Laboratory of applied microbiology


1-1 Rokkodai, Nada, Kobe 657-8501, Japan
Applied Microbiology, Bioproduction
Department of Science, Technology and Innovation
Graduate School of Science,Technology and Innovation
Kobe University Graduate School of Science,Technology and Innovation
Department of Agriculture BACELL meeting 2023 homepage

About US

Welcome! The Laboratory of applied microbiology, APPLMIC is engaged in reseach on bacteria with potential for biotechnological application.
Our research interests are:
・Basic research : elucidation of the function of beneficial genes in bacteria
・Applied Research : Microbial production of useful chemicals

We aim to create "new microbiology" with the latest technology and free thinking. Innovation starts here!!!


Ken-ichi YOSHIDA, Ph.D.

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Research interest:Professor Yoshida has been expanding his research broadly from Bacillus species to rhizobia and working on the elucidation of new metabolic pathways in bacteria. In particular, Prof.Yoshida is internationally recognized as a pioneer of research on bacterial inositol metaboism. For years, Prof. Yoshida has worked as a core member of iBioK programme to promote industry-academia collaboration. He is also working hard to promote the Kobe univisity to the European countries as an FEMS ambassador*, and as a general manager of Kobe University Brussels European Centre.


*Federation of European Microbiological Societies (FEMS) have commenced the creation of a network of honorary FEMS Ambassadors in selected non-European countries. As one of the FEMS Ambassadors, Prof. Ken-ichi Yoshida will help to promote the FEMS mission, vision, and activities of spreading microbiology knowledge, and connecting microbiologists and microbiological societies for benefit of humankind.

Academic Degree1987 Bachelor, Kyoto University
1989 Master, Kyoto University
1993 Ph. D.(Doctor of Agriculture), Kyoto University
Career1990 Assistant professor, Fukuyama University
1996-1997 Postdoc, INRA Jouy-en-Josas
1999 lecturer Fukuyama University
2003 Assosiate Professor, Fukuyama University
2004 Assosiate Professor, Kobe Unisersity
2009 Professor ,Kobe University
2013 Director, Center for EU Studies
2014 Executive director, Brussels European Centre, Kobe University
Affiliated academic organizations日本ゲノム微生物学会(庶務幹事)/日本農芸化学会(関西支部参与・全国代議員)/日本分子生物学会/日本生物工学会/植物微生物研究会/グラム陽性菌ゲノム機能会議/米国微生物学会(ASM)


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Research interest: Dr. Ishikawa has been studying the molecular mechanism and functions of the bacterial genes essential for cell growth (cell division and transcription). Based on that experience, he now aims to create general-purpose high-efficiency bio-process cells. In addition, he is developing a mothod to efficiently acquire useful bacterial genes from metagenome. He is also interested in the accelerated evolution of lactic acid bacteria.

Academic Degree1996-1999 Department of Applied Biology, Faculty of Textile Science and Technology, Shinshu University
Career1999-2001 Researcher, The Scripps Research Institute
2001 Research Fellowship, Japan Society for the Promotion of Science (JSPS)
2001 Assistant, Nara Institute of Science and Technology
2011 Assistant professor, Nara Institute of Science and Technology
2016 Associate professor, Kobe University
Affiliated academic organizations日本ゲノム微生物学会/日本乳酸菌学会/グラム陽性菌ゲノム機能会議

ProfKen-ichi Yoshida
Associate ProfShu Ishikawa
TraineeYuzheng Wu
D2Takahiko Kondo/Eri Kitagawa
D1Jyunya Yamamoto
M2Misaki Nakatsuji/Ryo Nishimura/Kohei Makino/Kazumasa Kanda
M1Kyosuke Kita/Koutarou Mori/Takahiro Yotsui/Cho
B4Kano Uda/Mizuki Kimura/Ryotaro Kido/Kaho Fukui/Kentaro Nishioka


・2019  河端 穂奈美/倉本 夏歩/堀川 拓真/山田 拓明/Le Phuong Quynh/木田 優士/西口 智也/西田光希(休学)
田中耕生 (助教)/石田 篤志/宮野 恵/松本 明日香/八木 悠夏/Christophe Michon(研究員)
Kang Don-min/岡田 大/加藤 みずき/木下 翔也/夏目 文音/西畑 省吾/森下 智代/西川 祐資
白江雄介/久世 純子(技術補佐員)
片本 康亮/辻 省吾/本窪田 章博/Sophia Karpenko(仏AgroParisTechより短期留学)/パラスト・マジディアン(INRAより滞在)
角 美有紀/田島 慎太郎/寺川 あやこ/山野 孝太郎/Thi Lan Thanh Bien/Daniel Reuss(独Gottingen大より技術補佐員)   




We are engaged in reseach aiming at production of useful chemicals by elucidating the genomic functions of Bacillus subtilis and other useuful bacteria. Below are the research topics that we are interested in.


Inositol stands for a group of cyclohexanehexol consisting of 9 stereoisomers epimerizing the six hydroxyl groups. Among them, myo-inositol is most abundant in nature and can be supplied at relatively low prices as produced from cheap materials such as rice bran. The other inositol stereoisomers are rare and expensive, but some are known to exert specific physiological effects beneficial for human health. For example, D-chiro-inositol and pinitol (3-O-methyl-D-chiro-inositol) have an insulin-like effect to lower the blood sugar level and are also useful to cure polycystic ovary syndrome. On the other hand, scyllo-inositol has an effect to suppress the aggregation of β-amyloid in the brain, and thus is expected as a remedy for Alzheimer's disease.

