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原著論文

2026

  1. The Japanese gut microbiome: ecology, uniqueness, and impact on health and disease
    筆頭著者責任著者
    Suguru Nishijima†, Masahira Hattori†, and Naoyoshi Nagata†
    Proceedings of the Japan Academy, Series B, Feb 2026
    プレスリリース Research Highlight

2025

  1. VIRE: a metagenome-derived, planetary-scale virome resource with environmental context
    共同筆頭著者責任著者
    Suguru Nishijima*†, Anthony Fullam*, Thomas SB Schmidt*, Michael Kuhn, and Peer Bork†
    Nucleic Acids Research, Nov 2025
    プレスリリース Research Highlight
  2. Metalog: curated and harmonised contextual data for global metagenomics samples
    Michael Kuhn, Thomas Sebastian B Schmidt, Pamela Ferretti, Anna Głazek, Shahriyar Mahdi Robbani, Wasiu Akanni, Anthony Fullam, Christian Schudoma, Ela Cetin, Mariam Hassan, Kasimir Noack, Anna Schwarz, Roman Thielemann, Leonie Thomas, Moritz Stetten, Renato Alves, Anandhi Iyappan, Ece Kartal, Ivan Kel, Marisa I Keller, Oleksandr Maistrenko, Anna Mankowski, Suguru Nishijima, Daniel Podlesny, Jonas Schiller, Sarah Schulz, Thea Van Rossum, and Peer Bork
    Nucleic Acids Research, Oct 2025
  3. The postbiotic ReFerm® versus standard nutritional support in advanced alcohol-related liver disease (GALA-POSTBIO): a randomized controlled phase 2 trial
    Johanne K Hansen, Mads Israelsen, Suguru Nishijima, Sara E Stinson, Peter Andersen, Stine Johansen, Camilla D Hansen, Maximilian Joseph Brol, Sabine Klein, Robert Schierwagen, Frank Erhard Uschner, Karolina Sulek, Ida F Villesen, Katrine P Lindvig, Katrine H Thorhauge, Nikolaj Torp, Jane M Jensen, Marisa Isabell Keller, Gitte H Jensen, Sönke Detlefsen, Diana J Leeming, Evelina Stankevic, Tommi Suvitaival, Andressa Zawadzki, Michael Kuhn, Lars Juhl Jensen, Morten Karsdal, Jonel Trebicka, Hans Israelsen, Cristina Legido-Quigley, Peer Bork, Manimozhiyan Arumugam, Torben Hansen, Maja Thiele, and Aleksander Krag
    Nature Communications, Jul 2025
  4. Fecal microbial load is a major determinant of gut microbiome variation and a confounder for disease associations
    筆頭著者
    Suguru Nishijima, Evelina Stankevic, Oliver Aasmets, Thomas S.B. Schmidt, Naoyoshi Nagata, Marisa Isabell Keller, Pamela Ferretti, Helene Bæk Juel, Anthony Fullam, Shahriyar Mahdi Robbani, Christian Schudoma, Johanne Kragh Hansen, Louise Aas Holm, Mads Israelsen, Robert Schierwagen, Nikolaj Torp, Anja Telzerow, Rajna Hercog, Stefanie Kandels, Diënty H.M. Hazenbrink, Manimozhiyan Arumugam, Flemming Bendtsen, Charlotte Brøns, Cilius Esmann Fonvig, Jens-Christian Holm, Trine Nielsen, Julie Steen Pedersen, Maja Sofie Thiele, Jonel Trebicka, Elin Org, Aleksander Krag, Torben Hansen, Michael Kuhn, and Peer Bork
    Cell, Jan 2025
    Research Highlight

