Exploring biomarker identification evaluating ecosystem fructuation in natural samples

• Project/Area Number: 25513012
• Research Category: Grant-in-Aid for Scientific Research (C)
• Allocation Type: Multi-year Fund
• Section: 一般
• Research Field: オミクス計測科学
• Research Institution: Institute of Physical and Chemical Research
• Principal Investigator: Kikuchi Jun 国立研究開発法人理化学研究所, 環境資源科学研究センター, チームリーダー (00321753)
• Project Period (FY): 2013-04-01 – 2016-03-31
• Project Status: Completed (Fiscal Year 2015)
• Budget Amount: ¥5,200,000 (Direct Cost: ¥4,000,000、Indirect Cost: ¥1,200,000); Fiscal Year 2015: ¥1,040,000 (Direct Cost: ¥800,000、Indirect Cost: ¥240,000); Fiscal Year 2014: ¥2,080,000 (Direct Cost: ¥1,600,000、Indirect Cost: ¥480,000); Fiscal Year 2013: ¥2,080,000 (Direct Cost: ¥1,600,000、Indirect Cost: ¥480,000)
• Keywords: NMR / 環境分析 / マイクロバイオーム / メタボローム / イオノーム / データサイエンス / 機械学習 / 共生システム / 複合微生物叢 / バイオマス / 栄養代謝 / 微生物発酵 / データ駆動型アプローチ / 元素分析 / ネットワーク解析 / パイロシーケンス

Outline of Final Research Achievements

Natural ecosystems can be conceptually thought of as interconnected environmental and metabolic systems. Humans and their activities affect and are a part of these ecosystems. Considering a more applied perspective of human activities within ecosystems, it is important to gain an understanding of natural ecology and its metabolic processes in various environments. We have shown the challenges of analytical approaches for molecular and microbial complexity in the ecosystem. The first challenge is macromolecular complexity to analyze structure and composition of polysaccharides. The second challenge is microbial complexity, namely concerning their metabolic activity. The third challenge is integrating molecular and microbial complexity, by using multi-omics approach. Our approach provides a foundation for evaluation of systemic effects of environmental fluctuation, and a step for opening up a new window that will clear up metabolic dynamics in the ecosystem.

Research Products

• [Journal Article] Artificial Autopolyploidization Modifies the Tricarboxylic Acid Cycle and GABA Shunt in Arabidopsis thaliana Col-0 (2016)
  • Author(s): Vergara, F. Kikuchi, J. Breuer, C.
  • Journal Title: Sci. Rep. Volume: XX
  • Peer Reviewed / Open Access / Int'l Joint Research / Acknowledgement Compliant
• [Journal Article] The effect of molecular conformation on the accuracy of theoretical 1H and 13C chemical shifts calculated by ab initio methods for NMR-based metabolomics databases (2016)
  • Author(s): Chikayama, E., Shinbo, Y., Komatsu, K. and Kikuchi, J.*
  • Journal Title: J. Phys. Chem Volume: 120 Issue: 14 Pages: 3479-3487
  • DOI: 10.1021/acs.jpcb.5b12748
  • Peer Reviewed / Acknowledgement Compliant
• [Journal Article] Structure and metabolic flow analysis of molecular complexity in 13C-labeled tree by 2D and 3D-NMR (2016)
  • Author(s): Komatsu, T., Ohishi, R., Shino, A. and Kikuchi, J.*
  • Journal Title: Angew. Chem. Int. Ed. Volume: XX Issue: 20 Pages: 6000-6003
  • DOI: 10.1002/anie.201600334
  • Peer Reviewed / Acknowledgement Compliant
• [Journal Article] Application of Maket Basket Analysis for Visualization of Transaction Data based on Human Lifestyle and Spectroscopic Measurements (2016)
  • Author(s): Shiokawa, Y., Misawa, T., Date, Y. and Kikuchi, J.*