●Inositol metabolism in B. subtilis

・Metabolic engineering of B. subtilis for the bio-production of rare inositol
・Understanding the mechanism of NADPH regeneration in B. subtilis
・Functional modification of inositol dehydrogenase
・Elucidation of enzymological and physiological significance of functionally unknown iolH gene

We have established metabolic engineering of B. subtilis to convert myo-inositol into scyllo-inositol, a promising therapeutic agent for Alzheimer's disease. In addition, to better understand the deeper cellular system required for the inositol conversion, we are elucidating the NADPH regeneration necessary as a coenzyme for the key enzyme IolW
An improved B. subtilis cell factory for producing scyllo-inositol, a promising therapeutic agent for Alzheimer’s disease

●Secretion of useful proteins by B. subtilis

B. subtilis cells displaying the artificially-designed cellulosome on the surface.

Cellulose and hemicellulose are main constituents of non-edible plant biomass and hardly decomposable materials. We aim to create a cellulose-degrading B. subtilis cells displaying the artificially designed cellulosome on the surface.

・Improvement of B. subtilis phytase secretion

Phytic acid is rich in rice bran as the major storage form of phosphates of cereals and legumes. We aim at improving the efficiency of secretory production of phytase, which produces myo-inositol by trimming off phosphate from phytic acid in rice bran.

●Inositol metabolism in thermophilic Geobacillus kaustophilus HTA426

・Elucidation of physiological significance of inositol metabolism in G. kaustophilus HTA426
・Regulation of the genes involved in inositol degradation in G. kaustophilus HTA426

G. kaustophilus can grow using myo-inositol as the sole carbon source. However, the genes and their regulation involved in the growth mechanism have not been fully elucidated. We are pursuing the possibility to utilize G. kaustophilus for the bio-production of rare inositol.
Three inositol dehydrogenases involved in the consumptionn and interconversion of inositol stereoisomers in a thermophilic bacterium, Geobacillus kaustophilus HTA426

●Development of efficient transformation method of thermophilic bacteria G. kaustophilus

G. kaustophilus is an industrially beneficial bacterium. Nevertheless, conventional transformation methods are inefficient and time consuming for this bacterium. We developed a novel method for transforming G. kaustophilus using conjugation plasmid pLS20cat.
A novel method for transforming the thermophilic bacterium Geobacillus kaustophilus

●Application of conjugative genetic transfer among Gram-positive bacteria

The conjugative plasmid, pLS20, isolated from B. subtilis natto, has an outstanding capacity for rapid self-transfer. In addition, it can function as a helper plasmid, mediating the mobilization of an independently replicating co-resident plasmid. The oriT sequence of pLS20cat (oriTLS20) was eliminated to obtain the plasmid, pLS20catΔoriT. pLS20catΔoriT was able to mobilize longer DNA segments, up to 113 kb of chromosomal DNA containing oriTLS20, after mixing the liquid cultures of the donor and recipient for only 15 min. This will allow us to develop a novel genetic tool for the rapid, easy, and repetitive mobilization of longer DNA segments into a recipient chromosome.
Rapid conjugative mobilization of a 100 kb segment of Bacillus subtilis chromosomal DNA is mediated by a helper plasmid with no ability for self-transfer

Bacillus velzensis S141: Promoting symbiotic nitrogen fixing capacity of soybean root nodule bacteria

Soybean symbiont Bradyrhizobium diazoefficience is known to form root nodules for a symbiotic nitrogen fixation with soybean. In a previous study, B. velzensis S141 was isolated as a plant growth-promoting rhizobacterium which enhances the beneficial effect of B. diazoefficience on soybean growth. We aim at revealing the underlying mechanism for the enhancement of the symbiotic nitrogen fixation of B. diazoefficience by B. velzensis S141, in collaboration with Suranaree University of Technology, Thailand.

●PHB production by B. diazoefficience

Soybean symbiont B. diazoefficience accumulates a large amount of poly-β-hydroxybutyrate (PHB) in cells, which is one of the promising bioplastics. PHB biosynthesis requires several enzymes involved in the synthesis and the decomposition of PHB. In addition, we found that other proteins called phasins, which stabilize the growing PHB granules, might play an important role in the PHB accumulation. We aim at elucidating the mechanism for the efficient PHB accumulation in B. diazoefficience.
PhaP phasins play a principal role in poly-β-hydroxybutyrate accumulation in free-living Bradyrhizobium japonicum
Bradyrhizobium diazoefficiens USDA110 PhaR functions for pleiotropic regulation of cellular processes besides PHB accumulation

●Transformation of Leuconostoc genus

Leuconostoc are obligatory heterofermentive lactic acid bacteria. In spite of its industrial importance, at present genetic manipulation of Leuconostoc is difficult because of its extremely low transformation efficiency. We aim at establishing its versatile transformation (mainly by protoplast method) using Leu. mesenteroides as a model organism.



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Since 2016, our lab belongs to the Graduate School of Science, Technoogy and Innovation.

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1-1 Rokkodai-cho, Nada-ku Kobe, JAPAN 657-8501
Graduate School of Science,Technology and Innovation

TEL: 078-807-5474
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1-1 Rokkodai, Nada, Kobe 657-8501, Kobe University, Graduate School of Agriculture Building E 6th Floor E601:labolatory, E654:professor's office

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