Shinji Fukuda

ORCID

Publication Activity (10 Years)

Years Active: 2019-2024
Publications (10 Years): 44

Top Venues

mSystems

Science advances

Nature communications

Microbiology resource announcements

Metabologenomics, Inc.

This page only lists publications with an associated author ORCID identifier.

Affiliation History

Metabologenomics, Inc. Mar 18 2015

Japan

CEO

Keio University Jun 01 2012

Japan

Project Professor :: Institute for Advanced Biosciences

Publications

Tomoya Tsukimi, Nozomu Obana, Suguru Shigemori, Kazuharu Arakawa, Eiji Miyauchi, Jiayue Yang, Isaiah Song, Yujin Ashino, Masataka Wakayama, Tomoyoshi Soga, Masaru Tomita, Hiroshi Ohno, Hirotada Mori, Shinji Fukuda
Genetic mutation in Escherichia coli genome during adaptation to the murine intestine is optimized for the host diet. mSystems 9 (2) (2024)
Isaiah Song, Jiayue Yang, Misa Saito, Tenagy Hartanto, Yasunori Nakayama, Takeshi Ichinohe, Shinji Fukuda
Prebiotic inulin ameliorates SARS-CoV-2 infection in hamsters by modulating the gut microbiome. NPJ science of food 8 (1) (2024)
Tomoya Tsukimi, Nozomu Obana, Suguru Shigemori, Kazuharu Arakawa, Eiji Miyauchi, Jiayue Yang, Isaiah Song, Yujin Ashino, Masataka Wakayama, Tomoyoshi Soga, Masaru Tomita, Hiroshi Ohno, Hirotada Mori, Shinji Fukuda
Genetic mutation in Escherichia coli genome during adaptation to the murine intestine is optimized for the host diet. mSystems (2024)
Tomoya Tsukimi, Nozomu Obana, Suguru Shigemori, Kazuharu Arakawa, Eiji Miyauchi, Jiayue Yang, Isaiah Song, Yujin Ashino, Masataka Wakayama, Tomoyoshi Soga, Masaru Tomita, Hiroshi Ohno, Hirotada Mori, Shinji Fukuda
Genetic mutation in Escherichia coli genome during adaptation to the murine intestine is optimized for the host diet. mSystems 9 (2) (2024)
Isaiah Song, Jiayue Yang, Misa Saito, Tenagy Hartanto, Yasunori Nakayama, Takeshi Ichinohe, Shinji Fukuda
Prebiotic inulin ameliorates SARS-CoV-2 infection in hamsters by modulating the gut microbiome. NPJ science of food 8 (1) (2024)
Alex Steimle, Mareike Neumann, Erica T Grant, Stéphanie Willieme, Alessandro De Sciscio, Amy Parrish, Markus Ollert, Eiji Miyauchi, Tomoyoshi Soga, Shinji Fukuda, Hiroshi Ohno, Mahesh S Desai
Gut microbial factors predict disease severity in a mouse model of multiple sclerosis. Nature microbiology (2024)
Tomoya Tsukimi, Nozomu Obana, Suguru Shigemori, Kazuharu Arakawa, Eiji Miyauchi, Jiayue Yang, Isaiah Song, Yujin Ashino, Masataka Wakayama, Tomoyoshi Soga, Masaru Tomita, Hiroshi Ohno, Hirotada Mori, Shinji Fukuda
Genetic mutation in Escherichia coli genome during adaptation to the murine intestine is optimized for the host diet. mSystems 9 (2) (2024)
Alex Steimle, Mareike Neumann, Erica T Grant, Stéphanie Willieme, Alessandro De Sciscio, Amy Parrish, Markus Ollert, Eiji Miyauchi, Tomoyoshi Soga, Shinji Fukuda, Hiroshi Ohno, Mahesh S Desai
Gut microbial factors predict disease severity in a mouse model of multiple sclerosis. Nature microbiology (2024)
Sayaka Mizutani, Ayako Tamaki, Satoshi Shiba, Felix Salim, Masayoshi Yamada, Hiroyuki Takamaru, Takeshi Nakajima, Naohisa Yoshida, Shoko Ikuta, Tatsuo Yachida, Tatsuhiro Shibata, Tomoyoshi Soga, Yutaka Saito, Shinji Fukuda, Hideki Ishikawa, Takuji Yamada, Hirotsugu Shiroma
