Updated on 2025/04/18

写真a

 
MACHIDA, Koshi
 
Affiliation
Faculty of Science and Engineering, School of Advanced Science and Engineering
Job title
Assistant Professor(non-tenure-track)

Research Areas

  • Molecular biology
 

Papers

  • Cultivation of previously uncultured sponge-associated bacteria using advanced cultivation techniques: A perspective on possible key mechanisms

    Dawoon Jung, Koshi Machida, Yoichi Nakao, Jeffrey S. Owen, Shan He, Tomonori Kindaichi, Akiyoshi Ohashi, Yoshiteru Aoi

    Frontiers in Marine Science   9  2022.08

     View Summary

    Most of the microbes from natural habitats cannot be cultivated with standard cultivation in laboratory, and sponge-associated microbes are no exception. We used two advanced methods based on a continuous-flow bioreactor (CF) and in situ cultivation (I-tip) to isolate previously uncultivated marine sponge-associated bacteria. We also characterized the physiological properties of the isolates from each method and attempted to clarify the mechanisms operating in each cultivation method. A greater number of novel bacteria were isolated using CF and in situ cultivation compared to standard direct plating (SDP) cultivation. Most isolates from CF cultivation were poor growers (with lower specific growth rates and saturated cell densities than those of isolates from SDP cultivation), demonstrating that it is effective to carry out pre-enrichment cultivation targeting bacteria that are less competitive on conventional cultivation, especially K-strategists and bacterial types inhibited by their own growth. Isolates from in situ cultivation showed a positive influence on cell recovery stimulated by chemical compounds in the extract of sponge tissue, indicating that some of the bacteria require a “growth initiation factor” that is present in the natural environment. Each advanced cultivation method has its own distinct key mechanisms allowing cultivation of physiologically and phylogenetically different fastidious bacteria for cultivation compared with conventional methods.

    DOI

    Scopus

    5
    Citation
    (Scopus)
  • Mutualistic relationship between Nitrospira and concomitant heterotrophs.

    Chiho Murakami, Koshi Machida, Yoichi Nakao, Tomonori Kindaichi, Akiyoshi Ohashi, Yoshiteru Aoi

    Environmental microbiology reports   14 ( 1 ) 130 - 137  2022.02  [International journal]

     View Summary

    Nitrifying chemoautotrophs support the growth of diverse concomitant heterotrophs in natural or engineered environments by supplying organic compounds. In this study, we aimed to investigate this microbial association, especially (i) to distinguish whether the relationship between nitrifying chemoautotrophs and heterotrophs is commensal or mutualistic, and (ii) to clarify how heterotrophs promote the growth of autotrophic nitrite-oxidizing bacteria (Nitrospira). Pure cultured Nitrospira (Nitrospira sp. ND1) was employed in this study. Heterotrophs growing with metabolic by-products of Nitrospira as a sole carbon source were isolated from several environmental samples and used to test the growth-promoting activity of Nitrospira. Furthermore, liquid chromatography-mass spectrometry analysis was conducted to evaluate how heterotrophs consumed chemical compounds produced by Nitrospira and newly produced during co-cultivation. Notably, Nitrospira growth was stimulated by co-cultivation with some heterotrophs and the addition of spent media of some strains, suggesting that not only heterotrophs but also Nitrospira received benefits from their mutual co-existence. Furthermore, the data suggested that some of the growth-promoting heterotrophs provided as-yet-unidentified growth-promoting factors to Nitrospira. Overall, Nitrospira and heterotrophs thus appear to exhibit a mutualistic relationship. Such mutualistic relationships between autotrophs and heterotrophs would contribute to the stability and diversity of microbial ecosystems.

    DOI PubMed

    Scopus

    6
    Citation
    (Scopus)
  • Triggering Growth via Growth Initiation Factors in Nature: A Putative Mechanism for in situ Cultivation of Previously Uncultivated Microorganisms.

