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RIKEN Center for Integrative Medical Sciences Laboratory for Microbiome Sciences

Team Leader: Hiroshi Ohno (M.D., Ph.D)

Research Summary

Hiroshi Ohno (M.D., Ph.D)

The aim of the microbiome research team (Laboratory for Microbiome Sciences) is to comprehensively elucidate the host-microbial interaction by the analysis of the ecological, functional, and medical features of the microbial communities such as human gut, oral, skin microbiomes, and various symbiotic communities in other species. Our team also develops technologies of bioinformatics and statistics for the analysis of large metagenomic and genomic datasets of microbiomes and microbes produced by the next-generation sequencers.

Main Research Fields

  • Biological Sciences

Related Research Fields

  • Informatics
  • Biological Sciences
  • Biology
  • Medicine, Dentistry & Pharmacy


  • Microbiome
  • Metagenome
  • Gut microbiota
  • Commensal bacteria
  • Bacterial genome

Selected Publications

Papers with an asterisk(*) are based on research conducted outside of RIKEN.

  • 1. Khasnobish A, Takayasu L, Watanabe KI, Nguyen TTT, Arakawa K, Hotta O, Joh K, Nakano A, Hosomi S, Hattori M, Suda W, Morita H.:
    "Dysbiosis in the Salivary Microbiome Associated with IgA Nephropathy-A Japanese Cohort Study"
    Microbes Environ. 36(2):ME21006 (2021).
  • 2. Takewaki D, Suda W, Sato W, Takayasu L, Kumar N, Kimura K, Kaga N, Mizuno T, Miyake S, Hattori M, Yamamura T.:
    "Alterations of the gut ecological and functional microenvironment in different stages of multiple sclerosis"
    Proc Natl Acad Sci U S A. 117:22402-22412 (2020).
  • 3. Miyauchi E, Kim SW, Suda W, Kawasumi M, Onawa S, Taguchi-Atarashi N, Morita H, Taylor TD, Hattori M, Ohno H.:
    "Gut microorganisms act together to exacerbate inflammation in spinal cords"
    Nature. 7823:102-106 (2020).
  • 4. Masuoka H, Suda W, Tomitsuka E, Shindo C, Takayasu L, Horwood P, Greenhill AR, Hattori M, Umezaki M, Hirayama K.:
    "The influences of low protein diet on the intestinal microbiota of mice."
    Sci Rep. 10:17077 (2020).
  • 5. Suzuki Y, Nishijima S, Furuta Y, Yoshimura J, Suda W, Oshima K, Hattori M, Morishita S.:
    "Long-read metagenomic exploration of extrachromosomal mobile genetic elements in the human gut."
    Microbiome 71:119(2019).
  • 6. *Atarashi K, Suda W, Luo C, Kawaguchi T, Motoo I, Narushima S, Kiguchi Y, Yasuma K, Watanabe E, Tanoue T, Thaiss CA, Sato M, Toyooka K, Said HS, Yamagami H, Rice SA, Gevers D, Johnson RC, Segre JA, Chen K, Kolls JK, Elinav E, Morita H, Xavier RJ, Hattori M, Honda K.:
    "Ectopic colonization of oral bacteria in the intestine drives TH1 cell induction and inflammation".
    Science. 358:359-365(2017).
  • 7. *Takayasu L, Suda W, Watanabe E, Fukuda S, Takanashi K, Ohno H, Takayasu M, Takayasu H, Hattori M.:
    "A 3-dimensional mathematical model of microbial proliferation that generates the characteristic cumulative relative abundance distributions in gut microbiomes."
    PLoS One. 12:e0180863 (2017).
  • 8. *Takayasu L, Suda W, Takanashi K, Iioka E, Kurokawa R, Shindo C, Hattori Y, Yamashita N, Nishijima S, Oshima K, Hattori M.:
    "Circadian oscillations of microbial and functional composition in the human salivary microbiome."
    DNA Res. 24:261-270 (2017).
  • 9. *Iwasawa K, Suda W, Tsunoda T, Oikawa-Kawamoto M, Umetsu S, Inui A, Fujisawa T, Morita H, Sogo T, Hattori M.:
    "Characterisation of the faecal microbiota in Japanese patients with paediatric-onset primary sclerosing cholangitis"
    Gut 66:1344-1346 (2017).
  • 10. *Nishijima S, Suda W, Oshima K, Kim SW, Hirose Y, Morita H, Hattori M.:
    "The gut microbiome of healthy Japanese and its microbial and functional uniqueness"
    DNA Res. 23:125-133 (2016).

Lab Members

Principal investigator

Hiroshi Ohno
Team Leader

Core members

Wataru Suda
Deputy Team Leader
Naveen Kumar
Senior Technical Scientist
Yusuke Ogata
Research Scientist
Taichi Umeyama
Research Scientist
Itsuka Kamimura
Postdoctoral Researcher
Hiroaki Masuoka
Postdoctoral Researcher
Tomo Kakihara
Junior Research Associate
Chie Shindo
Technical Staff I
Kaoru Kaida
Technical Staff I
Maki Tanokura
Technical Staff I
Joanna Christine Noack
Technical Staff II

Contact Information

West Research Building,
1-7-22 Suehiro-cho, Tsurumi-ku,
Yokohama City, Kanagawa,
230-0045, Japan
Tel: +81-(0)45-503-9302
Fax: +81-(0)45-503-9613