Dynamics of the gut microbiome in FAP patients undergoing intensive endoscopic reduction of polyp burden. Gut (2024)
Minami Nagai, Miyu Moriyama, Chiharu Ishii, Hirotake Mori, Hikaru Watanabe, Taku Nakahara, Takuji Yamada, Dai Ishikawa, Takamasa Ishikawa, Akiyoshi Hirayama, Ikuo Kimura, Akihito Nagahara, Toshio Naito, Shinji Fukuda, Takeshi Ichinohe
High body temperature increases gut microbiota-dependent host resistance to influenza A virus and SARS-CoV-2 infection. Nature communications 14 (1) (2023)
Shimpei Kawamoto, Ken Uemura, Nozomi Hori, Lena Takayasu, Yusuke Konishi, Kazutaka Katoh, Tomonori Matsumoto, Masae Suzuki, Yusuke Sakai, Tatsuyuki Matsudaira, Takahiro Adachi, Naoko Ohtani, Daron M Standley, Wataru Suda, Shinji Fukuda, Eiji Hara
Bacterial induction of B cell senescence promotes age-related changes in the gut microbiota. Nature cell biology (2023)
Yuxin Wang, Tatsuya Morishima, Maiko Sezaki, Ryo Sato, Gaku Nakato, Shinji Fukuda, Kouji Kobiyama, Ken J Ishii, Yuhua Li, Hitoshi Takizawa
Akkermansia muciniphila induces slow extramedullary hematopoiesis via cooperative IL-1R/TLR signals. EMBO reports (2023)
Minami Nagai, Miyu Moriyama, Chiharu Ishii, Hirotake Mori, Hikaru Watanabe, Taku Nakahara, Takuji Yamada, Dai Ishikawa, Takamasa Ishikawa, Akiyoshi Hirayama, Ikuo Kimura, Akihito Nagahara, Toshio Naito, Shinji Fukuda, Takeshi Ichinohe
High body temperature increases gut microbiota-dependent host resistance to influenza A virus and SARS-CoV-2 infection. Nature communications 14 (1) (2023)
Xiaolei Zhu, Shinji Sakamoto, Chiharu Ishii, Matthew D Smith, Koki Ito, Mizuho Obayashi, Lisa Unger, Yuto Hasegawa, Shunya Kurokawa, Taishiro Kishimoto, Hui Li, Shinya Hatano, Tza-Huei Wang, Yasunobu Yoshikai, Shin-Ichi Kano, Shinji Fukuda, Kenji Sanada, Peter A Calabresi, Atsushi Kamiya
Dectin-1 signaling on colonic γδ T cells promotes psychosocial stress responses. Nature immunology (2023)
Hiroto Morita, Chie Kano, Chiharu Ishii, Noriko Kagata, Takamasa Ishikawa, Akiyoshi Hirayama, Yoshihide Uchiyama, Susumu Hara, Teppei Nakamura, Shinji Fukuda
Bacteroides uniformis and its preferred substrate, α-cyclodextrin, enhance endurance exercise performance in mice and human males. Science advances 9 (4) (2023)
Kota Oshibuchi, Jiayue Yang, Nozomu Obana, Shinji Fukuda, Kazuharu Arakawa
Complete genome sequence of Solobacterium moorei JCM 10645 T isolated from a human stool sample. Microbiology resource announcements (2023)
Hiroto Morita, Chie Kano, Chiharu Ishii, Noriko Kagata, Takamasa Ishikawa, Akiyoshi Hirayama, Yoshihide Uchiyama, Susumu Hara, Teppei Nakamura, Shinji Fukuda
Bacteroides uniformis and its preferred substrate, α-cyclodextrin, enhance endurance exercise performance in mice and human males. Science advances 9 (4) (2023)
Kazuma Yama, Yuichiro Nishimoto, Kota Kumagai, Ryutaro Jo, Minori Harada, Yuki Maruyama, Yuto Aita, Narumi Fujii, Takuya Inokuchi, Ryosuke Kawamata, Misato Sako, Yuko Ichiba, Kota Tsutsumi, Mitsuo Kimura, Shinnosuke Murakami, Yasushi Kakizawa, Takashi Kumagai, Takuji Yamada, Shinji Fukuda
