Centers & Labs

RIKEN Center for Sustainable Resource Science

Environmental Metabolic Analysis Research team

Team Leader: Jun Kikuchi (Ph.D.)
Jun  Kikuchi(Ph.D.)

Our team intends to develop novel environmental analysis such as by a bird’s-eye view of metabolism caused by ecosystem biodiversity, based on technical advancements of our NMR approaches toward metabolite and biomass mixtures, as well as inorganic elements and microbial ecosystem analyses combined with bioinformatics and chemoinformatics approaches. Namely, we promote both international and industrial collaboration in order to contribute for effective utilization of chemical resources, by analyzing laboratory systems, industrial (agriculture, forestry, and fishery) process, and natural environment (hydrosphere and geosphere, as well as outer space).

Main Research Field

Complex systems

Related Research Fields

Informatics / Environmental science / Chemistry / Agricultural sciences

Keywords

  • Environmental analysis
  • Data science
  • Magnetic resonance
  • Symbiosis
  • Homeostasis

Selected Publications

  1. Ito, K., Obuchi, Y., Chikayama, E., Date, Y. and Kikuchi, J.*:
    “Exploratory machine-learned theoretical chemical shifts can closely predict metabolic mixture signals”
    Chem. Sci. (in press).
  2. Kikuchi, J.*, Ito, K. and Date, Y.:
    "Environmental metabolomics with data science as investigation of ecosystem homeostasis"
    Progress in NMR Spectroscopy 104, 56-88 (2018).
  3. Date, Y.*, and Kikuchi, J.*:
    "Application of a deep neural network to metabolomics studies and its performance in determining important variables"
    Anal. Chem. 90, 1805-1810 (2018).
  4. Oita, A., Oshima, T., Tsuboi, Y., Moriya, S., Date, Y. and Kikuchi, J.*:
    "Profiling physicochemical and planktonic features from discretely/continuously sampled surface water"
    Sci. Total Environ. 636, 12-19 (2018).
  5. Mekuchi, M., Sakata, K., Yamaguchi, T., Koiso, M. and Kikuchi, J.*:
    "Trans-omics approaches represented used to characterize fish nutritional biorhythms in Leopard coral groupers (Plectropomus leopardus)"
    Sci. Rep. 7, 9372 (2017).
  6. Komatsu, T., Ohishi, R., Shino, A. and Kikuchi, J.*:
    "Structure and metabolic flow analysis of molecular complexity in 13C-labeled tree by 2D and 3D-NMR"
    Angew. Chem. Int. Ed. 55, 6000-6003 (2016).
  7. Kikuchi, J.*, Tsuboi, Y., Komatsu, K., Gomi, M., Chikayama, E. and Date, Y.:
    "SpinCouple: Development of web-tool for analyzing metabolite mixtures via two-dimensional J-resolved NMR database"
    Anal. Chem. 88, 659-665 (2016).
  8. Komatsu, T., Kobayashi, T., Hatanaka, M. and Kikuchi, J.*:
    "Profiling planktonic biomass using element-specific, multicomponent nuclear magnetic resonance spectroscopy"
    Environ. Sci. Technol. 49, 7056-7062 (2015).
  9. Furusawa, Y., Obata, Y., Fukuda, S.*, Endo, T., Nakato, G., Takahashi, D., Nakanishi, Y., Uetake, C., Kato, K., Kato, T., Takahashi, M., Fukuda, N., Murakami, S., Miyauchi, E., Hino, S., Atarashi, K., Onawa, S., Fujimura, Y., Lockett, T., Clarke, J. M., Topping, D. L., Tomita, M., Hori, S., Ohara, O., Morita, T., Koseki, H., Kikuchi, J., Honda, K., Hase, K.* and Ohno, H.*:
    "Commensal microbe-derived butyrate induces colonic regulatory T cells"
    Nature 504, 446-450 (2013).
  10. Fukuda, S., Toh, H., Hase, K., Nakanishi, Y., Oshima, K., Yoshimura, K., Tobe, T., Clarke, J. M., Topping, D. L., Suzuki, T., Taylor, T. D., Itoh, K., Kikuchi, J., Morita, H., Hattori, M.* and Ohno, H.*:
    "Bifidobacteria protect from enteropathogenic infection through production of acetate."
    Nature 469, 543-547 (2011).

Lab Members

Principal Investigator

Jun Kikuchi
Team Leader

Core Members

Yasuhiro Date
Research Scientist
Kengo Ito
Postdoctoral Researcher
Atsushi Kurotani
Postdoctoral Researcher
Feifei Wei
Postdoctoral Researcher
Mario Uchimiya
Visiting Researcher
Yuho Sato
Junior Research Associate
Shunji Yamada
Junior Research Associate
Yuuri Tsuboi
Technical Staff I
kenji Sakata
Technical Staff I
Taiga Asakura
Technical Staff I
Tomoko Matsumoto
Technical Staff II