・ 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. (2019)

2018

・ Stein RR, Tanoue T, Szabady RL, Bhattarai SK, Olle B, Norman JM, Suda W, Oshima K, Hattori M, Gerber GK, Sander C, Honda K, Bucci V. Computer-guided design of optimal microbial consortia for immune system modulation. Elife. Apr 17;7. (2018) (doi: 10.7554/eLife.30916)

2017

・ 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 T(H)1 cell induction and inflammation. Science. 358(6361):359-365. (2017) (doi: 10.1126/science.aan4526)

・ Kim S, Kim H, Yim YS, Ha S, Atarashi K, Tan TG, Longman RS, Honda K, Littman DR, Choi GB, Huh JR. Maternal gut bacteria promote neurodevelopment abnormalities in mouse offspring. Nature. 549(7673):528-532. (2017) (doi: 10.1038/nature23910)

・ Doki N, Suyama M, Sasajima S, Ota J, Igarashi A, Mimura I, Morita H, Fujioka Y, Sugiyama D, Nishikawa H, Shimazu Y, Suda W, Takeshita K, Atarashi K, Hatori M, Sato E, Watakabe-Inamoto K, Yoshioka K, Najima Y, Kobayashi T, Kakihana K, Takahashi N, Sakamaki H, Honda K, Ohashi K. Clinical impact of pre-transplant gut microbial diversity on outcomes of allogeneic hematopoietic stem cell transplantation. Ann Hematol. 96(9):1517-1523. (2017) (doi: 10.1007/s00277-017-3069-8)

・ Chai JN, Peng Y, Rengarajan S, Solomon BD, Ai TL, Shen Z, Perry JSA, Knoop KA, Tanoue T, Narushima S, Honda K, Elson CO, Newberry RD, Stappenbeck TS, Kau AL, Peterson DA, Fox JG, Hsieh CS. Helicobacter species are potent drivers of colonic T cell responses in homeostasis and inflammation. Sci Immunol. Jul 21;2(13). (2017) (doi: 10.1126/sciimmunol.aal5068)

2016

・ Thaiss CA, Levy M, Korem T, Dohnalová L, Shapiro H, Jaitin DA, David E, Winter DR, Gury-BenAri M, Tatirovsky E, Tuganbaev T, Federici S, Zmora N, Zeevi D, Dori-Bachash M, Pevsner-Fischer M, Kartvelishvily E, Brandis A, Harmelin A, Shibolet O, Halpern Z, Honda K, Amit I, Segal E, Elinav E. Microbiota Diurnal Rhythmicity Programs Host Transcriptome Oscillations. Cell. 167(6):1495-1510. (2016) (doi: 10.1016/j.cell.2016.11.003)

・ Jones L, Ho WQ, Ying S, Ramakrishna L, Srinivasan KG, Yurieva M, Ng WP, Subramaniam S, Hamadee NH, Joseph S, Dolpady J, Atarashi K, Honda K, Zolezzi F, Poidinger M, Lafaille JJ, Curotto de Lafaille MA. A subpopulation of high IL-21-producing CD4(+) T cells in Peyer's Patches is induced by the microbiota and regulates germinal centers. Sci Rep. 6:30784. (2016) (doi: 10.1038/srep30784) 

・ Kakihana K, Fujioka Y, Suda W, Najima Y, Kuwata G, Sasajima S, Mimura I, Morita H, Sugiyama D, Nishikawa H, Hattori M, Hino Y, Ikegawa S, Yamamoto K, Toya T, Doki N, Koizumi K, Honda K, Ohashi K. Fecal microbiota transplantation for patients with steroid-resistant acute graft-versus-host disease of the gut. Blood. 128(16):2083-2088. (2016) (doi: 10.1182/blood-2016-05-717652)

・ Tanoue T, Atarashi K, Honda K. Development and maintenance of intestinal regulatory T cells. Nat Rev Immunol. 16(5):295-309. (2016) (doi: 10.1038/nri.2016.36) Review.

・ Honda K, Littman DR. The microbiota in adaptive immune homeostasis and disease. Nature. 535: 75-84 (2016) (doi: 10.1038/nature18848) Review.

