Microbial Systems biology lab


Microbial Systems Biology Laboratory

at the Graduate School of Pharmaceutical Sciences, Kyoto University


Latest updates

April 7

This week Tristan Edwards is joining us for an internship while on exchange from ULC (London) Welcome aboard!

April 2

This week we welcome two new students: Mitsuki Suzuki (iD2) and Misaki Sasayama (B4) both joined the MSB lab. Welcome aboard!

March 26 (graduation week)

Congratulations to Yukiko and Yusuke for the successful completion of their Master's and Bachelor's degree, respectively!

All the best for the next step!

December 11

We are just back from the Molecular Biology Society of Japan conference held last week in Kobe (December 6-8). Three successful poster presentations by Yukiko (M2), Yifan (D1) and Ryunosuke (D2). お疲れ様。


November 24

M. Robert presented at BACELL 2023 in Kobe last week: A short talk about "Biofilming beyond B. subtilis" at this international conference on B. subtilis mainly held in Europe but this year in Japan. A very well organized event. #BACELL

September 29

Ryunosuke Sakai (D2 student) won one of the poster awards for his presentation at the Third Research Networking Salon co-organized by the Faculties of Medicine, Pharmaceutical Sciences, and Biostudies at Kyoto University on September 27-29. Great that his imaging system attracted interest!

Networking Salon web site

September 20

Martin Robert was in Asamushi, Aomori for the popular inter-university Interactive short course in marine biology. A great success after a four-year hiatus. A total of 32 students from Tohoku University, University of Tokyo, University of Tsukuba, and Kyoto University participated in this immersive and unique science experience in beautiful Asamushi.

July 7, 2023 (Happy Tanabata!)

Three students and MR represented the MSB lab at the 19th E. coli workshop in beautiful Yunohama onsen, Yamagata. Very fruitful event! https://ecolimtg2023.wixsite.com/main #大腸菌研究会

April 14, 2023

Last week Yusuke Hoshiba officially joined the MSB lab as a B4 undergraduate student.

Welcome aboard!

March 24, 2023 (Graduation day)

Congratulations to Yifan Zhao, our B4 student graduating this spring with a Bachelor degree in Pharmaceutical Sciences!

Stay tuned as he will continue with us for his Ph.D, degree from April.

Youtube video of a presentation for the TEDxTohokuUniversity 2020 conference about the Hidden Life of bacteria. 

News about the conference

We believe microorganisms can help us answer big questions about living processes and organisms

What we do

We study the simple model bacterium E. coli, through its genes, proteins and metabolites and how they interact in the living cell. We aim at a better understanding of bacterial metabolic function, a fundamental cellular process that is deeply connected to all other cellular activities.  All energy and mass/molecular transformations happening in the cell are what metabolism is all about.  We are also trying to better understand how metabolic function is reorganised during adaption to new environments, during growth in large colonies and biofilms, Finally, we hope to uncover how the dynamics of bacterial populations are shaped by cell-cell and metabolic interactions.

While these are fundamental research objectives, they have broad potential applications for metabolic engineering and human/animal health because E. coli is a major ally for bio-production and for human digestive and metabolic function.

With E. coli we can perform experiments safely, rapidly, and conveniently often in a matter of hours or days, a task that could otherwise take weeks, months, if not years, using most other organisms. Moreover, basic functional discoveries made in E. coli can usually apply to most other living organisms.


We are interested in bacterial metabolism, the study of mass and energy transfer in the cell in the form of biochemical reactions.

Complex systems

Complex systems are made up of many components that interact and generate non-intuitive behavior displaying properties that the individual components do not. Bacterial collectives are part of this, as are insect colonies, brains,  societies, etc.

Biofilm development

Biofilms are structures formed by microorganisms when growing in large colonies that result in the production of a complex extracellular matrix. Biofilms have unique properties that are thought to protect the cells from various environmental challenges.


Keywords: E. coli, metabolomics, proteomics, biochemistry, biofilms, cellular dynamics, systems biology, complex systems, socio-biology, adaptive evolution

M. Robert 2021-2023