2024

  1. Multi-biome analysis identifies distinct gut microbial signatures and their crosstalk in ulcerative colitis and Crohn’s disease
    責任著者
    Shintaro Akiyama, Suguru Nishijima†, Yasushi Kojima, Moto Kimura, Mitsuru Ohsugi, Kohjiro Ueki, Masashi Mizokami, Masahira Hattori, Kiichiro Tsuchiya, Naomi Uemura, Takashi Kawai, Peer Bork, and Naoyoshi Nagata
    Nature Communications, Nov 2024
    プレスリリース
  2. Opportunities and barriers in omics-based biomarker discovery for steatotic liver diseases
    Maja Thiele, Ida Falk Villesen, Lili Niu, Stine Johansen, Karolina Sulek, Suguru Nishijima, Lore Van Espen, Marisa Keller, Mads Israelsen, Tommi Suvitaival, Andressa Zawadzki, Helene Bæk Juel, Maximilian Joseph Brol, Sara Elizabeth Stinson, Yun Huang, Maria Camilla Alvarez Silva, Michael Kuhn, Ema Anastasiadou, Diana Julie Leeming, Morten Karsdal, Jelle Matthijnssens, Manimozhiyan Arumugam, Louise Torp Dalgaard, Cristina Legido-Quigley, Matthias Mann, Jonel Trebicka, Peer Bork, Lars Juhl Jensen, Torben Hansen, and Aleksander Krag
    Journal of Hepatology, Aug 2024

2023

  1. Sphingolipids Are Depleted in Alcohol-Related Liver Fibrosis
    Maja Thiele, Tommi Suvitaival, Kristina Trošt, Mijin Kim, Andressa Zawadzki, Mikkel Kjaergaard, Dorte N. Rasmussen, Katrine P. Lindvig, Mads Israelsen, Sören Detlefsen, Peter Andersen, Helene B. Juel, Trine Nielsen, Sofia Georgiou, Valentina Filippa, Michael Kuhn, Suguru Nishijima, Luís Moitinho-Silva, Peter Rossing, Jonel Trebicka, Ema Anastasiadou, Peer Bork, Torben Hansen, Cristina Legido-Quigley, Aleksander Krag, Matthias Mann, Jelle Matthijnssens, Manimozhiyan Arumugam, Rob Henrar, Hans Israelsen, Morten Karsdal, and Hans Olav Melberg
    Gastroenterology, Jun 2023
  2. Consistency across multi-omics layers in a drug-perturbed gut microbial community
    共同筆頭著者
    Sander Wuyts*, Renato Alves*, Maria Zimmermann-Kogadeeva*, Suguru Nishijima*, Sonja Blasche, Marja Driessen, Philipp E. Geyer, Rajna Hercog, Ece Kartal, Lisa Maier, Johannes B. Müller, Sarela Garcia Santamarina, Thomas Sebastian B. Schmidt, Daniel C. Sevin, Anja Telzerow, Peter V. Treit, Tobias Wenzel, Athanasios Typas, Kiran R. Patil, Matthias Mann, Michael Kuhn, and Peer Bork
    Molecular Systems Biology, Jul 2023