  • Journal Title: Anal. Chem. Volume: 88 Issue: 5 Pages: 2714-2719
  • DOI: 10.1021/acs.analchem.5b04182
  • Acknowledgement Compliant
• [Journal Article] Visualization of microfloral metabolism for marine waste recycling (2016)
  • Author(s): Ogura, T., Hoshino, R., Date, Y. and Kikuchi, J.*
  • Journal Title: Metabolites Volume: 6 Issue: 1 Pages: 7-7
  • DOI: 10.3390/metabo6010007
  • Peer Reviewed / Open Access / Acknowledgement Compliant
• [Journal Article] Fragment Assembly Approach Based on Graph/Network Theory with Quantum Chemistry Verifications for Assigning Multidimensional NMR Signals in Metabolite Mixtures (2016)
  • Author(s): Ito, K., Tsutsumi, Y., Date, Y. and Kikuchi, J.*
  • Journal Title: ACS Chem. Biol. Volume: 11 Issue: 4 Pages: 1030-1038
  • DOI: 10.1021/acschembio.5b00894
  • Peer Reviewed / Acknowledgement Compliant
• [Journal Article] SENSI: Signal ENhancement by Spectral Integration for Analysis of Metabolic Mixtures (2016)
  • Author(s): Misawa, T., Komatsu, T., Date, Y. and Kikuchi, J.*
  • Journal Title: Chem. Commun. Volume: 52 Issue: 14 Pages: 2964-2967
  • DOI: 10.1039/c5cc09442a
  • Peer Reviewed / Acknowledgement Compliant
• [Journal Article] Organosolv pretreatment of sorghum bagasse using a low concentration of hydrophobic solvents such as 1-butanol or 1-pentanol (2016)
  • Author(s): Teramura, H., Kikuchi, J. (14人中13番目）
  • Journal Title: Biotech. Biofuels Volume: 9 Issue: 1 Pages: 27-27
  • DOI: 10.1186/s13068-016-0427-z
  • Peer Reviewed
• [Journal Article] SpinCouple: Development of web-tool for analyzing metabolite mixtures via 2D-J resolved NMR spectra (2016)
  • Author(s): Kikuchi, J.* Tsuboi, Y., Komatsu, K., Gomi, M., Chikayama, E. and Date, Y.
  • Journal Title: Anal. Chem. Volume: 88 Issue: 1 Pages: 659-665
  • DOI: 10.1021/acs.analchem.5b02311
  • Peer Reviewed / Acknowledgement Compliant
• [Journal Article] Polysaccharides as major carbon sources in environmental biodiversity (2016)
  • Author(s): Kikuchi, J.* and Komatsu, T.
  • Journal Title: NMR in Glycoscience and Glycotechnology Volume: XX
• [Journal Article] Identification of reliable components in multivariate curve resolution-alternating least squares (MCR-ALS) for a data-driven approach across metabolic processes (2015)
  • Author(s): Motegi, H., Kikuchi, J* (9人中9番目）
  • Journal Title: Sci. Rep. Volume: 5 Issue: 1 Pages: 16710-16710
  • DOI: 10.1038/srep15710
  • Peer Reviewed / Open Access / Acknowledgement Compliant
• [Journal Article] Methylated cytokinins from phytopathogen Rhodococcus fascians mimic plant hormone activity (2015)
  • Author(s): Radhika, V., Kikuchi, J., (7人中5番目）
  • Journal Title: Plant Physiol Volume: 169 Issue: 2 Pages: 1118-1126
  • DOI: 10.1104/pp.15.00787
  • Peer Reviewed
• [Journal Article] Precipitate obtained following membrane separation of hydrothermally pretreated rice straw liquid revealed by 2D NMR to have high lignin content (2015)
  • Author(s): Sasaki, K., Kikuchi, J. (12人中11番目）
  • Journal Title: Biotech. Biofuels Volume: 8 Issue: 1 Pages: 88-88
  • DOI: 10.1186/s13068-015-0273-4
  • Peer Reviewed
• [Journal Article] Probiotic Bifidobacterium longum alters gut luminal metabolism through modification of the gut microbial community. (2015)
  • Author(s): Sugahara, H., Odamaki, T., Fukuda, S., Kato, T., Xiao, J.Z., Abe, F., Kikuchi, J., Ohno, H.