Dysbiosis of oral microbiome persists after dental treatment-induced remission of periodontal disease and dental caries. mSystems (2023)
Hiroto Morita, Chie Kano, Chiharu Ishii, Noriko Kagata, Takamasa Ishikawa, Akiyoshi Hirayama, Yoshihide Uchiyama, Susumu Hara, Teppei Nakamura, Shinji Fukuda
Bacteroides uniformis and its preferred substrate, α-cyclodextrin, enhance endurance exercise performance in mice and human males. Science advances 9 (4) (2023)
Minami Nagai, Miyu Moriyama, Chiharu Ishii, Hirotake Mori, Hikaru Watanabe, Taku Nakahara, Takuji Yamada, Dai Ishikawa, Takamasa Ishikawa, Akiyoshi Hirayama, Ikuo Kimura, Akihito Nagahara, Toshio Naito, Shinji Fukuda, Takeshi Ichinohe
High body temperature increases gut microbiota-dependent host resistance to influenza A virus and SARS-CoV-2 infection. Nature communications 14 (1) (2023)
Hiroto Morita, Chie Kano, Chiharu Ishii, Noriko Kagata, Takamasa Ishikawa, Akiyoshi Hirayama, Yoshihide Uchiyama, Susumu Hara, Teppei Nakamura, Shinji Fukuda
Bacteroides uniformis and its preferred substrate, α-cyclodextrin, enhance endurance exercise performance in mice and human males. Science advances 9 (4) (2023)
Shimpei Kawamoto, Ken Uemura, Nozomi Hori, Lena Takayasu, Yusuke Konishi, Kazutaka Katoh, Tomonori Matsumoto, Masae Suzuki, Yusuke Sakai, Tatsuyuki Matsudaira, Takahiro Adachi, Naoko Ohtani, Daron M Standley, Wataru Suda, Shinji Fukuda, Eiji Hara
Bacterial induction of B cell senescence promotes age-related changes in the gut microbiota. Nature cell biology (2023)
Akimasa Kure, Tomoya Tsukimi, Chiharu Ishii, Wanping Aw, Nozomu Obana, Gaku Nakato, Akiyoshi Hirayama, Haruna Kawano, Toshiyuki China, Fumitaka Shimizu, Masayoshi Nagata, Shinji Isotani, Satoru Muto, Shigeo Horie, Shinji Fukuda
Gut environment changes due to androgen deprivation therapy in patients with prostate cancer. Prostate cancer and prostatic diseases (2022)
Sayaka Ishihara, Tsuyoshi Sato, Noriyuki Fujikado, Haruka Miyazaki, Takayuki Yoshimoto, Hiromitsu Yamamoto, Shinji Fukuda, Koko Katagiri
Rap1 prevents colitogenic Th17 cell expansion and facilitates Treg cell differentiation and distal TCR signaling. Communications biology 5 (1) (2022)
Maiko Sezaki, Yoshikazu Hayashi, Gaku Nakato, Yuxin Wang, Sayuri Nakata, Subinoy Biswas, Tatsuya Morishima, Md Fakruddin, Jieun Moon, Soyeon Ahn, Pilhan Kim, Yuji Miyamoto, Hideo Baba, Shinji Fukuda, Hitoshi Takizawa
Hematopoietic stem and progenitor cells integrate microbial signals to promote post-inflammation gut tissue repair. The EMBO journal 41 (22) (2022)
Hirotsugu Shiroma, Satoshi Shiba, Pande Putu Erawijantari, Hiroyuki Takamaru, Masayoshi Yamada, Taku Sakamoto, Yukihide Kanemitsu, Sayaka Mizutani, Tomoyoshi Soga, Yutaka Saito, Tatsuhiro Shibata, Shinji Fukuda, Shinichi Yachida, Takuji Yamada
Surgical Treatment for Colorectal Cancer Partially Restores Gut Microbiome and Metabolome Traits. mSystems 7 (2) (2022)
Katsuma Miyaho, Kenji Sanada, Shunya Kurokawa, Arisa Tanaka, Tomoyuki Tachibana, Chiharu Ishii, Yoshihiro Noda, Shinichiro Nakajima, Shinji Fukuda, Masaru Mimura, Taishiro Kishimoto, Akira Iwanami
