Centers & Labs

RIKEN Center for Integrative Medical Sciences

Laboratory for Microbiome Sciences

Team Leader: Masahira Hattori (Ph.D.)
Masahira  Hattori(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 Field


Related Research Fields

Biology & Biochemistry / Molecular Biology & Genetics / Immunology / Clinical Medicine / Computer Science / Environment & Ecology

Research Subjects

  • Metagenomics of human microbiomes
  • Computational Biology of bacterial communities
  • Metagenomics of symbiotic communities

Selected Publications

Papers with an asterisk(*) are based on research conducted outside of RIKEN.
  1. *Takayasu L, Suda W, Takanashi K, Erica Iioka E, Kurokawa R, Shindo C, Hattori Y, Yamashita N, Nishijima S, Oshima K, and Hattori M:
    "Circadian oscillations of microbial and functional composition in the human salivary microbiome"
    DNA Res., in press (2017).
  2. *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, in press (2016).
  3. *Nishijima S, Suda W, Oshima K, Kim S-W, Hirose Y, Morita H, Hattori M:
    "The gut microbiome of healthy Japanese and its microbial and functional uniqueness"
    DNA Res. 23(2), 125-133 (2016).
  4. *Atarashi K, Tanoue T, Ando M, Kamada N, Nagano Y, Narushima S, Suda W, Imaoka A, Setoyama H, Nagamori T, Ishikawa E, Shima T, Hara T, Kado S, Jinnohara T, Ohno H, Kondo T, Toyooka K, Watanabe E, Yokoyama SI, Tokoro S, Mori H, Noguchi Y, Morita H, Ivanov II, Sugiyama T, Nuñez G, Camp JG, Hattori M, Umesaki Y, Honda K:
    "Th17 Cell Induction by Adhesion of Microbes to Intestinal Epithelial Cells"
    Cell 163, 367-380 (2015).
  5. *Miyake S, Kim S, Suda W, Oshima K, Nakamura M, Matsuoka T, Chihara N, Tomita A, Sato W, Kim SW, Morita H, Hattori M, Yamamura T:
    "Dysbiosis in the Gut Microbiota of Patients with Multiple Sclerosis, with a Striking Depletion of Species Belonging to Clostridia XIVa and IV Clusters"
    PLoS One. 10(9): e0137429 (2015).
  6. *Kawamoto S, Maruya M, Kato LM, Suda W, Atarashi K, Doi Y, Tsutsui Y, Qin H, Honda K, Okada T, Hattori M, Fagarasan S:
    "Symbiotic regulatory loop between Foxp3+ T cells, IgA and gut microbiota"
    Immunity 41: 152-65 (2014).
  7. *Said HS, Suda W, Nakagome S, Chinen H, Oshima K, Kim S, Kimura R, Iraha A, Ishida H, Fujita J, Mano S, Morita H, Dohi T, Oota H, Hattori M:
    "Dysbiosis of salivary microbiota in inflammatory bowel diseases and its association with oral immunological biomarkers"
    DNA Res. 21: 15-25 (2014).
  8. *Atarashi K, Tanoue T, Oshima K, Suda W, Nagano Y, Kim S, Narushima S, Fukuda S, Hase K, Ohno H, Olle B, Taniguchi T, Morita H, Hattori M, Honda K:
    "Treg induction by a rationally selected mixture of Clostridia strains from the human microbiota"
    Nature 500: 232-236 (2013).
  9. *Kim SW, Suda W, Kim S, Oshima K, Fukuda S, Ohno H, Morita H, Hattori M:
    "Robustness of gut microbiota of healthy adult in response to probiotic intervention revealed by high-throughput pyrosequencing"
    DNA Res. 20: 241-253 (2013).Nature 499: 97-101 (2013).
  10. *Prakash T, Oshima K, Morita H, Fukuda S, Imaoka A, Kumar N, Sharma VK, Takahashi M, Saitou N, Taylor TD, Ohno H, Umesaki Y, Hattori M:
    "Complete genome sequences of rat and mouse segmented filamentous bacteria, a potent inducer of Th17 cell differentiation"
    Cell Host Microbe 10: 273-284 (2011).

Contact information

North Research Building,
1-7-22 Suehiro-cho, Tsurumi-ku,
Yokohama City, Kanagawa,
230-0045, Japan

Email: masahira.hattori [at]


Further information