Just published!: Sakai, R., Zhao, Y. and Robert, M. LOTUS: A low-cost time-lapse automated imaging system for spatio-temporal analysis of microbial colony or biofilm development. PLOS ONE 21, e0339652 (2026).
We study the simple model bacterium E. coli, through its genes, proteins and metabolites and how they interact in the living cell, especially in biofilms. 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 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.
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.
Youtube video of a presentation for the TEDxTohokuUniversity 2020 conference about the Hidden Life of bacteria.
Keywords: E. coli, metabolomics, proteomics, biochemistry, biofilms, cellular dynamics, systems biology, complex systems, socio-biology, adaptive evolution
M. Robert 2021-2025