The Potential Impact of Age on Gut Microbiota in Patients with Major Depressive Disorder: A Secondary Analysis of the Prospective Observational Study. Journal of personalized medicine 12 (11) (2022)
Katsuma Miyaho, Kenji Sanada, Shunya Kurokawa, Arisa Tanaka, Tomoyuki Tachibana, Chiharu Ishii, Yoshihiro Noda, Shinichiro Nakajima, Shinji Fukuda, Masaru Mimura, Taishiro Kishimoto, Akira Iwanami
The Potential Impact of Age on Gut Microbiota in Patients with Major Depressive Disorder: A Secondary Analysis of the Prospective Observational Study. Journal of personalized medicine 12 (11) (2022)
Ryota Yamagishi, Fumitaka Kamachi, Masaru Nakamura, Shota Yamazaki, Tomonori Kamiya, Masaki Takasugi, Yi Cheng, Yoshiki Nonaka, Yoshimi Yukawa-Muto, Le Thi Thanh Thuy, Yohsuke Harada, Tatsuya Arai, Tze Mun Loo, Shin Yoshimoto, Tatsuya Ando, Masahiro Nakajima, Hayao Taguchi, Takamasa Ishikawa, Hisaya Akiba, Sachiko Miyake, Masato Kubo, Yoichiro Iwakura, Shinji Fukuda, Wei-Yu Chen, Norifumi Kawada, Alexander Y Rudensky, Susumu Nakae, Eiji Hara, Naoko Ohtani
Gasdermin D-mediated release of IL-33 from senescent hepatic stellate cells promotes obesity-associated hepatocellular carcinoma. Science immunology 7 (72) (2022)
Shinri Sato, Eisuke Shimizu, Jingliang He, Mamoru Ogawa, Kazuki Asai, Hiroyuki Yazu, Robert Rusch, Mio Yamane, Fan Yang, Shinji Fukuda, Yutaka Kawakami, Masayuki Ohta, Yoko Ogawa
Positive Effects of Oral Antibiotic Administration in Murine Chronic Graft-Versus-Host Disease. International journal of molecular sciences 22 (7) (2021)
Samuel Connell, Motoko Kawashima, Shigeru Nakamura, Toshihiro Imada, Hiromitsu Yamamoto, Masayuki Ohta, Shinji Fukuda
Lactoferrin Ameliorates Dry Eye Disease Potentially through Enhancement of Short-Chain Fatty Acid Production by Gut Microbiota in Mice. International journal of molecular sciences 22 (22) (2021)
Atsuo Nakamura, Shin Kurihara, Daisuke Takahashi, Wakana Ohashi, Yutaka Nakamura, Shunsuke Kimura, Masayoshi Onuki, Aiko Kume, Yukiko Sasazawa, Yukihiro Furusawa, Yuuki Obata, Shinji Fukuda, Shinji Saiki, Mitsuharu Matsumoto, Koji Hase
Symbiotic polyamine metabolism regulates epithelial proliferation and macrophage differentiation in the colon. Nature communications 12 (1) (2021)
Ryuta Ejima, Masahiro Akiyama, Hiroki Sato, Sawako Tomioka, Kyosuke Yakabe, Tatsuki Kimizuka, Natsumi Seki, Yumiko Fujimura, Akiyoshi Hirayama, Shinji Fukuda, Koji Hase, Yun-Gi Kim
Seaweed Dietary Fiber Sodium Alginate Suppresses the Migration of Colonic Inflammatory Monocytes and Diet-Induced Metabolic Syndrome via the Gut Microbiota. Nutrients 13 (8) (2021)
Haruno Takahashi, Jiayue Yang, Hiromitsu Yamamoto, Shinji Fukuda, Kazuharu Arakawa
Complete Genome Sequence of Adlercreutzia equolifaciens subsp. celatus DSM 18785. Microbiology resource announcements 10 (19) (2021)
Yoko Yokoyama, Kawori Shinohara, Naho Kitamura, Anna Nakamura, Ai Onoue, Kazuki Tanaka, Akiyoshi Hirayama, Wanping Aw, Shigeru Nakamura, Yoko Ogawa, Shinji Fukuda, Masayuki Ohta, Mitsuhiro Watanabe
Metabolic Effects of Bee Larva-Derived Protein in Mice: Assessment of an Alternative Protein Source. Foods (Basel, Switzerland) 10 (11) (2021)