2022

  1. Extensive gut virome variation and its associations with host and environmental factors in a population-level cohort
    共同筆頭著者責任著者
    Suguru Nishijima*†, Naoyoshi Nagata†*, Yuya Kiguchi, Yasushi Kojima, Tohru Miyoshi-Akiyama, Moto Kimura, Mitsuru Ohsugi, Kohjiro Ueki, Shinichi Oka, Masashi Mizokami, Takao Itoi, Takashi Kawai, Naomi Uemura, and Masahira Hattori
    Nature Communications, Sep 2022
    プレスリリース
  2. Metagenomic Identification of Microbial Signatures Predicting Pancreatic Cancer From a Multinational Study
    共同筆頭著者責任著者
    Naoyoshi Nagata†*, Suguru Nishijima†*, Yasushi Kojima, Yuya Hisada, Koh Imbe, Tohru Miyoshi-Akiyama, Wataru Suda, Moto Kimura, Ryo Aoki, Katsunori Sekine, Mitsuru Ohsugi, Kuniko Miki, Tsuyoshi Osawa, Kohjiro Ueki, Shinichi Oka, Masashi Mizokami, Ece Kartal, Thomas S.B. Schmidt, Esther Molina-Montes, Lidia Estudillo, Nuria Malats, Jonel Trebicka, Stephan Kersting, Melanie Langheinrich, Peer Bork, Naomi Uemura, Takao Itoi, and Takashi Kawai
    Gastroenterology, Mar 2022
    プレスリリース
  3. Population-level metagenomics uncovers distinct effects of multiple medications on the human gut microbiome
    共同筆頭著者責任著者
    Naoyoshi Nagata*†, Suguru Nishijima†*, Tohru Miyoshi-Akiyama, Yasushi Kojima, Moto Kimura, Ryo Aoki, Mitsuru Ohsugi, Kohjiro Ueki, Kuniko Miki, Eri Iwata, Kayoko Hayakawa, Norio Ohmagari, Shinichi Oka, Masashi Mizokami, Takao Itoi, Takashi Kawai, Naomi Uemura, and Masahira Hattori
    Gastroenterology, Jul 2022
    プレスリリース 新聞記事

2021

  1. Long-read metagenomics of multiple displacement amplified DNA of low-biomass human gut phageomes by SACRA pre-processing chimeric reads
    Yuya Kiguchi, Suguru Nishijima, Naveen Kumar, Masahira Hattori, and Wataru Suda
    DNA Research, Sep 2021

2020

  1. Emergence of the novel aminoglycoside acetyltransferase variant Aac(6’)-ib-d179y and acquisition of colistin heteroresistance in carbapenem-resistant Klebsiella pneumoniae due to a disrupting mutation in the DNA repair enzyme muts
    Takuya Sato, Takashi Wada, Suguru Nishijima, Yoko Fukushima, Chie Nakajima, Yasuhiko Suzuki, Shinya Takahashi, and Shin-Ichi Yokota
    mBio, Dec 2020
  2. Revealing the microbial assemblage structure in the human gut microbiome using latent Dirichlet allocation
    Shinichiro Hosoda, Suguru Nishijima, Taku Fukunaga, Masahira Hattori, and Michiaki Hamada
    Microbiome, Dec 2020
    プレスリリース

2019

  1. Effects of storage temperature, storage time, and Cary-Blair transport medium on the stability of the gut microbiota
    Naoyoshi Nagata, Mari Tohya, Fumihiko Takeuchi, Wataru Suda, Suguru Nishijima, Mitsuru Ohsugi, Kohjiro Ueki, Tetsuro Tsujimoto, Tomoka Nakamura, Takashi Kawai, Tohru Miyoshi-Akiyama, Naomi Uemura, and Masahira Hattori
    Drug Discoveries & Therapeutics, Oct 2019
  2. Long-read metagenomic exploration of extrachromosomal mobile genetic elements in the human gut
    共同筆頭著者
    Yoshihiko Suzuki*, Suguru Nishijima*, Yoshikazu Furuta, Jun Yoshimura, Wataru Suda, Kenshiro Oshima, Masahira Hattori, and Shinichi Morishita
    Microbiome, Aug 2019
  3. Effects of bowel preparation on the human gut microbiome and metabolome
    Naoyoshi Nagata, Mari Tohya, Shinji Fukuda, Wataru Suda, Suguru Nishijima, Fumihiko Takeuchi, Mitsuru Ohsugi, Tetsuro Tsujimoto, Tomoka Nakamura, Akira Shimomura, Naohiro Yanagisawa, Yuya Hisada, Kazuhiro Watanabe, Koh Imbe, Junichi Akiyama, Masashi Mizokami, Tohru Miyoshi-Akiyama, Naomi Uemura, and Masahira Hattori
    Scientific Reports, Mar 2019

