Publications

2026

1. The Japanese gut microbiome: ecology, uniqueness, and impact on health and disease

   First authorCorresponding author

   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

   Co-first authorCorresponding author

   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

   First author

   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

   Corresponding author

   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

   Co-first author

   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

   Co-first authorCorresponding author

   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

   Co-first authorCorresponding author

   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

   Co-first authorCorresponding author

   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

   Co-first author

   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

   First author

   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