  • Journal Title: Scientific Reports Volume: 5 Issue: 1 Pages: 13548-13548
  • DOI: 10.1038/srep13548
  • Peer Reviewed / Open Access
• [Journal Article] Metabolic dynamics analysis by massive data integration: application to tsunami-affected field soils in Japan (2015)
  • Author(s): Ogura, T., Date, Y., Tsuboi, Y. and Kikuchi, J.*
  • Journal Title: ACS Chem. Biol. Volume: 10 Issue: 8 Pages: 1908-1915
  • DOI: 10.1021/cb500609p
  • Peer Reviewed / Acknowledgement Compliant
• [Journal Article] Profiling planktonic biomass using element-specific, multicomponent nuclear magnetic resonance spectroscopy (2015)
  • Author(s): Komatsu, T., Kobayashi, T., Hatanaka, M. and Kikuchi, J.*
  • Journal Title: Environ. Sci. Technol Volume: 49 Issue: 11 Pages: 7056-7062
  • DOI: 10.1021/acs.est.5b00837
  • Peer Reviewed / Acknowledgement Compliant
• [Journal Article] Multidimensional High-Resolution Magic Angle Spinning and Solution-State NMR Characterization of (13)C-labeled Plant Metabolites and Lignocellulose. (2015)
  • Author(s): Mori T, Tsuboi Y, Ishida N, Nishikubo N, Demura T, Kikuchi J.
  • Journal Title: Scientific Report Volume: 5 Issue: 1 Pages: 11848-11848
  • DOI: 10.1038/srep11848
  • Peer Reviewed / Open Access
• [Journal Article] Profiling contents of water-soluble metabolites and mineral nutrients to evaluate the effects of pesticides and organic and chemical fertilizers on tomato fruit quality (2015)
  • Author(s): Watanabe, M., Ohta, Y., Sun, L., Motoyama, N. and Kikuchi, J.
  • Journal Title: Food Chem. Volume: 169 Pages: 387-395
  • DOI: 10.1016/j.foodchem.2014.07.155
  • Peer Reviewed
• [Journal Article] A NMR-based, non-targeted multistep metabolic profiling revealed L-rhamnitol as a metabolite that characterised apples from different geographic origins (2015)
  • Author(s): Satoru Tomita, Tadashi Nemoto, Yosuke Matsuo, Toshihiko Shoji, Fukuyo Tanaka, Hiroyuki Nakagawa, Hiroshi Ono, Jun Kikuchi, Mayumi Ohnishi-Kameyama, Yasuyo Sekiyama
  • Journal Title: Food Chemistry Volume: 174 Pages: 163-172
  • DOI: 10.1016/j.foodchem.2014.11.028
  • Peer Reviewed / Acknowledgement Compliant
• [Journal Article] Human metabolic, mineral and microbiota fluctuations across daily nutritional intakes visualized by data-driven approach (2015)
  • Author(s): Misawa, T., Date, Y. and Kikuchi, J
  • Journal Title: J. Proteome Res. Volume: 14 Issue: 3 Pages: 1526-1534
  • DOI: 10.1021/pr501194k
  • Peer Reviewed / Acknowledgement Compliant
• [Journal Article] Pretreatment and integrated analysis of spectral data reveal seaweed similarity based on chemical diversity (2015)
  • Author(s): Wei, F., Ito, K., Sakata, K., Date, Y. and Kikuchi, J.
