
  • Organizer: XX International Congress of Genetics(Oral)
  • Place of Presentation: Berlin, Germany)
  • Year and Date: 2008-07-17
• [Book] Wiley & Sons(Sequences from prokaryotic, eukaryotic and viral genomes currently available clustered according to phylotype on a large-scale Self-Organizing Map., Knowledge Based Bioinformatics)(Eds.Gil Alterovites, Marco Ramoni), Ltd. (2010)
  • Author(s): Takashi Abe, Shigehiko Kanaya, Toshimichi Ikemura
  • Total Pages: 233-249
• [Book] マリンメタゲノムの有効利用(環境巾来大量DNA配列を利用した難培養性生物群の系統推定のための新規情報学手法)(松永是、竹山春子監修) (2009)
  • Author(s): 阿部貴志、上原啓史、金谷重彦、池村淑道
  • Total Pages: 228-239
  • Publisher: シーエムシー出版
• [Book] 生物の科学遺伝(遺伝分野の教育における高校と大学の連携の能性,Vol.63,No.1) (2009)
  • Author(s): 上原啓史、阿部貴志、池村淑道
  • Total Pages: 92-96
  • Publisher: エヌ・ティー・エス
• [Book] 公的データベースからの有用遺伝子の発掘:持続可能型社会への貢献遺伝子データベースの構築と世界最高水準スーパーコンピュータの利用」、日本化学会情報科学部会誌、Vol.26 (2008)
  • Author(s): 池村淑道、上原啓史、棚橋佳代、阿部貴志
  • Total Pages: 40-44
• [Book] データベースに蓄積の著しい機能未知のタンパク質類の機能推定のための自己組織化マップ法による新規情報学的手法の開発 日本化学会情報化学部会誌、Vol.26 (2008)
  • Author(s): 阿部貴志、金谷重彦、池村淑道
  • Total Pages: 31-33
• [Book] ゲノム配列情報からの効率的な知識発見のための情報学的手法の確立 『日本化学会情報化学部会誌』Vol.26 (2008)
  • Author(s): 阿部貴志、金谷重彦、池村淑道
  • Total Pages: 20-22
• [Book] 持続可能型社会への貢献遺伝子データベース 日本化学会情報化学部会誌 (2008)
  • Author(s): 上原啓史、棚橋佳代、阿部貴志、池村淑道
  • Total Pages: 17-19
• [Book] エキスパートがキュレートしたtRNAデータベース 日本化学会情報化学部会誌 Vol.26 (2008)
  • Author(s): 井口八郎、小原康雄、武藤あきら、山田優子、木ノ内誠、前野聖、金谷重彦、池村淑道、阿部貴志
  • Total Pages: 11-16
• [Book] 第18バイオ情報学研究会(オリゴヌクレオチド組成を用いた一括学習型自己組織化地図法によるA型インフルエンザウイルスの府目敢的な特徴解明)、Vo1.2009-BIO-18 No5
  • Author(s): 岩崎裕貴、池村淑道、伊藤正恵、阿部貴志
  • Total Pages: 1-6
• [Remarks] ホームページ等
  • URL: http://trna.nagahama-i-bio.ac.jp/