2018

  1. Collaborative environmental DNA sampling from petal surfaces of flowering cherry Cerasus × yedoensis ’Somei-yoshino’ across the Japanese archipelago
    Takahiro Ohta, Takeshi Kawashima, Naoaki O. Shinozaki, Atsushi Dobashi, Satoshi Hiraoka, Tomohiro Hoshino, Kenta Kanno, Takashi Kataoka, Sayaka Kawashima, Masaru Matsui, Wakana Nemoto, Suguru Nishijima, Naoya Suganuma, Hiroshi Suzuki, Y.-H. Taguchi, Yuji Takenaka, Yuko Tanigawa, Masaki Tsuneyoshi, Keisuke Yoshitake, Yoshihiro Sato, Ryuichiro Yamashita, Kazuharu Arakawa, and Wataru Iwasaki
    Journal of Plant Research, Jun 2018

2017

  1. Circadian oscillations of microbial and functional composition in the human salivary microbiome
    Lena Takayasu, Wataru Suda, Kageyasu Takanashi, Erica Iioka, Rina Kurokawa, Chie Shindo, Yasue Hattori, Naoko Yamashita, Suguru Nishijima, Kenshiro Oshima, and Masahira Hattori
    DNA Research, Jun 2017

2016

  1. Nitrogen fixation and nifH diversity in human gut microbiota
    Katsura Igai, Manabu Itakura, Suguru Nishijima, Hirohito Tsurumaru, Wataru Suda, Takumi Tsutaya, Eriko Tomitsuka, Kiyoshi Tadokoro, Jun Baba, Shingo Odani, Kazumi Natsuhara, Ayako Morita, Minoru Yoneda, Andrew R. Greenhill, Paul F. Horwood, Jun-ichi Inoue, Moriya Ohkuma, Yuichi Hongoh, Taro Yamamoto, Peter M. Siba, Masahira Hattori, Kiwamu Minamisawa, and Masahiro Umezaki
    Scientific Reports, Aug 2016
  2. The gut microbiome of healthy Japanese and its microbial and functional uniqueness
    筆頭著者
    Suguru Nishijima, Wataru Suda, Kenshiro Oshima, Seok-Won Kim, Yuu Hirose, Hidetoshi Morita, and Masahira Hattori
    DNA Research, Mar 2016
    プレスリリース 日本語記事 新聞記事

日本語総説

2025

  1. Cover image for “環境因子（食事，生活習慣，薬剤）や疾患とヒトマイクロバイオームの関連解析”
    環境因子（食事，生活習慣，薬剤）や疾患とヒトマイクロバイオームの関連解析
    西嶋傑 永田尚義
    実験医学別冊 達人直伝 マイクロバイオーム研究実践プロトコール, Jun 2025
  2. Cover image for “腸内真菌叢のマイクロバイオーム解析”
    腸内真菌叢のマイクロバイオーム解析
    秋山慎太郎 , 西嶋傑 , 永田尚義
    実験医学別冊 達人直伝 マイクロバイオーム研究実践プロトコール, Jun 2025

2020

  1. Cover image for “メタゲノムデータを用いた腸内細菌叢への影響因子の解明”
    メタゲノムデータを用いた腸内細菌叢への影響因子の解明
    永田尚義 西嶋傑
    ヒトマイクロバイオーム Vol.2 ～解析技術の進展とデータ駆動型・ターゲット機能型研究最前線～, Jun 2020
  2. Cover image for “ロングリードメタゲノミクス”
    ロングリードメタゲノミクス
    鈴木慶彦 , 西嶋傑 , 森下真一
    ヒトマイクロバイオーム Vol.2 ～解析技術の進展とデータ駆動型・ターゲット機能型研究最前線～, Jun 2020