・ Bucci V, Tzen B, Li N, Simmons M, Tanoue T, Bogart E, Deng L, Yeliseyev V,Delaney ML, Liu Q, Olle B, Stein RR, Honda K, Bry L, Gerber GK. MDSINE: Microbial Dynamical Systems INference Engine for microbiome time-series analyses. Genome Biol.17(1):121.(2016) (doi: 10.1186/s13059-016-0980-6)
 

・ Saito T, Nishikawa H, Wada H, Nagano Y, Sugiyama D, Atarashi K, Maeda Y, Hamaguchi M, Ohkura N, Sato E, Nagase H, Nishimura J, Yamamoto H, Takiguchi S, Tanoue T, Suda W, Morita H, Hattori M, Honda K, Mori M, Doki Y, Sakaguchi S.  Two FOXP3(+)CD4(+) T cell subpopulations distinctly control the prognosis of colorectal cancers. Nat Med. 22(6):679-84 (2016) (doi: 10.1038/nm.4086)

・ Ramanan D, Bowcutt R, Lee SC, Tang MS, Kurtz ZD, Ding Y, Honda K, Gause WC, Blaser MJ, Bonneau RA, Lim YA, Loke P, Cadwell K. Helminth infection promotes colonization resistance via type 2 immunity. Science. 352(6285):608-12 (2016) (doi: 10.1126/science.aaf3229)

・ Mathewson ND, Jenq R, Mathew AV, Koenigsknecht M, Hanash A, Toubai T, Oravecz-Wilson K, Wu SR, Sun Y, Rossi C, Fujiwara H, Byun J, Shono Y, Lindemans C, Calafiore M, Schmidt TC, Honda K, Young VB, Pennathur S, van den Brink M, Reddy P. Gut microbiome-derived metabolites modulate intestinal epithelial cell damage and mitigate graft-versus-host disease. Nat Immunol. 17(5):505-13 (2016) (doi: 10.1038/ni.3400)

2015

・ 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(2):367-80 (2015) (doi: 10.1016/j.cell.2015.08.058)

→ Keio Research Highlights: Sticky bacteria switch on immune cells.

・ Ohnmacht C, Park JH, Cording S, Wing JB, Atarashi K, Obata Y, Gaboriau-Routhiau V, Marques R, Dulauroy S, Fedoseeva M, Busslinger M, Cerf-Bensussan N, Boneca IG, Voehringer D, Hase K, Honda K, Sakaguchi S, Eberl G. The microbiota regulates type 2 immunity through RORγt+ T cells. Science. 349(6251):989-93. (2015) (doi: 10.1126/science.aac4263)

・ Horai R, Zárate-Bladés CR, Dillenburg-Pilla P, Chen J, Kielczewski JL, Silver PB, Jittayasothorn Y, Chan CC, Yamane H, Honda K, Caspi RR. Microbiota-Dependent Activation of an Autoreactive T Cell Receptor Provokes Autoimmunity in an Immunologically Privileged Site. Immunity. 43:343-53. (2015) (doi: 10.1016/j.immuni.2015.07.014)

・ Honda K. TFH-IgA responses keep microbiota in check. Cell Host Microbe. 17(2):144-6. (2015) (doi: 10.1016/j.chom.2015.01.009)

2014

・ Narushima S, Sugiura Y, Oshima K, Atarashi K, Hattori M, Suematsu M, Honda K. Characterization of the 17 strains of regulatory T cell-inducing human-derived Clostridia. Gut Microbes. 5(3):333-9. (2014) (doi: 10.4161/gmic.28572)

2013

・ Furusawa Y, Obata Y, Fukuda S, Endo TA, Nakato G, Takahashi D, Nakanishi Y, Uetake C, Kato K, Kato T, Takahashi M, Fukuda NN, Murakami S, Miyauchi E, Hino S, Atarashi K, Onawa S, Fujimura Y, Lockett T, Clarke JM, Topping DL, Tomita M, Hori S, Ohara O, Morita T, Koseki H, Kikuchi J, Honda K, Hase K, Ohno H. Commensal microbe-derived butyrate induces the differentiation of colonic regulatory T cells. Nature. 504(7480):446-50. (2013) (doi: 10.1038/nature12721)

・ 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) (doi: 10.1038/nature12331)

・ Yoshimoto S, Loo TM, Atarashi K, Kanda H, Sato S, Oyadomari S, Iwakura Y, Oshima K, Morita H, Hattori M, Honda K, Ishikawa Y, Hara E, Ohtani N. Obesity-induced gut microbial metabolite promotes liver cancer through senescence secretome. Nature 499:97-101. (2013) (doi: 10.1038/nature12347)

