Researcher Information
researchmap URL
Research History
- Apr. 2024 - Present
Japan Agency for Marine-Earth Science and Technology, Research Institute for Marine Resource Utilization (MRU), Research Center for Bioscience and Nanoscience (CeBN), Project Researcher - Apr. 2021 - Mar. 2024
Japan Agency for Marine-Earth Science and Technology, X-STAR, Young Research Fellow - Apr. 2019 - Mar. 2021
National Institute of Advanced Industrial Science and Technology, 生物プロセス研究部門 生物資源情報基盤研究グループ, JSPS Young Research Fellow (PD) - Apr. 2018 - Mar. 2019
The University of Tokyo, Atmosphere and Ocean research Institute, Project Researcher
Research activity information
Papers
- Yu Nakajima; Shu-Kuan Wong; Yuki Muramatsu; Marie Johanna Cuadra; Kei Zenimoto; Keigi Ou; Hiroshi Xavier Chiura; Keiji Nakamura; Yasuhiro Gotoh; Tetsuya Hayashi; Yasuyoshi Nakagawa; Susumu Yoshizawa
Phylogenomic reclassification of Cellulophaga species to Paracellulophaga gen. nov. and description of Allocellulophaga tsushimaensis gen. nov., sp. nov., a novel bacterium from coastal seawater of Tsushima Island, Japan
Antonie van Leeuwenhoek, 09 Mar. 2026
119, 4
[Reviewed]
Lead, Corresponding - Chiho Sukigara; Taichi Yokokawa; Akiko Makabe; Kaho Mori; Yu Nakajima; Shinya Kouketsu; Eiji Tasumi; Masumi Hasegawa-Takano; Naoto F. Ishikawa; Chunqi Jiang; Siyu Jiang; Riku Miyase; Satoshi Nishino; Youta Sugai; Kento Tominaga; Hiroshi Uchida; Yu Yoshida; Susumu Yoshizawa; Shinsuke Kawagucci
Diel and daily changes of water mass structure and biogeochemical processes in early spring in the western subtropical North Pacific
Progress in Earth and Planetary Science, 20 Nov. 2025
12, 1
[Reviewed] - Takaomi Ito; Takao Segawa; Kazuto Takasaki; Takahiro Matsudaira; Itsuki Kiyatake; Hiroyuki Irino; Yu Nakajima
Comparison of the Fecal Microbiota from Long-term Captive and Newly Captured Whale Sharks (Rhincodon typus)
Microbes and Environments, Oct. 2025
40, 3
[Reviewed]
Last, Corresponding - Takao Segawa; Yu Nakajima; Keiko Yamamoto; Shoko Kishima; Takuya Itou
Ureaplasma ceti sp. nov. isolated from the gastric fluid of a spotted dolphin (Stenella attenuata)
International Journal of Systematic and Evolutionary Microbiology, 11 Mar. 2025
75, 3
[Reviewed] - Mako Takada; Chunqi Jiang; Youta Sugai; Masumi Hasegawa-Takano; Takayoshi Fujiwara; Yuya Tsukamoto; Yu Nakajima; Yosuke Nishimura; Susumu Yoshizawa
Draft genome sequences of three rhodopsin possessing Croceitalea sp. strains, isolated from the sea surface microlayer in Japan.