  • Journal Title: Anal. Chem. Volume: 87 Issue: 5 Pages: 2819-2826
  • DOI: 10.1021/ac504211n
  • Peer Reviewed
• [Journal Article] Strengthening of the intestinal epithelial tight junction by Bifidobacterium bifidum (2015)
  • Author(s): Chen-Yu Hsieh, Toshifumi Osaka, Eri Moriyama1, Yasuhiro Date, Jun Kikuchi, Satoshi Tsuneda
  • Journal Title: Physiological Reports Volume: 3 Issue: 3 Pages: e12327-e12327
  • DOI: 10.14814/phy2.12327
  • Peer Reviewed / Open Access / Acknowledgement Compliant
• [Journal Article] Introduction of chemically labile substructures in Arabidopsis lignin through the use of the Ca dehydrogenase from Sphingobium sp. Strain SYK-6 (2015)
  • Author(s): Kikuchi, J (22中15番目)
  • Journal Title: Plant Biotechnol. J. Volume: - Issue: 6 Pages: 821-832
  • DOI: 10.1111/pbi.12316
  • Peer Reviewed
• [Journal Article] Changes in lignin and polysaccharide components in 13 cultivars of rice straw following dilute acid pretreatment as studied by solution-state 2D 1H-13C NMR (2015)
  • Author(s): Teramura, H., Sasaki, K., Oshima, T., Aikawa, S., Matsuda, F., Kawaguchi, H., Ogino, C., Yamazaki, M., Shirai, T., Okamoto, M., Kikuchi, J. and Kondo, A
  • Journal Title: PLoS ONE Volume: -
  • Peer Reviewed
• [Journal Article] Comparative analysis of chemical and microbial profiles of estuarine sediments sampled from Kanto and Tohoku regions in Japan (2014)
  • Author(s): Asakura, T., Date, Y. and Kikuchi, J
  • Journal Title: Anal. Chem. Volume: 86 Issue: 11 Pages: 5425-5432
  • DOI: 10.1021/ac5005037
  • Peer Reviewed / Acknowledgement Compliant
• [Journal Article] Multiple omics uncovers host-gut microbial mutualism during prebiotic fructooligosaccharide supplementation (2014)
  • Author(s): Kato, T., Fukuda, S., Fujiwara, A., Suda, W., Hattori, M., Kikuchi, J. and Ohno, H..
  • Journal Title: DNA Res. Volume: 21 Issue: 5 Pages: 469-480
  • DOI: 10.1093/dnares/dsu013
  • Peer Reviewed
• [Journal Article] Metabolomic profiling of 13C-cellulose digestion in a lower termite: insights into symbiont function (2014)
  • Author(s): Tokuda, T., Tsuboi, Y., Kihara, K. Saito, S. Moriya, S. Lo, N. and Kikuchi, J
  • Journal Title: Proc. Royal Soc. B Volume: 281 Issue: 1789 Pages: 20140990-20140990
  • DOI: 10.1098/rspb.2014.0990
  • Peer Reviewed / Open Access / Acknowledgement Compliant
• [Journal Article] Comparative metabolomic and ionomic approach for abundant fishes in estuarine environments of Japan (2014)
  • Author(s): Yoshida, S., Date, Y. and Kikuchi, J
  • Journal Title: Sci. Rep. Volume: 4 Issue: 1 Pages: 7005-7005
  • DOI: 10.1038/srep07005
  • Peer Reviewed / Open Access / Acknowledgement Compliant
• [Journal Article] Chemical profiling of Jatropha tissues under different torrefaction conditions: application to biomass waste recovery (2014)
  • Author(s): Watanabe, T., Shino, A., Akashi, K. and Kikuchi, J.
  • Journal Title: PLoS One Volume: 9 Issue: 9 Pages: e106893-e106893
  • DOI: 10.1371/journal.pone.0106893
  • Peer Reviewed / Open Access / Acknowledgement Compliant
• [Journal Article] Biogeochemical Typing of Paddy Field by a Data-Driven Approach Revealing Sub-Systems within a Complex Environment - A Pipeline to Filtrate, Organize and Frame Massive Dataset from Multi-Omics Analyses (2014)
  • Author(s): Ogawa DM, Moriya S, Tsuboi Y, Date Y, Prieto-da-Silva AR, Rádis-Baptista G, Yamane T, Kikuchi J.
