Basic Information

Email Address

• Email Address

  nakajima.aruto.5xkyoto-u.ac.jp

Academic Degree

• 23 Mar. 2021

  京都大学修士（生命科学）
• 23 May 2025

  京都大学博士（生命科学）

Academic Resume (Undergraduate School/Majors)

• 京都大学, 農学部食品生物科学科, 卒業

Research History

• From Jun. 2025, To Present

  Kyoto University, Graduate School of Biostudies, 特定研究員, 特任助教
• From Apr. 2025, To May 2025

  Kyoto University, Graduate School of Biostudies, 研究員

ID,URL

• ORCID ID

  0000-0002-5354-2394

• J-Global ID

  202501011533262141

researchmap URL

• https://researchmap.jp/arutonakajima

Research

Papers

• Total Chemical Synthesis of the Human Milk Oligosaccharide Disialyllacto- N -tetraose and Its Degradation by Bifidobacterium bifidum Sialidases

  Maiko Tanase; Aruto Nakajima; Naoko Komura; Hidenori Tanaka; Hiromune Ando; Hideharu Ishida; Takane Katayama; Toshihiko Katoh; Akihiro Imamura

  Organic Letters, 07 May 2026, Peer-reviewed

  
• Human milk oligosaccharides and infant gut microbiome in Mongolian mother-infant dyads

  Enkhtuul Davaanyam; Undarmaa Otgonbaatar; Aruto Nakajima; Mikiyasu Sakanaka; Miriam N. Ojima; Tomoya Kozakai; Toshihiko Katoh; Toshitaka Odamaki; Batkhuu Javzan; Enkhmaa Dagvadorj; Davaapurev Bekh-Ochir; Takane Katayama

  Journal of Dairy Science, Nov. 2025

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• Uptake of fucosylated type I human milk oligosaccharide blocks by Bifidobacterium longum subsp. infantis

  Morten Ejby Hansen; Mikiyasu Sakanaka; Mathias Jensen; Hiroka Sakanaka; Michael Jakob Pichler; Shingo Maeda; Julie Franck Høvring; Aruto Nakajima; Sonja Kunstmann; Tine Sofie Nielsen; Günther Herbert Johannes Peters; Dirk Jan Slotboom; Jens Preben Morth; Takane Katayama; Maher Abou Hachem

  mBio, 14 Jul. 2025

  
• Ecological insights into the assembly of bifidobacterial communities in the infant gut

  Miriam N. Ojima; Mikiyasu Sakanaka; Aruto Nakajima; Toshitaka Odamaki; Takane Katayama

  Ecological Research, 22 Jul. 2025

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• In vitro competition with Bifidobacterium strains impairs potentially pathogenic growth of Clostridium perfringens on 2′-fucosyllactose

  Aruto Nakajima; Aleksandr A. Arzamasov; Mikiyasu Sakanaka; Ryuta Murakami; Tomoya Kozakai; Keisuke Yoshida; Toshihiko Katoh; Miriam N. Ojima; Junko Hirose; Saeko Nagao; Jin-Zhong Xiao; Toshitaka Odamaki; Dmitry A. Rodionov; Takane Katayama

  Gut Microbes, 18 Mar. 2025

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• Suppression of fecal phenol production by oral supplementation of sesamol: inhibition of tyrosine phenol-lyase by sesamol

  Daiki Oikawa; Zion Byun; Bunzo Mikami; Aina Gotoh; Toshihiko Katoh; Ryo Ueno; Aruto Nakajima; Satoshi Yamashita; Wakako Ikeda-Ohtsubo; Seiji Takahashi; Toshiyuki Waki; Koichi Kikuchi; Takaaki Abe; Takane Katayama; Toru Nakayama

  Food & Function, 2025

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• An improved temperature-sensitive shuttle vector system for scarless gene deletion in human gut-associated Bifidobacterium species