Microbiology resource announcements, 16 Feb. 2024
e0003824
[Reviewed] - Masumi Hasegawa-Takano; Toshiaki Hosaka; Keiichi Kojima; Yosuke Nishimura; Marie Kurihara; Yu Nakajima; Yoshiko Ishizuka-Katsura; Tomomi Kimura-Someya; Mikako Shirouzu; Yuki Sudo; Susumu Yoshizawa
Cyanorhodopsin-II represents a yellow-absorbing proton-pumping rhodopsin clade within cyanobacteria
The ISME Journal, 08 Jan. 2024
18, 1
[Reviewed] - Yuki Sato-Takabe; Yu Nakajima; Yuya Tsukamoto; Koji Hamasaki; Takuhei Shiozaki
Draft Genome Sequence of the Aerobic Anoxygenic Phototrophic Bacterium Roseobacter sp. Strain OBYS 0001, Isolated from Coastal Seawater in Otsuchi Bay, Japan
Microbiology Resource Announcements, 15 Jul. 2021
10, 28
[Reviewed] - Yuki Sato-Takabe; Yu Nakajima; Satoru Suzuki; Kota Sekiguchi; Satoshi Hanada; Takuhei Shiozaki
Draft Genome Sequences of Putative Aerobic Anoxygenic Phototrophic Bacterial Strains Jannaschia sp. Strains AI_61 and AI_62, Isolated from Seawater around a Coastal Aquaculture Area
Microbiology Resource Announcements, 15 Jul. 2021
10, 28
[Reviewed] - Yu Nakajima; Keiichi Kojima; Yuichiro Kashiyama; Satoko Doi; Ryosuke Nakai; Yuki Sudo; Kazuhiro Kogure; Susumu Yoshizawa
Bacterium Lacking a Known Gene for Retinal Biosynthesis Constructs Functional Rhodopsins
Microbes and Environments, Dec. 2020
35, 4
[Reviewed]
Lead, Corresponding - Masumi Hasegawa; Toshiaki Hosaka; Keiichi Kojima; Yosuke Nishimura; Yu Nakajima; Tomomi Kimura-Someya; Mikako Shirouzu; Yuki Sudo; Susumu Yoshizawa
A unique clade of light-driven proton-pumping rhodopsins evolved in the cyanobacterial lineage
Scientific Reports, Dec. 2020
10, 1, 16752, 16752
[Reviewed] - David M Needham; Susumu Yoshizawa; Toshiaki Hosaka; Camille Poirier; Chang Jae Choi; Elisabeth Hehenberger; Nicholas A T Irwin; Susanne Wilken; Cheuk-Man Yung; Charles Bachy; Rika Kurihara; Yu Nakajima; Keiichi Kojima; Tomomi Kimura-Someya; Guy Leonard; Rex R Malmstrom; Daniel R Mende; Daniel K Olson; Yuki Sudo; Sebastian Sudek; Thomas A Richards; Edward F DeLong; Patrick J Keeling; Alyson E Santoro; Mikako Shirouzu; Wataru Iwasaki; Alexandra Z Worden
A distinct lineage of giant viruses brings a rhodopsin photosystem to unicellular marine predators.
Proceedings of the National Academy of Sciences of the United States of America, 08 Oct. 2019
116, 41, 20574, 20583
[Reviewed] - Atsushi Shibukawa; Keiichi Kojima; Yu Nakajima; Yosuke Nishimura; Susumu Yoshizawa; Yuki Sudo
Photochemical Characterization of a New Heliorhodopsin from the Gram-Negative Eubacterium Bellilinea caldifistulae (BcHeR) and Comparison with Heliorhodopsin-48C12.
Biochemistry, 02 Jul. 2019
58, 26, 2934, 2943
[Reviewed] - Shu-Kuan Wong; Susumu Yoshizawa; Yu Nakajima; Marie Johanna Cuadra; Yuichi Nogi; Keiji Nakamura; Hideto Takami; Yoshitoshi Ogura; Tetsuya Hayashi; Hiroshi Xavier Chiura; Koji Hamasaki
Amylibacter kogurei sp. nov., a novel marine alphaproteobacterium isolated from the coastal sea surface microlayer of a marine inlet.
International journal of systematic and evolutionary microbiology, Sep. 2018
68, 9, 2872, 2877
[Reviewed] - Masumi Hasegawa; Yu Nakajima; Shu-Kuan Wong; Keiji Nakamura; Yoshitoshi Ogura; Tetsuya Hayashi; Kazuhiro Kogure; Susumu Yoshizawa
Draft Genome Sequence of Saccharospirillum sp. Strain MSK14-1, Isolated from Surface Seawater Collected at Aburatsubo Inlet in Japan.
Genome announcements, 31 May 2018
6, 22
[Reviewed] - Yohei Kumagai; Susumu Yoshizawa; Yu Nakajima; Mai Watanabe; Tsukasa Fukunaga; Yoshitoshi Ogura; Tetsuya Hayashi; Kenshiro Oshima; Masahira Hattori; Masahiko Ikeuchi; Kazuhiro Kogure; Edward F DeLong; Wataru Iwasaki
Solar-panel and parasol strategies shape the proteorhodopsin distribution pattern in marine Flavobacteriia.