    Dawoon Jung, Koshi Machida, Yoichi Nakao, Tomonori Kindaichi, Akiyoshi Ohashi, Yoshiteru Aoi

    Frontiers in microbiology   12   537194 - 537194  2021  [International journal]

     View Summary

    Most microorganisms resist cultivation under standard laboratory conditions. On the other hand, cultivating microbes in a membrane-bound device incubated in nature (in situ cultivation) can be an effective approach to overcome this limitation. In the present study, we applied in situ cultivation to isolate diverse previously uncultivated marine sponge-associated microbes and comparatively analyzed this method's efficiencies with those of the conventional method. Then, we attempted to investigate the key and previously unidentified mechanism of growing uncultivated microorganisms by in situ cultivation focusing on growth triggering via growth initiation factor. Significantly more novel and diverse microbial types were isolated via in situ cultivation than by standard direct plating (SDP). We hypothesized that some of environmental microorganisms which resist cultivation are in a non-growing state and require growth initiation factors for the recovery and that these can be provided from the environment (in this study from marine sponge). According to the hypothesis, the effect of the sponge extract on recovery on agar medium was compared between strains derived from in situ and SDP cultivation. Adding small amounts of the sponge extracts to the medium elevated the colony-formation efficiencies of the in situ strains at the starvation recovery step, while it showed no positive effect on that of SDP strains. Conversely, specific growth rates or saturated cell densities of all tested strains were not positively affected. These results indicate that, (1) the sponge extract contains chemical compounds that facilitate recovery of non-growing microbes, (2) these substances worked on the in situ strains, and (3) growth initiation factor in the sponge extract did not continuously promote growth activity but worked as triggers for regrowth (resuscitation from non-growing state).

    DOI PubMed

    Scopus

    14
    Citation
    (Scopus)
  • Peptide precursors that acquire denatured collagen-hybridizing ability by O-to-N acyl migration at physiological pH.

    Sayaka Kanai, Koshi Machida, Ryo Masuda, Takaki Koide

    Organic & biomolecular chemistry   18 ( 15 ) 2823 - 2827  2020.04  [International journal]

     View Summary

    Here, we report peptide probes with either single or cyclic double stranded collagen-like sequences that spontaneously acquire collagen-hybridizing ability at physiological pH. These peptides have ester bonds derived from O-acyl isopeptide units that are converted to amide bonds via intramolecular O-to-N acyl migration by a pH shift. The peptides that do not require pre-treatment for disassembly will be useful as prodrugs in theranostic treatments targeting unfolded collagen.

    DOI PubMed

    Scopus

    5
    Citation
    (Scopus)
  • Sameuramide A, a new cyclic depsipeptide isolated from an ascidian of the family Didemnidae.

    Koshi Machida, Daisuke Arai, Ryosuke Katsumata, Satoshi Otsuka, Jun K Yamashita, Tao Ye, Shoubin Tang, Nobuhiro Fusetani, Yoichi Nakao

    Bioorganic & medicinal chemistry   26 ( 13 ) 3852 - 3857  2018.07  [International journal]

     View Summary

    Sameuramide A (1), a new cyclic depsipeptide encompassing one each of alanine, N-methyl alanine, N-methyl dehydroalanine, N,O-dimethyl threonine, phenyllactic acid, three β-hydroxy leucines, and two propionates, was isolated from a didemnid ascidian collected at the northern part of Japan. The planar structure was established based on the interpretation of MS and NMR data. The absolute configuration of the subunits was determined by the advanced Marfey's method and the chiral LC-MS analysis. Compound 1 exhibited the activity of maintaining colony formation of murine embryonic stem (mES) cells without leukemia inhibitory factor (LIF). Down regulation of the gene expression of Krüppel-like transcription factor 4 (Klf4) indicated that 1 itself was not able to maintain the undifferentiated state of the mES cells. However, the expression levels of the marker genes (Nestin, T, Sox17) for three germ layers were upregulated in embryoid bodies (EBs) after treatment of 1 together with LIF, suggesting that 1 plays a supportive role for LIF in maintaining the multipotency of mES cells.

    DOI PubMed

    Scopus

    11
    Citation
    (Scopus)
  • Dolabellol A, a New Halogenated Diterpene Isolated from the Opisthobranch Dolabella auricularia

    Koshi Machida, Takuro Matsumoto, Nobuhiro Fusetani, Yoichi Nakao

    CHEMISTRY LETTERS   46 ( 11 ) 1676 - 1678  2017.09

     View Summary

    A new halogenated diterpene, dolabellol A (1), was isolated from the opisthobranch Dolabella auricularia. The planar structure of dolabellol A was elucidated by NMR spectroscopic analysis and chemical reactions. The absolute stereochemistry was determined by single-crystal X-ray diffraction studies.

    DOI

    Scopus

    6
    Citation
    (Scopus)
  • Cinanthrenol A, an estrogenic steroid containing phenanthrene nucleus, from a marine sponge Cinachyrella sp.