  • Journal Title: PLOS ONE Volume: 9 Issue: 10 Pages: e110723-e110723
  • DOI: 10.1371/journal.pone.0110723
  • Peer Reviewed / Open Access / Acknowledgement Compliant
• [Journal Article] Multi-spectroscopic analysis of seed quality and 13C-stable-isotopologue monitoring in initial growth metabolism of Jatropha curcas L. using stable-isotope labeling (2014)
  • Author(s): Komatsu, T., Oishi, R., Shino, A. Akashi, K. and Kikuchi, J
  • Journal Title: Metabolites Volume: 4 Issue: 4 Pages: 1018-1033
  • DOI: 10.3390/metabo4041018
  • Peer Reviewed / Open Access / Acknowledgement Compliant
• [Journal Article] 安定同位体標識による生体分子混合物ならびに代謝経路解析 (2014)
  • Author(s): 菊地淳
  • Journal Title: 生物工学会誌 Volume: 92 Pages: 100-109
• [Journal Article] 食と代謝のメタボノミクス (2014)
  • Author(s): 菊地 淳
  • Journal Title: 実験医学 Volume: 32 Pages: 699-705
• [Journal Article] NMRにおけるイノベーション (2014)
  • Author(s): 菊地 淳
  • Journal Title: 生物工学会誌 Volume: 92 Pages: 561-561
• [Journal Article] NMRで挑む複雑系の分子宇宙 (2014)
  • Author(s): 三澤拓真、伊藤研悟、菊地 淳
  • Journal Title: 生物工学会誌 Volume: 92 Pages: 504-510
• [Journal Article] 複雑系高分子群に挑むバイオマスNMRの世界 (2014)
  • Author(s): 小松功典、菊地 淳
  • Journal Title: 細胞工学 Volume: 33 Pages: 843-849
• [Journal Article] 分子複雑系 (2014)
  • Author(s): 菊地 淳
  • Journal Title: NMR Volume: 5 Pages: 78-82
  • NAID: 40020568027
• [Journal Article] 食の来た道還る道 (2014)
  • Author(s): 菊地 淳
  • Journal Title: バイオインダストリー Volume: 31 Pages: 37-44
• [Journal Article] Toward better annotation in plant metabolomics: isolation and structure elucidation of 36 specialized metabolites from Oryza sativa (rice) by using MS/MS and NMR analyses (2014)
  • Author(s): Zhigang Yang, Ryo Nakabayashi, Yozo Okazaki, Tetsuya Mori, Satoshi Takamatsu, Susumu Kitanaka, Jun Kikuchi, Kazuki Saito
  • Journal Title: Metabolomics Volume: 10 Issue: 4 Pages: 543-555
  • DOI: 10.1007/s11306-013-0619-5
  • Peer Reviewed / Open Access
• [Journal Article] Visualizing microbial dechlorination processes in underground ecosystem by statistical correlation and network analysis approach (2014)
  • Author(s): Yamazawa, A., Date, Y., Ito, K. and Kikuchi, J.
  • Journal Title: J. Biosci. Bioeng. Volume: 117 Issue: 3 Pages: 305-309
  • DOI: 10.1016/j.jbiosc.2013.08.010
  • NAID: 110009815381
  • Peer Reviewed
• [Journal Article] In vitro evaluation method for screening of candidate prebiotic foods (2014)
  • Author(s): Date, Y., Nakanishi, Y., Fukuda, S. et al.
  • Journal Title: Food Chemistry Volume: 152 Pages: 251-260
  • DOI: 10.1016/j.foodchem.2013.11.126
  • Peer Reviewed
• [Journal Article] Cellulose digestion and metabolisms induced biocatalytic transitions in anaerobic microbial ecosystems (2014)
  • Author(s): Yamazawa, A., Iikura, T., Morioka, Y., Shino, A., Ogata, Y., Date, Y. and Kikuchi, J.
  • Journal Title: Metabolites Volume: 4 Issue: 1 Pages: 36-52
  • DOI: 10.3390/metabo4010036
  • Peer Reviewed
• [Journal Article] Integrated analysis of seaweed components in seasonal fluctuation by data mining across heterogeneous chemical measurements with network visualization (2014)
  • Author(s): Ito, K., Sakata, K., Date, Y. and Kikuchi, J.
  • Journal Title: Anal. Chem. Volume: 86 Issue: 2 Pages: 1098-1105
  • DOI: 10.1021/ac402869b
  • Peer Reviewed
• [Journal Article] Solid, solution and gas-state NMR monitoring of 13C-cellulose degradation in an anaerobic microbial ecosystem (2013)
  • Author(s): Yamazawa, A., Iikura, T., Shino, A., Date, Y., and Kikuchi, J.
  • Journal Title: Molecules Volume: 18 Issue: 8 Pages: 9021-9033
  • DOI: 10.3390/molecules18089021
  • Peer Reviewed
• [Journal Article] Differences in cellulosic supramolecular structure of compositionally similar rice straw affect biomass metabolism by paddy soil microbiota (2013)
  • Author(s): Ogura, T., Date, Y. and Kikuchi, J.