The ISME journal, May 2018
12, 5, 1329, 1343
[Reviewed] - Yu Nakajima; Takashi Tsukamoto; Yohei Kumagai; Yoshitoshi Ogura; Tetsuya Hayashi; Jaeho Song; Takashi Kikukawa; Makoto Demura; Kazuhiro Kogure; Yuki Sudo; Susumu Yoshizawa
Presence of a Haloarchaeal Halorhodopsin-Like Cl- Pump in Marine Bacteria.
Microbes and environments, 29 Mar. 2018
33, 1, 89, 97
[Reviewed]
Lead, Corresponding - Saki Inoue; Susumu Yoshizawa; Yu Nakajima; Keiichi Kojima; Takashi Tsukamoto; Takashi Kikukawa; Yuki Sudo
Spectroscopic characteristics of Rubricoccus marinus xenorhodopsin (RmXeR) and a putative model for its inward H+ transport mechanism.
Physical chemistry chemical physics : PCCP, 31 Jan. 2018
20, 5, 3172, 3183
[Reviewed] - Yu Nakajima; Susumu Yoshizawa; Sanghwa Park; Yohei Kumagai; Shu-Kuan Wong; Yoshitoshi Ogura; Tetsuya Hayashi; Kazuhiro Kogure
Draft Genome Sequence of Rubricoccus marinus SG-29T, a Marine Bacterium within the Family Rhodothermaceae, Which Contains Two Different Rhodopsin Genes.
Genome announcements, 21 Sep. 2017
5, 38
[Reviewed]
Lead - Yu Nakajima; Susumu Yoshizawa; Keiji Nakamura; Yoshitoshi Ogura; Tetsuya Hayashi; Kazuhiro Kogure
Draft Genome Sequences of Tersicoccus phoenicis DSM 30849T, Isolated from a Cleanroom for Spacecraft Assembly, and Tersicoccus sp. Strain Bi-70, Isolated from a Freshwater Lake.
Genome announcements, 30 Mar. 2017
5, 13
[Reviewed]
Lead - Akiko Niho; Susumu Yoshizawa; Takashi Tsukamoto; Marie Kurihara; Shinya Tahara; Yu Nakajima; Misao Mizuno; Hikaru Kuramochi; Tahei Tahara; Yasuhisa Mizutani; Yuki Sudo
Demonstration of a Light-Driven SO42- Transporter and Its Spectroscopic Characteristics.
Journal of the American Chemical Society, 29 Mar. 2017
139, 12, 4376, 4389
[Reviewed] - Toshiaki Hosaka; Susumu Yoshizawa; Yu Nakajima; Noboru Ohsawa; Masakatsu Hato; Edward F DeLong; Kazuhiro Kogure; Shigeyuki Yokoyama; Tomomi Kimura-Someya; Wataru Iwasaki; Mikako Shirouzu
Structural Mechanism for Light-driven Transport by a New Type of Chloride Ion Pump, Nonlabens marinus Rhodopsin-3.
The Journal of biological chemistry, 19 Aug. 2016
291, 34, 17488, 17495
[Reviewed] - Shu-Kuan Wong; Susumu Yoshizawa; Yu Nakajima; Yoshitoshi Ogura; Tetsuya Hayashi; Koji Hamasaki
Draft Genome Sequence of Lewinella sp. Strain 4G2 Isolated from the Coastal Sea Surface Microlayer.
Genome announcements, 28 Jul. 2016
4, 4
[Reviewed]
Misc.
- 富永賢人; 森香穂; 森香穂; 中島悠; 中島悠; 長谷川万純; 長谷川万純; 横川太一; 横川太一; 鋤柄千穂; 川口慎介; 吉澤晋; 吉澤晋
高解像メタトランスクリプトームが照らし出す多様な海洋ウイルスの日周転写動態
日本微生物生態学会大会(Web), 2025
38th - 中島悠
The Fifth Meeting of Bergey’s International Society for Microbial Systematics (BISMiS)・Marine Microbes Gordon Research Conference (GRC) 2024への参加報告
日本微生物生態学会誌, Sep. 2024
39, 2, 93, 94 - 岡崎友輔; 中島悠; 井上真男; 金子博人; 志野裕亮; 峯田航; 山下大祐; 熊谷洋平
Frontiers of microbial ecology
日本地球化学会年会要旨集(Web), 2020
67th - Hasegawa Masumi; Hosaka Toshiaki; Kojima Keiichi; Nishimura Yosuke; Nakajima Yu; Kimura―Someya Tomomi; Shirouzu Mikako; Sudo Yuki; Yoshizawa Susumu
The light-utilization mechanisms different from photosynthesis in cyanobacteria: The discovering of cyanorhodopsin.