    Koshi Machida, Takahiro Abe, Daisuke Arai, Mayumi Okamoto, Isao Shimizu, Nicole J de Voogd, Nobuhiro Fusetani, Yoichi Nakao

    Organic letters   16 ( 6 ) 1539 - 41  2014.03  [International journal]

     View Summary

    Cinanthrenol A (1), a new steroid composed of a phenanthrene and a spiro[2,4]heptane system, was isolated from the marine sponge Cinachyrella sp. It is the first phenathrene-containing steroid with estrogen activity.

    DOI PubMed

    Scopus

    23
    Citation
    (Scopus)

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Research Projects

  • Integrated platform for analyzing the modes of actions of natural products

    Japan Society for the Promotion of Science  Grants-in-Aid for Scientific Research

    Project Year :

    2021.04
    -
    2024.03
     

  • International collaborative study on foods, microbiota, and life style diseases of Asians

    Japan Society for the Promotion of Science  Grants-in-Aid for Scientific Research

    Project Year :

    2020.10
    -
    2024.03
     

  • Search for bioactive compounds from unutilized microbes of marine sponge

    Japan Society for the Promotion of Science  Grants-in-Aid for Scientific Research

    Project Year :

    2020.04
    -
    2023.03
     

Misc

  • 難培養性微生物Nitrospiraに共存する従属栄養細菌による増殖促進メカニズムの解明

    村上千穂, 村上千穂, 金田一智規, 町田光史, 中尾洋一, 大橋晶良, 青井議輝

    日本微生物生態学会大会(Web)   33rd  2019

    J-GLOBAL

  • 新規環状デプシペプチドsameuramide Aの生物活性

    町田光史, 勝俣亮介, 新井大祐, 大塚悟史, 山下潤, TANG Shoubin, YE Tao, 中尾洋一, 中尾洋一

    日本分子生物学会年会プログラム・要旨集(Web)   42nd  2019

    J-GLOBAL

  • 新規天然化合物shinanthrene Aとそのエストロゲン活性

    町田光史, 岡本真由美, 清水功雄, 新井大祐, 伏谷伸宏, 中尾洋一

    日本分子生物学会年会プログラム・要旨集(Web)   36th  2013

    J-GLOBAL

  • Shinanthrene Aの立体化学研究と生物活性

    町田光史, 岡本真由美, 清水功雄, 中尾洋一

    日本化学会講演予稿集   93rd ( 4 )  2013

    J-GLOBAL

 

Syllabus

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Internal Special Research Projects

  • 発酵味噌からの抗高血圧活性物質の探索

    2024  

     View Summary

    高血圧は日本における代表的な生活習慣病であり、多くの人々が悩まされている。高血圧は心血管疾患のリスクを高め、健康寿命を脅かす要因のひとつとされている。したがって、日常的に高血圧の予防や悪化を防ぐ食品成分を摂取することが重要である。日本の伝統的な大豆発酵食品である醤油、味噌、納豆には、アンジオテンシン変換酵素(ACE)阻害作用があり、血圧上昇を抑制する効果があることが知られている。ACEはレニン-アンジオテンシン系において中心的な役割を果たす酵素であり、アンジオテンシンIを血管収縮作用の強いアンジオテンシンIIに変換し、血管拡張物質であるブラジキニンを不活化させることで血圧を上昇させる。これまでに、大豆発酵食品に含まれるACE阻害ペプチドとして、ニコチアナミン、Ser-Trp、Phe-Phe-Tyr-Tyr、Ile-Ala-Valなどが報告されており、それらの半数阻害濃度(IC50)は1.9 μMから880 μMの範囲にある。本研究では、新たな機能性食品成分の探索の一環として、味噌からACE阻害活性を持つ成分を探索した。ODSフラッシュカラムクロマトグラフィーを用いた分画により、70%メタノールで溶出されたFr.15-5がACE阻害活性を示すことが明らかになった。一方で、これまで報告されている味噌由来のACE阻害ペプチドは、30%メタノールで溶出されていたことから、Fr.15-5は既知のペプチドとは極性が異なる成分を含むと考えられる。この結果は、味噌に含まれるACE阻害成分が多様であり、これまで知られていなかった新規成分が存在する可能性を示唆している。今後、Fr.15-5に含まれる有効成分の構造解析が進めば、より高機能な高血圧予防食品の開発につながることが期待される。