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Naoto Tanaka Professor |
From Graduate School 【 display / non-display 】
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Tokyo University of Agriculture Doctoral program (second term) Completed
1998.04 - 2001.03
Country：Japan
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Tokyo University of Agriculture Doctoral program (first term) Completed
1996.04 - 1998.03
Country：Japan
Degree 【 display / non-display 】
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博士（農芸化学） ( 2001.03 東京農業大学 )
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修士（農芸化学） ( 1998.03 東京農業大学 )
Employment Record in Research 【 display / non-display 】
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Tokyo University of Agriculture Faculty of Applied Bio-Science Department of Applied Biology and Chemistry
2001.04 - 2001.06
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Tokyo University of Agriculture Faculty of Applied Bio-Science Culture Collection Center Lecturer
2007.04 - 2010.09
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Tokyo University of Agriculture Graduate School of Agriculture Department of Environmental Symbiotic Studies Lecturer
2009.04 - 2010.09
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Tokyo University of Agriculture Graduate School of Agriculture Department of Environmental Symbiotic Studies Associate Professor
2010.10 - 2013.03
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Tokyo University of Agriculture Faculty of Applied Bio-Science Associate Professor
2010.10 - 2015.03
Papers 【 display / non-display 】
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Magnesium enhances the expression of arthroconidia-related genes in Trichosporon asahii Reviewed International journal
K. Aoki, M. Matsutani, M. Ohkuma, T. Sugita, Y. Kobayashi, N. Tanaka, M. Takashima
Microbiol Spectr 14 ( 7 ) e0345925 2026.06
Language：English Publishing type：Research paper (scientific journal)
Trichosporon asahii is a pleomorphic basidiomycetous yeast that causes deep-seated mycoses in immunocompromised individuals. T. asahii exhibits three morphological types: hyphae, yeasts, and arthroconidia. Hyphal formation is related to virulence and is accelerated by the addition of magnesium. However, the effects of magnesium on gene expression have not been elucidated. In this study, we aimed to investigate whether gene expression is affected by magnesium. RNA sequencing and genetic analyses revealed that magnesium addition increased the expression of genes related to arthroconidia formation in T. asahii. We identified 11 magnesium-enhanced expression (mee) genes, whose expressions increased more than 5-fold. Deletion of mee4, mee5, mee6, and mee11 decreased arthroconidia formation. Furthermore, increased mee6 expression depended on mee4 and mee5, which lie downstream of the TOR pathway, and increased mee11 expression depended on mee4. In addition, mee11 inhibited the expression of other mee genes, and mee6 inhibited the expression of mee4. Overall, we identified a gene expression network related to arthroconidia formation in T. asahii, providing insights into the transition from hypha to arthroconidia and enhancing our understanding of fungal pathogenesis.
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Qipengyuania triglochinis sp. nov. and Alteriqipengyuania triglochinis sp. nov.: two novel Erythrobacteraceae members isolated from rhizosphere and root in Triglochin maritima L. Reviewed International journal
Kosuke Yamamoto, Fumiya Watanabe, Riku Murakami, Hinako Kubo, Takao Iino, Moriya Ohkuma, Minenosuke Matsutani, Hikaru Sakamoto, Hiromasa Saitoh and Naoto Tanaka
International Journal of Systematic and Evolutionary Microbiology 76 ( 4 ) 1 - 10 2026.04
Language：English Publishing type：Research paper (scientific journal) Publisher：Microbiology Society
Two novel bacterial strains, designated as strains 483ᵀ and 357ᵀ, were isolated from the rhizosphere and root, respectively, of Triglochin maritima L. collected from Lake Notoro, Hokkaido, Japan. Strain 357ᵀ was motile, whereas strain 483ᵀ was non-motile. Both strains grew at 10–40 °C (optimum, 30 °C), pH 5.5–9.0 (optimum, pH 6.0) and 0–15.94% (w/v) NaCl (optimum, 1.94%). Based on 16S rRNA gene sequences, strain 483ᵀ was most similar to Qipengyuania aestuarii GH1ᵀ (99.7%), while strain 357ᵀ was closely related to Alteriqipengyuania abyssalis NZ-12Bᵀ and Alteriqipengyuania lutimaris S-5ᵀ (both 98.7%). Phylogenetic analysis based on 16S rRNA gene sequences revealed that strains 483ᵀ and 357ᵀ clustered with Q. aestuarii GH1ᵀ and A. abyssalis NZ-12Bᵀ, respectively. Whole-genome phylogeny showed consistent results. DNA G+C contents were 59.9 mol% (strain 483ᵀ) and 65.4 mol% (strain 357ᵀ). The average nucleotide identity (ANI), fastANI and digital DNA–DNA hybridization values between the novel strains and their closest relatives were 82.8–85.5%, 82.8–85.5% and 25.2–26.3%, respectively. Both strains contained ubiquinone-10 as the sole respiratory quinone. The major fatty acids in strain 483ᵀ were C14 : 0 2-OH and summed feature 8 (C18 : 1 ω7c), differing from Q. aestuarii. In strain 357ᵀ, C17 : 1 ω6c and summed feature 8 predominated, similar to A. abyssalis and A. lutimaris. Polar lipids of strain 483ᵀ were mainly phosphatidylcholine, phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol, sphingoglycolipid and five unidentified lipids, whereas strain 357ᵀ mainly contained phosphatidylcholine, phosphatidylglycerol, diphosphatidylglycerol, sphingoglycolipid and three unidentified lipids. Based on these results, strains 483ᵀ and 357ᵀ represent novel species of Qipengyuania and Alteriqipengyuania, for which the names Qipengyuania triglochinis sp. nov. and Alteriqipengyuania triglochinis sp. nov. are proposed. The type strains are strain 483ᵀ (=NRIC 2006ᵀ=JCM 36263ᵀ=NCIMB 15619ᵀ=DSM 120134T) and strain 357ᵀ (=NRIC 2005ᵀ=JCM 36262ᵀ=NCIMB 15618ᵀ=DSM 120133T).
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Phylogenomic insights into Taphrinomycotina and genomic features of Saitoella coloradoensis based on whole-genome sequencing at the chromosome level, with a proposal of the new class Saitoellomycetes Reviewed International journal
Yuuki Kobayashi, Junta Sugiyama, Rahul Sk , Yuh Shiwa, Keita Aoki, Naoto Tanaka, Masako Takashima
Micologia 28 1 - 18 2026.01
Language：English Publishing type：Research paper (scientific journal) Publisher：Taylor $ Francis
Taphrinomycotina, a subphylum of the phylum Ascomycota, comprises fungi with diverse morphologies and ecologies. Saitoella and Savitreella are genera of red-colored yeasts within Taphrinomycotina, but their precise phylogenetic positions have remained controversial. In this study, we sequenced the whole genomes of Saitoella coloradoensis and Savitreella phatthalungensis in order to elucidate their phylogenetic relationships using a phylogenomic approach based on chromosome-level genome assemblies generated by long-read sequencing technologies. Our phylogenetic analyses suggest that Saitoella is distinct from all currently described classes within Taphrinomycotina, whereas Savitreella seems to belong to the class Taphrinomycetes. Furthermore, Saitoella shares high average amino acid identity with all other classes in Taphrinomycotina, suggesting that it retains ancient gene sequences. Our findings enable us to propose a new class, order, and family-namely, Saitoellomycetes, Saitoellales, and Saitoellaceae-automatically typified by the genus Saitoella. Our chromosome-level assembly reveals that Saitoella coloradoensis possesses 38 chromosomes, the highest number of chromosomes among fungi reported to date. We also identify structural differences between two Saitoella species and a chromosome structure lacking the canonical palindromic centromeric repeat sequence.
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Chromosome-resolved genome assemblies of Rhodotorula toruloides reveal abnormal chromosomal evolution under artificial culture conditions Reviewed International journal
Yuuki Kobayashi, Moriya Ohkuma, Keita Aoki, Naoto Tanaka, Masako Takashima
scientific reports 16 1732 2025.12
Language：English Publishing type：Research paper (scientific journal) Publisher：Nature Portfolio
Rhodotorula toruloides is a basidiomycete yeast known for accumulating lipids within its cells. Owing to its oil-producing potential, many strains of this species have been isolated and studied. However, substantial genetic diversity has been reported within this species, making the true taxonomic boundaries of R. toruloides ambiguous. In this study, we sequenced the whole genomes of multiple strains of R. toruloides and related species, generated complete chromosome-level assemblies, and conducted comparative analyses. We found that the genomes of Rhodotorula and Rhodosporidiobolus generally comprise 17 chromosomes with conserved chromosomal synteny. However, some strains of R. toruloides exhibited chromosomal shuffling. Notably, several of these rearrangements were observed among strains that had diverged under laboratory conditions, suggesting that irregular structural mutations occurred in artificial culture environments. Our findings revealed such abnormal chromosomal evolution under artificial conditions and underscore the potential for cryptic mutations, which are undetectable by phenotype or gene sequence comparisons, to arise in laboratory strains. We also found that the genome of the haploid strain NP11, which is a descendant of the type strain of R. toruloides, comprises only one parental genome.