Abstracts of Annual Meeting of the Geochemical Society of Japan, 2020
67, 186 - 海老原 諒子; 鈴木 研志; 田上 諒; 中島 悠; 鈴木 重勝; 平井 美穂; 大竹 遥; 佐野 友紀; 中小路 菫; 安田 まり奈; 石井 拳人; 後藤 栞; 渡辺 宏紀; 執行 宣彦
環境微生物系合同大会2017ポスター賞受賞者の声
日本微生物生態学会誌, 2018
33, 1, 2, 8 - 中島 悠; 江崎 和音; 菊池 結貴子; 宮武 広直; 安藤 康伸; 生出 秀行; 横山 広美; 音野 瑛俊
Back-to-Alma matter Project (BAP) : Consideration on 9 years Activities and Future Prospects
科学技術コミュニケーション = Japanese journal of science communication, Jun. 2017
21, 59, 75 - 菊池 結貴子; 江崎 和音; 中島 悠; 石川 遼子; 伊與木 健太; 正田 亜八香; 音野 瑛俊
BAP cafe : Meeting Place for Enthusiasts
科学技術コミュニケーション, Jan. 2017
20, 3, 13 - Yamada Takahito; Nakajima Yu; Ezaki Kazune; Shinogi Shingo; Shoda Ayaka; Yokoyama Hiromi; BAP collaboration
27aAG-7 Present activity of Back to Alma matter Project(BAP)
Meeting Abstracts of the Physical Society of Japan, 2014
69, 0, 442, 442 - 中島 悠; 吉澤 晋; 木暮 一啓
PG-017 Vibrio属細菌におけるプロテオロドプシンの発現条件および生理的役割の解明(生理・代謝・増殖,ポスター発表)
日本微生物生態学会講演要旨集, 2013
29, 128, 128
Presentations
- 瀬川太雄; 中島悠; 古川恭平; 佐藤多美; 犬丸皓貴; 村上郁月; 伊藤琢也
イルカとUreaplasma cetiの共生関係～進化の代償を支払う共生細菌～
第31回 日本野生動物医学会大会, 28 Sep. 2025 - 齋藤柚月; 瀬川太雄; 中島悠; 伊東隆臣; 喜屋武樹; 芳井祐友; 伊藤琢也
ジンベエザメ（Rhincodon typus）より分離された新種ウレアプラズマ
第31回 日本野生動物医学会大会, 27 Sep. 2025 - 瀬川 太雄; 中島 悠; 古川 恭平; 伊藤 琢也
イルカはなぜ前胃を持つのか：Ureaplasma ceti との共生が解く進化の謎
第38回日本微生物生態学会東京大会, 09 Sep. 2025 - 森 香穂; 富永 賢人; 中島 悠; 長谷川 万純; 西野 聡; 蒋 春啓; 横川 太一; 鋤柄 千穂; 川口 慎介; 吉澤 晋
黒潮続流域における海洋原核生物代謝の日周期性
第38回日本微生物生態学会東京大会, 08 Sep. 2025 - 髙橋 優乃; 藤原 敬允; 中島 悠; 富永 賢人; 吉澤 晋
Cl- ポンプ型ロドプシンの生理的役割から探る海洋細菌の新たな光エネルギー利用戦略
第38回日本微生物生態学会東京大会, 08 Sep. 2025 - 富永 賢人; 森 香穂; 中島 悠; 長谷川 万純; 横川 太一; 鋤柄 千穂; 川口 慎介; 吉澤 晋
高時間解像メタトランスクリプトームが照らし出す多様な海洋ウイルスの日周転写動態
第38回日本微生物生態学会東京大会, 08 Sep. 2025 - Masumi Hasegawa-Takano; Yohei Matsui; Miho Hirai; Karin Inoue; Tsuyoshi Takano; Yu Nakajima; Susumu Yoshizawa; Yosuke Nishimura
Exploring microbial diversity and carbon storage capacity of mangrove sediments through spatiotemporal studies
JpGU - 森 香穂; 中島 悠; 長谷川 万純; 富永 賢人; 西野 聡; 蒋 春啓; 横川 太一; 鋤柄 千穂; 川口 慎介; 吉澤 晋
Diel Patterns of Microbial Communities;Depth-Driven Genomic Shifts in the;Kuroshio Extension Observatory
JpGU - 齋藤 柚月; 瀬川 太雄; 中島 悠; 伊東 隆臣; 喜屋武 樹; 芳井 祐友; 伊藤 琢也
ジンベエザメ腸内から分離した新種ウレアプラズマと共生関係の検討