・ Schlitzer A, McGovern N, Teo P, Zelante T, Atarashi K, Low D, Ho AW, See P, Shin A, Wasan PS, Hoeffel G, Malleret B, Heiseke A, Chew S, Jardine L, Purvis HA, Hilkens CM, Tam J, Poidinger M, Stanley ER, Krug AB, Renia L, Sivasankar B, Ng LG, Collin M, Ricciardi-Castagnoli P, Honda K, Haniffa M, Ginhoux F. IRF4 transcription factor-dependent CD11b+ dendritic cells in human and mouse control mucosal IL-17 cytokine responses. Immunity. 38(5):970-83. (2013) (doi: 10.1016/j.immuni.2013.04.011)

・ Mucida D, Husain MM, Muroi S, van Wijk F, Shinnakasu R, Naoe Y, Reis BS, Huang Y, Lambolez F, Docherty M, Attinger A, Shui JW, Kim G, Lena CJ, Sakaguchi S, Miyamoto C, Wang P, Atarashi K, Park Y, Nakayama T, Honda K, Ellmeier W, Kronenberg M, Taniuchi I, Cheroutre H. Transcriptional reprogramming of mature CD4⁺helper T cells generates distinct MHC class II-restricted cytotoxic T lymphocytes. Nat Immunol. 14:281-9. (2013) (doi: 10.1038/ni.2523)

2012

・ Honda K. IL-22 from T cells: better late than never. Immunity. 37(6):952-4. (2012) (doi: 10.1016/j.immuni.2012.11.006)

・ Ivanov II, Honda K. Intestinal commensal microbes as immune modulators. Cell Host Microbe. 12:496-508. (2012) (doi: 10.1016/j.chom.2012.09.009) Review.

・ Honda K, Littman DR. The microbiome in infectious disease and inflammation. Ann Rev Immunol. 30:759-95. (2012) (doi: 10.1146/annurev-immunol-020711-074937)

2011

・ Honda K. Porphyromonas gingivalis sinks teeth into the oral microbiota and periodontal disease. Cell Host Microbe. 10(5):423-5. (2011) (doi: 10.1016/j.chom.2011.10.008)
 

・ Atarashi K, Tanoue T, Shima T, Imaoka A, Kuwahara T, Momose Y, Cheng G, Yamasaki S, Saito T, Ohba Y, Taniguchi T, Takeda K, Hori S, Ivanov II, Umesaki Y, Itoh K and Honda K. Induction of colonic regulatory T cells by indigenous Clostridium species. Science. 331(6015):337-341 (2011) (doi: 10.1126/science.1198469)

2009

・ 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(3):485-98. (2009) (doi: 10.1016/j.cell.2009.09.033)

・ Yanai H, Ban T, Wang Z, Choi MK, Kawamura T, Negishi H, Nakasato M, Lu Y, Hangai S, Koshiba R, Savitsky D, Ronfani L, Akira S, Bianchi ME, Honda K, Tamura T, Kodama T, Taniguchi T. HMGB proteins function as universal sentinels for nucleic-acid-mediated innate immune responses. Nature. 462(7269):99-103. (2009) (doi: 10.1016/j.vaccine.2010.09.026)

2008

・ Negishi H, Osawa T, Ogami K, Ouyang X, Sakaguchi S, Koshiba R, Yanai H, Seko Y, Shitara H, Bishop K, Yonekawa H, Tamura T, Kaisho T, Taya C, Taniguchi T, Honda K. A critical link between Toll-like receptor 3 and type II interferon signaling pathways in antiviral innate immunity. Proc Natl Acad Sci U S A. 105(51):20446-51. (2008) (doi: 10.1073/pnas.0810372105)

・ Atarashi K, Nishimura J, Shima T, Umesaki Y, Yamamoto M, Onoue M, Yagita H, Ishii N, Evans R, Honda K, Takeda K. ATP drives lamina propria T(H)17 cell differentiation. Nature 455(7214):808-12. (2008) (doi: 10.1038/nature07240)

・ Kano SI, Sato K, Morishita Y, Vollstedt S, Kim S, Bishop K, Honda K, Kubo M, Taniguchi T. The contribution of transcription factor IRF1 to the interferon-gamma-interleukin 12 signaling axis and T(H)1 versus T(H)-17 differentiation of CD4(+) T cells. Nature Immunology 9(1): 34–41. (2008) (doi: 10.1038/ni1538)

2007

・ Takaoka A, Wang Z, Choi MK, Yanai H, Negishi H, Ban T, Lu Y, Miyagishi M, Kodama T, Honda K, Ohba Y, Taniguchi T. DAI (DLM-1/ZBP1) is a cytosolic DNA sensor and an activator of innate immune response. Nature 448(7152):501-5. (2007) (doi: 10.1038/nature06013)

