Research Summary

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

• 

  Jan. 23, 2023
  Gut microbe degrades digestive enzyme trypsin in the large intestine

• 

  Dec. 3, 2021
  The distinct microbiome of centenarians may partially account for their longevity

• 

  Feb. 19, 2016
  Good neighbors make good defenses

• 

  Sep. 27, 2013
  Intestinal bacteria show ‘community spirit’

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