2019

  1. Cover image for “メタゲノムデータからの微生物ゲノムの再構成”
    メタゲノムデータからの微生物ゲノムの再構成
    西嶋傑
    実験医学増刊 シングルセルゲノミクス, Dec 2019

2018

  1. Cover image for “日本人腸内細菌叢のユニークさと国間多様性”
    日本人腸内細菌叢のユニークさと国間多様性
    服部正平 西嶋傑
    週間医学のあゆみ, Oct 2018
  2. Cover image for “大規模シークエンスデータを用いたヒトマイクロバイオーム研究”
    大規模シークエンスデータを用いたヒトマイクロバイオーム研究
    須田亙 , 緒方勇亮 , 西嶋傑
    CLINICAL CALCIUM, Sep 2018
  3. Cover image for “メタゲノム解析によるヒト腸内マイクロバイオームの国レベル多様性”
    メタゲノム解析によるヒト腸内マイクロバイオームの国レベル多様性
    服部正平 西嶋傑
    最新醫學, Apr 2018

2017

  1. Cover image for “日本人腸内細菌叢の特徴と国間多様性”
    日本人腸内細菌叢の特徴と国間多様性
    服部正平 西嶋傑
    糖尿病診療マスター, Jun 2017
  2. Cover image for “ヒト腸内細菌叢のメタゲノム解析”
    ヒト腸内細菌叢のメタゲノム解析
    大島健志朗 , 西嶋傑 , 服部正平
    生体の科学, Apr 2017
  3. Cover image for “ヒト腸内マイクロバイオームのメタゲノム解析”
    ヒト腸内マイクロバイオームのメタゲノム解析
    大島健志朗 西嶋傑
    ファルマシア, Nov 2017

2016

  1. Cover image for “腸内細菌叢のメタゲノム解析・メタ16S 解析”
    腸内細菌叢のメタゲノム解析・メタ16S 解析
    須田亙 , 西嶋傑 , 高安玲奈 , 大島健志朗
    実験医学別冊 今すぐ始める! メタゲノム解析実験プロトコール, Dec 2016
  2. Cover image for “日本人腸内細菌叢のメタゲノム解析と特徴解明”
    日本人腸内細菌叢のメタゲノム解析と特徴解明
    西嶋傑 服部正平
    実験医学別冊 今すぐ始める! メタゲノム解析実験プロトコール, Dec 2016
  3. Cover image for “ヒト腸内細菌叢のメタゲノムデータのインフォマティクス”
    ヒト腸内細菌叢のメタゲノムデータのインフォマティクス
    西嶋傑
    実験医学別冊 今すぐ始める! メタゲノム解析実験プロトコール, Dec 2016
  4. Cover image for “次世代シーケンサーを用いた腸内細菌叢の解析手法と日本人腸内細菌叢の特徴”
    次世代シーケンサーを用いた腸内細菌叢の解析手法と日本人腸内細菌叢の特徴
    須田亙 , 西嶋傑 , 服部正平
    The Lipid, Apr 2016
  5. Cover image for “メタゲノム解析・16S 解析とその解析技術”
    メタゲノム解析・16S 解析とその解析技術
    大島健志朗 , 西嶋傑 , 須田亙
    ヒトマイクロバイオーム研究最前線 〜常在菌の解析技術から生態、医療分野、食品への応用研究まで〜, Mar 2016
  6. Cover image for “日本人腸内細菌叢のメタゲノム解析”
    日本人腸内細菌叢のメタゲノム解析
    西嶋傑 服部正平
    ヒトマイクロバイオーム研究最前線 〜常在菌の解析技術から生態、医療分野、食品への応用研究まで〜, Mar 2016

2014

  1. Cover image for “ヒト腸内細菌マイクロバイオームの特徴”
    ヒト腸内細菌マイクロバイオームの特徴
    服部正平 西嶋傑
    G.I. Research, Feb 2014

2013

  1. Cover image for “ヒトの腸内マイクロバイオーム”
    ヒトの腸内マイクロバイオーム
    西嶋傑 服部正平
    細胞工学, Oct 2013