  • Journal Title: PLoS ONE Volume: 8 Issue: 6 Pages: e66919-e66919
  • DOI: 10.1371/journal.pone.0066919
  • Peer Reviewed
• [Journal Article] Selective signal detection in solid-state NMR using rotor synchronized dipolar dephasing for the analysis of hemicellulose in lignocellulosic biomass (2013)
  • Author(s): Komatsu, T and Kikuchi, J.
  • Journal Title: J. Phys. Chem. Lett. Volume: 4 Issue: 14 Pages: 2279-2283
  • DOI: 10.1021/jz400978g
  • Peer Reviewed
• [Journal Article] Comprehensive signal assignment of 13C-labeled lignocellulose using multidimensional solution NMR and 13C chemical shift comparison with solid-state NMR (2013)
  • Author(s): Komatsu, T and Kikuchi, J.
  • Journal Title: Anal. Chem. Volume: 85 Issue: 18 Pages: 8857-8865
  • DOI: 10.1021/ac402197h
  • Peer Reviewed
• [Journal Article] Commensal microbe-derived butyrate induces colonic regulatory T cells (2013)
  • Author(s): Yukihiro Furusawa, Yuuki Obata, Shinji Fukuda, Takaho A. Endo, Gaku Nakato, Daisuke Takahashi, Yumiko Nakanishi, Chikako Uetake, Keiko Kato, Tamotsu Kato, Masumi Takahashi, Noriko N. Fukuda, Shinnosuke Murakami, Eiji Miyauchi, Shingo Hino, Koji Atarashi, Satoshi Onawa, Yumiko Fujimura, Trevor Lockett, Julie M. Clarke, David L. Topping, Masaru Tomita, Shohei Hori, Osamu Ohara, Tatsuya Morita, Haruhiko Koseki, J un Kikuchi, Kenya Honda, Koji Hase and Hiroshi Ohno
  • Journal Title: Nature Volume: 506 Issue: 7480 Pages: 446-450
  • DOI: 10.1038/nature12721
  • Peer Reviewed
• [Presentation] Analysis of metabolite structure and its turnover by multi-dimensional NMR (2014)
  • Author(s): Kikuchi, J
  • Organizer: Annotation and Identification of Small Biological Molecules
  • Place of Presentation: Gif-Sur-Yvitte, France
  • Year and Date: 2014-10-23
  • Invited
• [Presentation] Analysis of microbial metabolism in the gut ecosystem (2014)
  • Author(s): Kikuchi, J
  • Organizer: Korean Society for Biotechnolgy and Bioengineering
  • Place of Presentation: Gyeongjyu, Korea
  • Year and Date: 2014-04-11
  • Invited
• [Presentation] Visualizing metabolic system catalyzed by microbial ecosystem using statistical correlation analysis (2013)
  • Author(s): Kikuchi, J
  • Organizer: ISMAR2013
  • Place of Presentation: Rio de Janeiro, Brazil
• [Book] ヒトマイクロビオーム研究の最前線 (2016)
  • Author(s): 菊地淳
  • Total Pages: 472
  • Publisher: エヌティーエス出版
• [Book] セルロースナノファイバーの調製、分散・複合化と製品応用 (2015)
  • Author(s): 菊地淳
  • Total Pages: 535
  • Publisher: 技術情報協会
• [Book] セルロースナノファイバーの前処理、分散技術と応用事例 (2015)
  • Author(s): 菊地 淳 （分筆）
  • Total Pages: 244
  • Publisher: 技術情報協会
• [Book] 常在菌が操るヒトの健康と疾患 (2014)
  • Author(s): 菊地 淳 （分筆）
  • Total Pages: 834
  • Publisher: 羊土社
• [Book] 植物細胞壁 (2013)
  • Author(s): 菊地 淳 （分筆）
  • Total Pages: 349
  • Publisher: 講談社
• [Remarks] 横浜市立大学大学院生命医科学研究科 生命分析科学研究室
  • URL: http://www.tsurumi.yokohama-cu.ac.jp/bas/publications2015.html