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2025年シンポジウム「微生物の分離とその利活用─食と健康へのアプローチ─」
田中 尚人
日本微生物資源学会誌 41 ( 2 ) 100 - 102 2025.12
Books and Other Publications 【 display / non-display 】
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田中尚人（ Role： Joint author , 東京農業大学の乳酸菌コレクション）
(株)エヌ・ティー・エス 2023.09 （ ISBN:978-4-86043-858-6 ）
Language：Japanese Book type：General book, introductory book for general audience
生物資源として、生きた研究材料として重要性が高まる中、研究の発展に寄与する微生物資源の利活用について解説している。また、微生物メタゲノム情報の解析や環境サンプルの直接研究により明らかになりつつ微生物の多様性・生態について記載している。
Misc 【 display / non-display 】
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公益財団法人発酵研究所 学会・研究部会助成 駒形和男先生追悼公開シンポジウム 「新たな時代を拓く微生物分類学：現状と展望」
田中 尚人, 飯野 隆夫, 石田 達也, 伊藤 隆, 乙黒 美彩, 河地 正伸, 鈴木 誠, 高島 昌子
日本微生物資源学会誌 39 ( 1 ) 41 - 45 2023
Authorship：Lead author, Corresponding author Language：Japanese Publishing type：Meeting report Publisher：日本微生物資源学会
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乳酸菌を分離するための基本 Invited Reviewed
田中尚人
日本乳酸菌学会誌 30 ( 1 ) 3 - 7 2019.03
Authorship：Lead author Language：Japanese Publishing type：Article, review, commentary, editorial, etc. (scientific journal)
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ユーザーの求める機能性乳酸菌株のオンライン選抜システムの開発
田中尚人，宮崎智，鈴木智典，冨田理，梶川揚申，内野昌孝，五十君靜信，岡田早苗
日本微生物資源学会誌 33 ( 1 ) 31 - 37 2017.06
Authorship：Lead author Language：English Publishing type：Rapid communication, short report, research note, etc. (scientific journal)
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デルブレッキー菌は変な乳酸菌
田中尚人
生物工学会会誌 95 ( 4 ) 207 2017.04
Language：Japanese Publishing type：Article, review, commentary, editorial, etc. (bulletin of university, research institution)
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これからのハラール研究
阿部尚樹、内野昌孝、野口治子、田中尚人、岡大貴
食品機械装置 2016.05
Authorship：Lead author Language：Japanese Publishing type：Article, review, commentary, editorial, etc. (trade magazine, newspaper, online media)
Past of Cooperative Research 【 display / non-display 】
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発酵食品由来微生物の分類学的研究
2014.09 - 2017.03
独立行政法人製品評価技術基盤機構 国内共同研究 Cooperative Research within Japan
国内外発酵食品由来乳酸菌の系統分布の解析および新種提唱
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新規機能性乳酸菌資源開発の共同事業
2011.08 - 2014.03
独立行政法人製品評価技術基盤機構 国内共同研究 Cooperative Research within Japan
モンゴルの乳酸菌の分離及び系統解析による系統的分布と応用利用のための性状解析
Presentations 【 display / non-display 】
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Comparative genomics for reclassification of Stenotrophomonas maltophilia reference strains and biovar II group International conference
2022.03
Event date： 2022.03
Language：Japanese Presentation type：Oral presentation (general)
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Characterization of biofilm formation and constituent bacterial species by addition of siderophores to environmental samples International conference
2022.03
Event date： 2022.03
Language：Japanese Presentation type：Oral presentation (general)
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Analysis of mating-type loci of Cutaneotrichosporon cavernicola strains by comparative genomics International conference
2022.03
Event date： 2022.03
Language：Japanese Presentation type：Oral presentation (general)
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Effects of biodegradable plastic on river microbiome International conference
2019.03
Event date： 2019.03
Language：Japanese Presentation type：Oral presentation (general)
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Effects of bacterial community in the river water by degradation of bioplastic International conference
2019.03
Event date： 2019.03
Language：Japanese Presentation type：Oral presentation (general)
Committee Memberships 【 display / non-display 】
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日本微生物資源学会 理事（会計）
2014.09
Committee type：Academic society
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日本微生物資源学会 理事（編集副委員長）
2009.04 - 2014.08
Committee type：Academic society
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日本微生物系統分類研究会 理事（会計）
2008.01 - 2015.03