第52回日本マイコプラズマ学会学術集会, 24 May 2025 - 瀬川 太雄; 中島 悠; 古川 恭平; 佐藤 多美; 犬丸 皓貴; 村上 郁月; 伊藤 琢也
Ureaplasma cetiの代謝産物から推定するイルカとの新たな共生関係
第52回日本マイコプラズマ学会学術集会, 24 May 2025 - 長谷川 万純; 松井 洋平; 平井 美穂; 井上 香鈴; 髙野 剛史; 中島 悠; 吉澤晋; 西村 陽介
Exploring microbial diversity and carbon storage capacity of mangrove sediments from spatio-temporal studies
37th JSME, 30 Oct. 2024 - 森香穂; 中島悠; 谷川万純; 蒋春啓; 横川太一; 鋤柄千穂; 川口慎介; 吉澤晋
Daily fluctuations of marine microorganism communities in the Black Sea subduction zone
37th JSME, 30 Oct. 2024 - 中島悠; 瀬川太雄
Comparative genomic analysis of a novel marine animal symbiontic Ureaplasma
37th JSME, 29 Oct. 2024 - Masumi Hasegawa-Takano; Miho Hirai; Karin Inoue; Tsuyoshi Takano; Yu Nakajima; Susumu Yoshizawa; Yosuke Nishimura
Spatiotemporal metagenomic surveys uncovered diverse microbial communities in mangrove sediments
ISME19 - Yu Nakajima
Ecogenomics of multiple rhodopsin encoding prokaryotes inhabiting marine environment
Marine Microbes 2024 Gordon Research Seminar, 08 Jun. 2024 - Nakajima, Y; Sato, Y; Ohkubo, S; Hirai, M; Urayama, S-I; Okano, K; Kimura, H; Honda, K; Nunoura, T; Nobu, M., K; Tamaki, H; Takai, K
Tera base hot spring metagenomes illuminate novel and diverse microbiomes
The Fifth meeting of Bergey’s International Society for Microbial Systematics (BISMiS), 07 Nov. 2023 - Nakajima, Y; Sato, Y; Ohkubo, S; Hirai, M; Okano, K; Kimura, H; Honda, K; Nobu, M., K; Tamaki, H; Takai, K
Tera base hot spring metagenomes illuminate novel and diverse microbiomes
17th SAME Symposium of Aquatic Microbial Ecology, 22 Aug. 2023 - 佐藤 悠; 中島 悠; 大久保 智司; 岡野 憲司; 木村 浩之; 本田, 孝祐
深部流体に含まれる微生物の多様性と代謝特性
日本微生物生態学会 第35回大会, 01 Nov. 2022 - 小林 香苗, 眞壁 明子, 中島 悠, 平岡 聡史, 宮崎 征行, 津田 美和子, 澄田 智美, 野牧 秀隆, 布浦 拓郎, 川口 慎介
深海表層堆積物中の窒素代謝を担う微生物の鉛直分布と窒素循環への寄与の評価
日本微生物生態学会 第35回大会, 01 Nov. 2022 - 中島 悠; 中原 望; 玉木 秀幸
イルカ口腔内に共生する特異な細菌群集
日本微生物生態学会 第35回大会, 01 Nov. 2022 - 中島悠
多様なロドプシン保有微生物の光利用戦略
第63回日本植物生理学会関連集会 原核光合成生物シンポジウム, 21 Mar. 2022, [Invited] - 中島悠; Masaru Konishi Nobu; 西村 陽介; 吉澤 晋; 玉木 秀幸
暗黒環境の光受容体？機能未知ロドプシンを保有する微生物の比較ゲノム解析
日本微生物生態学会 第34回大会, 31 Oct. 2021 - 中島悠; 微生物生態学会若手会世話人
私の考える最強のラボ選手権
日本微生物生態学会 第34回大会, 30 Oct. 2021 - 長谷川万純; 保坂俊彰; 小島慧一; 西村陽介; 中島 悠; 染谷友美; 白水美香子; 須藤雄気; 吉澤晋