Ki-Hyeon Seong, Nhung Hong Ly, Yuki Katou, Naoko Yokota, Ryuichiro Nakato, Shinnosuke Murakami, Akiyoshi Hirayama, Shinji Fukuda, Siu Kang, Tomoyoshi Soga, Katsuhiko Shirahige, Shunsuke Ishii
Publisher Correction: Paternal restraint stress affects offspring metabolism via ATF-2 dependent mechanisms in Drosophila melanogaster germ cells. Communications biology 3 (1) (2020)
Hikaru Inoue, Sayaka Shibata, Konosuke Ii, Joe Inoue, Shinji Fukuda, Kazuharu Arakawa
Complete Genome Sequence of Bifidobacterium longum Strain Jih1, Isolated from Human Feces. Microbiology resource announcements 9 (22) (2020)
Pande Putu Erawijantari, Sayaka Mizutani, Hirotsugu Shiroma, Satoshi Shiba, Takeshi Nakajima, Taku Sakamoto, Yutaka Saito, Shinji Fukuda, Takuji Yamada
Influence of gastrectomy for gastric cancer treatment on faecal microbiome and metabolome profiles. Gut 69 (8) (2020)
Hiroshi Fujishima, Naoko Okada, Kenji Matsumoto, Eisuke Shimizu, Shinji Fukuda, Masaru Tomita
Conjunctival Injection Reduction in Patients with Atopic Keratoconjunctivitis Due to Synergic Effect of Bovine Enteric-Coated Lactoferrin in 0.1% Tacrolimus Ophthalmic Suspension. Journal of clinical medicine 9 (10) (2020)
Eikan Mishima, Mariko Ichijo, Takeshi Kawabe, Koichi Kikuchi, Yukako Akiyama, Takafumi Toyohara, Takehiro Suzuki, Chitose Suzuki, Atsuko Asao, Naoto Ishii, Shinji Fukuda, Takaaki Abe
Germ-Free Conditions Modulate Host Purine Metabolism, Exacerbating Adenine-Induced Kidney Damage. Toxins 12 (9) (2020)
Hiroko Nagao-Kitamoto, Jhansi L Leslie, Sho Kitamoto, Chunsheng Jin, Kristina A Thomsson, Merritt G Gillilland, Peter Kuffa, Yoshiyuki Goto, Robert R Jenq, Chiharu Ishii, Akiyoshi Hirayama, Anna M Seekatz, Eric C Martens, Kathryn A Eaton, John Y Kao, Shinji Fukuda, Peter D R Higgins, Niclas G Karlsson, Vincent B Young, Nobuhiko Kamada
Interleukin-22-mediated host glycosylation prevents Clostridioides difficile infection by modulating the metabolic activity of the gut microbiota. Nature medicine 26 (4) (2020)
Ki-Hyeon Seong, Nhung Hong Ly, Yuki Katou, Naoko Yokota, Ryuichiro Nakato, Shinnosuke Murakami, Akiyoshi Hirayama, Shinji Fukuda, Siu Kang, Tomoyoshi Soga, Katsuhiko Shirahige, Shunsuke Ishii
Paternal restraint stress affects offspring metabolism via ATF-2 dependent mechanisms in Drosophila melanogaster germ cells. Communications biology 3 (1) (2020)
Sho Kitamoto, Christopher J Alteri, Michael Rodrigues, Hiroko Nagao-Kitamoto, Kohei Sugihara, Stephanie D Himpsl, Malak Bazzi, Mao Miyoshi, Tatsuki Nishioka, Atsushi Hayashi, Tina L Morhardt, Peter Kuffa, Helmut Grasberger, Mohamad El-Zaatari, Shrinivas Bishu, Chiharu Ishii, Akiyoshi Hirayama, Kathryn A Eaton, Belgin Dogan, Kenneth W Simpson, Naohiro Inohara, Harry L T Mobley, John Y Kao, Shinji Fukuda, Nicolas Barnich, Nobuhiko Kamada
Dietary L-serine confers a competitive fitness advantage to Enterobacteriaceae in the inflamed gut. Nature microbiology 5 (1) (2019)
Wanping Aw, Shinji Fukuda
Protective effects of bifidobacteria against enteropathogens. Microbial biotechnology 12 (6) (2019)

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Publication Activity (10 Years)

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Shinji Fukuda