RIKEN Center for Integrative Medical Sciences Laboratory for Gut Homeostasis
Team Director: Kenya Honda (M.D., Ph.D)
Research Summary

Trillions of microorganisms, termed the “microbiota”, reside in the mammalian gastrointestinal tract, and collectively generate thousands of small molecules. These microbial metabolites can accumulate both locally and systemically and potentially influence nearly all aspects of mammalian physiology, including the regulation of immune system, metabolism, and nervous systems. To understand the role of gut microbiota in host physiology, we are doing research using various approaches and techniques.
Main Research Fields
- Medicine, Dentistry & Pharmacy
Related Research Fields
- Chemistry
- Biological Sciences
- Biology
Keywords
- Gut microflora
- Bacteria-derived metabolites
- Longevity
- Enteric and central nervous system
- Mucosal immune system
Selected Publications
Papers with an asterisk(*) are based on research conducted outside of RIKEN.
- 1.
Furuichi M, Kawaguchi T, Pust MM, Yasuma-Mitobe K, Plichta DR, Hasegawa N, Ohya T, Bhattarai SK, Sasajima S, Aoto Y, Tuganbaev T, Yaginuma M, Ueda M, Okahashi N, Amafuji K, Kiridoshi Y, Sugita K, Stražar M, Avila-Pacheco J, Pierce K, Clish CB, Skelly AN, Hattori M, Nakamoto N, Caballero S, Norman JM, Olle B, Tanoue T, Suda W, Arita M, Bucci V, Atarashi K, Xavier RJ, Honda K:
"Commensal consortia decolonize Enterobacteriaceae via ecological control."
Nature, 633:878-886(2024). - 2.
Johansen J, Atarashi K, Arai Y, Hirose N, Sørensen SJ, Vatanen T, Knip M, Honda K, Xavier RJ, Rasmussen S, Plichta DR:
"Centenarians have a diverse gut virome with the potential to modulate metabolism and promote healthy lifespan"
Nat Microbiol., 8:1064-1078(2023). - 3.
Sato Y, Atarashi K, Plichta DR, Arai Y, Sasajima S, Kearney SM, Suda W, Takeshita K, Sasaki T, Okamoto S, Skelly AN, Okamura Y, Vlamakis H, Li Y, Tanoue T, Takei H, Nittono H, Narushima S, Irie J, Itoh H, Moriya K, Sugiura Y, Suematsu M, Moritoki N, Shibata S, Littman DR, Fischbach MA, Uwamino Y, Inoue T, Honda A, Hattori M, Murai T, Xavier RJ, Hirose N, Honda K:
"Novel bile acid biosynthetic pathways are enriched in the microbiome of centenarians."
Nature, 599:458-464(2021). - 4.
Li Y, Watanabe E, Kawashima Y, Plichta DR, Wang Z, Ujike M, Ang QY, Wu R, Furuichi M, Takeshita K, Yoshida K, Nishiyama K, Kearney SM, Suda W, Hattori M, Sasajima S, Matsunaga T, Zhang X, Watanabe K, Fujishiro J, Norman JM, Olle B, Matsuyama S, Namkoong H, Uwamino Y, Ishii M, Fukunaga K, Hasegawa N, Ohara O, Xavier RJ, Atarashi K, Honda K:
"Identification of trypsin-degrading commensals in the large intestine."
Nature, 609:582-589(2022). - 5.
Ivanov II, Tuganbaev T, Skelly AN, Honda K:
"T Cell Responses to the Microbiota."
Annu Rev Immunol., 40:559-587(2022). - 6.
Tanoue T, Morita S, Plichta DR, Skelly AN, Suda W, Sugiura Y, Narushima S, Vlamakis H, Motoo I, Sugita K, Shiota A, Takeshita K, Yasuma-Mitobe K, Riethmacher D, Kaisho T, Norman JM, Mucida D, Suematsu M, Yaguchi T, Bucci V, Inoue T, Kawakami Y, Olle B, Roberts B, Hattori M, Xavier RJ, Atarashi K, Honda K:
"A defined commensal consortium elicits CD8 T cells and anti-cancer immunity."
Nature, 565: 600-605(2019). - 7.
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). - 8.
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 S, 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). - 9.
* Atarashi K, Tanoue T, Oshima K, Suda W, Nagano Y, Nishikawa H, Fukuda S, Saito T, Narushima S, Hase K, Kim S, Fritz JV, Wilmes P, Ueha S, Matsushima K, Ohno H, Olle B, Sakaguchi S, 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). - 10.
* Ivanov II, Atarashi K, Manel N, Brodie EL, Shima T, Karaoz U, Wei D, Goldfarb KC, Santee CA, Lynch SV, Tanoue T, Imaoka A, Itoh K, Takeda K, Umesaki Y, Honda K, Littman DR:
"Induction of intestinal Th17 cells by segmented filamentous bacteria."
Cell, 139:485-98 (2009).
Recent Research Results
Feb. 19, 2016
Good neighbors make good defensesSep. 27, 2013
Intestinal bacteria show ‘community spirit’
Related Links
Lab Members
Principal investigator
- Kenya Honda
- Team Director
Core members
- Prabha Tiwari
- Senior Visiting Scientist
- Hui Fang
- Postdoctoral Researcher
- Koji Atarashi
- Senior Visiting Scientist
- Takeshi Tanoue
- Senior Visiting Scientist
- Kozue Takeshita
- Senior Visiting Scientist
- Hideki Terajima
- Visiting Scientist
- Munehiro Furuichi
- Visiting Scientist
- Timur Tuganbaev
- Visiting Scientist
- Saki Kasai
- Technical Staff II
- Xiaoxi Zhang
- Student Trainee
- Koji Yoshida
- Student Trainee
Contact Information
4F, North Research Building
1-7-22 Suehiro-cho, Tsurumi-ku,
Yokohama City, Kanagawa,
230-0045, Japan
Tel: +81-(0)45-503-9682
Email: kenya.honda@riken.jp