  Tomoya Kozakai; Aruto Nakajima; Keisuke Miyazawa; Yuki Sasaki; Toshitaka Odamaki; Toshihiko Katoh; Takeshi Fukuma; Jin-zhong Xiao; Tohru Suzuki; Takane Katayama; Mikiyasu Sakanaka

  iScience, 15 Nov. 2024

  
• Human gut-associated Bifidobacterium species salvage exogenous indole, a uremic toxin precursor, to synthesize indole-3-lactic acid via tryptophan

  Cheng Chung Yong; Takuma Sakurai; Hiroki Kaneko; Ayako Horigome; Eri Mitsuyama; Aruto Nakajima; Toshihiko Katoh; Mikiyasu Sakanaka; Takaaki Abe; Jin-Zhong Xiao; Miyuki Tanaka; Toshitaka Odamaki; Takane Katayama

  Gut Microbes, 05 May 2024

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• Human Milk Oligosaccharide Utilization in Intestinal Bifidobacteria Is Governed by Global Transcriptional Regulator NagR

  Aleksandr A. Arzamasov; Aruto Nakajima; Mikiyasu Sakanaka; Miriam N. Ojima; Takane Katayama; Dmitry A. Rodionov; Andrei L. Osterman

  mSystems, 12 Sep. 2022

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• Priority effects shape the structure of infant-type Bifidobacterium communities on human milk oligosaccharides

  Miriam N Ojima; Lin Jiang; Aleksandr A Arzamasov; Keisuke Yoshida; Toshitaka Odamaki; Jinzhong Xiao; Aruto Nakajima; Motomitsu Kitaoka; Junko Hirose; Tadasu Urashima; Toshihiko Katoh; Aina Gotoh; Douwe van Sinderen; Dmitry A Rodionov; Andrei L Osterman; Mikiyasu Sakanaka; Takane Katayama

  The ISME Journal, 01 Sep. 2022

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• A simple method that enhances minority species detection in the microbiota: 16S metagenome-DRIP (Deeper Resolution using an Inhibitory Primer)

  Aruto Nakajima; Keisuke Yoshida; Aina Gotoh; Toshihiko Katoh; Miriam N. Ojima; Mikiyasu Sakanaka; Jin-Zhong Xiao; Toshitaka Odamaki; Takane Katayama

  Microbiome Research Reports, 30 May 2022

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• Diversification of a Fucosyllactose Transporter within the Genus Bifidobacterium

  Miriam N. Ojima; Yuya Asao; Aruto Nakajima; Toshihiko Katoh; Motomitsu Kitaoka; Aina Gotoh; Junko Hirose; Tadasu Urashima; Satoru Fukiya; Atsushi Yokota; Maher Abou Hachem; Mikiyasu Sakanaka; Takane Katayama

  Applied and Environmental Microbiology, 25 Jan. 2022

  

Books and Other Publications

• シンバイオティクスによる病原性細菌制御の可能性～より安全なヒトミルクオリゴ糖の利用に向けて～

  中島有登; 片山高嶺, Joint work

  バイオサイエンスとインダストリー, Mar. 2026

  

External funds: Kakenhi

• 株間多様性を生む新たな因子の同定：他種細菌との共存時に顕現する新奇遺伝子機能解明

  Grant-in-Aid for Early-Career Scientists

  Basic Section 38020:Applied microbiology-related

  Kyoto University

  中島 有登

  From 01 Apr. 2026, To 31 Mar. 2028, Adopted

  https://kaken.nii.ac.jp/grant/KAKENHI-PROJECT-26K17982/
• Mechanism of environment-dependent human milk oligosaccharide assimilation in opportunistic gut pathogens

  Grant-in-Aid for Research Activity Start-up

  0601:Agricultural chemistry and related fields

  Kyoto University

  中島 有登

  From 31 Jul. 2025, To 31 Mar. 2027, Granted

  乳児腸内細菌;母乳オリゴ糖;Clostridium perfringens;2′-フコシルラクトース;環境応答

  https://kaken.nii.ac.jp/grant/KAKENHI-PROJECT-25K23623/