・ Yanai H, Chen HM, Inuzuka T, Kondo S, Mak TW, Takaoka A, Honda K, Taniguchi T. Role of IRF5 transcription factor in antiviral immunity and tumor suppression. Proc Natl Acad Sci U S A. 104:3402-3407. (2007) (doi: 10.1073/pnas.0611559104)

2006

・ Negishi H, Fujita Y, Yanai H, Sakaguchi S, Ouyang X, Shinohara M, Takayanagi H, Ohba Y, Taniguchi T, Honda K. Evidence for licensing of IFN-γ-induced IRF1 transcription factor by MyD88 in TLR-dependent gene induction program.  Proc Natl Acad Sci U S A. 103(41):15136-15141. (2006) (doi: 10.1073/pnas.0607181103)

・ Honda K, Takaoka A, Taniguchi T. Type I interferon gene induction by the interferon regulatory factor family of transcription factors.  Immunity 25(3):349-360. (2006) (doi: 10.1016/j.immuni.2006.08.009)

・ Honda K, Taniguchi T.  IRFs: master regulators of signalling by Toll-like receptors and cytosolic pattern-recognition receptors. Nature Reviews Immunology 6(9):644-658. (2006)(doi: 10.1038/nri1900) Review.

2005

・ Negishi H, Ohba Y, Yanai H, Takaoka A, Honma K, Yui K, Matsuyama T, Taniguchi T, Honda K.  Negative regulation of Toll-like-receptor signaling by IRF-4.  Proc Natl Acad Sci U S A. 102(44):15989-15994. (2005) (doi: 10.1073/pnas.0508327102)

・ Takaoka A, Yanai H, Kondo S, Duncan G, Negishi H, Mizutani T, Kano S, Honda K, Ohba Y, Mak TW, Taniguchi T. Integral role of IRF-5 in the gene induction programme activated by Toll-like receptors. Nature 434(7030):243-249. (2005) (doi: 10.1038/nature03308)

・ Honda K, Yanai H, Negishi H, Asagiri M, Sato M, Mizutani T, Shimada N, Ohba Y, Takaoka A, Yoshida N, Taniguchi T. IRF-7 is the master regulator of type-I interferon-dependent immune responses. Nature 434(7034):772-777. (2005) (doi: 10.1038/nature03464)

・ Honda K, Ohba Y, Yanai H, Negishi H, Mizutani T, Takaoka A, Taya C, Taniguchi T. Spatiotemporal regulation of MyD88-IRF-7 signalling for robust type-I interferon induction. Nature 434(7036):1035-1040. (2005) (doi: 10.1038/nature03547)

2004

・ Honda K, Yanai H, Mizutani T, Negishi H, Shimada N, Suzuki N, Ohba Y, Takaoka A, Yeh WC, Taniguchi T. Role of a transductional- transcriptional processor complex involving MyD88 and IRF-7 in Toll-like receptor signaling. Proc Natl Acad Sci U S A. 101(43):15416-15421. (2004) (doi: 10.1073/pnas.0406933101)

・ Honda K, Mizutani T, Taniguchi T. Negative regulation of IFN-α/β signaling by IFN regulatory factor 2 for homeostatic development of dendritic cells. Proc Natl Acad Sci U S A. 101(8):2416-2421. (2004)

2003

・ Takaoka A, Hayakawa S, Yanai H, Stoiber D, Negishi H, Kikuchi H, Sasaki S, Imai K, Shibue T, Honda K, Taniguchi T. Integration of interferon-α/β signalling to p53 responses in tumour suppression and antiviral defence. Nature 424(6948):516-523. (2003) (doi: 10.1038/nature01850)

・ Honda K, Sakaguchi S, Nakajima C, Watanabe A, Yanai H, Matsumoto M, Ohteki T, Kaisho T, Takaoka A, Akira S, Seya T, Taniguchi T. Selective contribution of IFN-α/β signaling to the maturation of dendritic cells induced by double-stranded RNA or viral infection. Proc Natl Acad Sci U S A. 100(19):10872-10877. (2003) (doi: 10.1073/pnas.1934678100)

2001

・ Honda K, Nakano H, Yoshida H, Nishikawa S, Rennert P, Ikuta K, Tamechika M, Yamaguchi K, Fukumoto T, Chiba T, and Nishikawa SI. Molecular basis for hematopoietic / mesenchymal interaction during initiation of Peyer’s patch organogenesis. J. Exp. Med. 193(5):621-630 (2001)

Publications

Honda Lab

Department of Microbiology and Immunology

School of Medicine

Keio University 

Laboratory for Gut Homeostasis

RIKEN Center for Integrative Medical Science