シアノバクテリアの光合成とは異なる光利用：シアノロドプシンの発見
日本地球化学会 第 67 回オンライン年会, 19 Nov. 2020 - 岡崎友輔; 中島悠; 井上真男; 金子博人; 志野裕亮; 峯田航; 山下大祐; 熊谷洋平
微生物生態学の最前線
日本地球化学会 第 67 回オンライン年会, 19 Nov. 2020 - 永田 崇; 烏山 昌幸; 竹内 一郎; 中島 悠; 吉澤 晋; 井上 圭一
Mutational analysis of the mechanism of an absorption red shift in a marine bacterial Cl–-pumping rhodopsin
第58回日本生物物理学会年会 - Yu Nakajima; Keiichi Kojima; Satoko Doi; Yuichiro Kashiyama; Ryosuke Nakai; Yuki Sudo; Kazuhiro Kogure; Susumu Yoshizawa
Is the possession of retinal-synthesis gene (blh) essential for the function of rhodopsin?
16th SAME Symposium of Aquatic Microbial Ecology, 01 Sep. 2019 - Susumu Yoshizawa; Yu Nakajima; Kazuhiro Kogure
A haloarchaeal halorhodopsin-like Cl– pump in marine bacteria
17th International Symposium on Microbial Ecology (ISME17), 12 Aug. 2018 - Yu Nakajima; Satoko Doi; Keiichi Kojima; Yuki Sudo; Kazuhiro Kogure; Susumu Yoshizawa
Is the retinal-synthesizing gene (blh) essential for rhodopsin-containing bacteria?
32th JSME, 11 Jul. 2018 - Yu Nakajima; Susumu Yoshizawa; Kazuhiro Kogure
ロドプシンを保有するUltra-small actinobacteriaの光利用戦略
環境微生物系学会合同大会2017, 29 Aug. 2017 - 中島悠; 吉澤晋; Edward; F. DeLong; 木暮一啓
複数のロドプシンを保有する細菌の比較トランスクリプトーム解析
水圏微生物研究フォーラム2016, 09 Aug. 2016 - Yu Nakajima; Susumu Yoshizawa; Kazuhiro Kogure
プロテオロドプシン保有発光細菌における発光量の調節
BMB2015, 01 Dec. 2015 - Yu Nakajima; Susumu Yoshizawa; Kazuhiro Kogure
Physiological advantage of bacteria possessing multiple rhodopsins
14th SAME Symposium for Aquatic Microbial Ecology, 23 Aug. 2015 - Yu Nakajima; Susumu Yoshizawa; Kazuhiro Kogure
Physiological advantage of Rhodopsin-possessing bacteria: unseen residents of marine euphotic zone
Kyoto University International workshop Microbes beyond borders, 05 Mar. 2015 - Yu Nakajima; Susumu Yoshizawa; Kazuhiro Kogure
Vibrio属細菌におけるプロテオロドプシンの活性評価および生理的役割の解明
29th JSME, 22 Nov. 2013 - Yu Nakajima; Susumu Yoshizawa; Kazuhiro Kogure
Quantification of the proton pump activity of proteorhodopsin in Vibrio campbellii
13th SAME Symposium for Aquatic Microbial Ecology, 08 Sep. 2013 - 山田崇人; 中島悠; 江崎和音; 篠木新吾; 正田亜八香; 横山広美; 他BAP collaboration
大学院生出張授業プロジェクト(BAP) 活動報告III
日本物理学会第69回年次大会, 27 Mar. 2013
