Staff

OHMURA TakuyaAssistant Professor

Laboratory
Laboratory of Physical Ethology
Research Theme
Mechanics under microbial ecology in fluid system
Research Keywords

ciliate, biofilm, cell swimming, microrheology, microfluidics, fluid dynamics simulation, live-cell imaging, image analysis with machine learning

Overview of Research

Many microorganisms inhabit on Earth, playing a crucial role as part of the ecosystem. When observed under a microscope, their behaviors are diverse, such as swimming freely and forming colonies. What they all have in common is their survival strategies, adapted to external environments. Microorganisms that thrive in high or low temperatures, perform photosynthesis, or possess anaerobic properties can be said to have internal metabolic systems that adapt to the external environment. While molecular biology has advanced our understanding of metabolism, we cannot ignore the mechanical influences of external environments, such as boundary conditions like water surfaces and walls, or the flow within the environment, as microorganisms live in real-world. This raises the question: Is the ecology of microorganisms optimized not only at the level of cellular metabolism but also from a mechanical perspective?

To address this question, we are conducting research to quantify the behavior of microorganisms at the single-cell level using live-cell imaging and image analysis, and to uncover the mechanical mechanisms underlying microbial ecology by validating observational results with various physical models. For example, using fluid dynamics models, we have found that two mechanical conditions explain why freshwater ciliates are not swept into the sea. By applying soft matter physics models, we can measure that bacterial colonies have both soft and hard regions within the same colony. By appropriately selecting physical theories depending on the research subject, we approach the diverse ecological phenomena exhibited by microorganisms.

Charge

Message

From a biological perspective, microorganisms are classified into various groups, including eukaryotes like Paramecium and Euglena, as well as prokaryotes such as bacteria. Focusing on the movement of microorganisms, if we classify them based on their “swimming methods” from a fluid dynamics standpoint, they can be divided into three distinct lineages. One of these lineages includes some spieces among bacteria, archaea, protists, and even (though not microorganisms) mammalian sperm, allowing us to view living organisms through a completely different framework than genetic taxonomy.

I would like to share with everyone the joy of systematizing the behavior of observed organisms through physics and mathematics, and creating new classification criteria that have never existed before.

Representative Publications

Takuya Ohmura, Dominic J. Skinner, Konstantin Neuhaus, Gary PT Choi, Jörn Dunkel, Knut Drescher: “In vivo microrheology reveals local elastic and plastic responses inside three‐dimensional bacterial biofilms”
Advanced Materials, 36(29), 2314059 (2024). doi: 10.1002/adma.202314059
– editor’s choice

Eric Jelli*, Takuya Ohmura*, Niklas Netter*, Martin Abt, Eva Jiménez‐Siebert, Konstantin Neuhaus, Daniel K. H. Rode, Carey D. Nadell, Knut Drescher: “Single‐cell segmentation in bacterial biofilms with an optimized deep learning method enables tracking of cell lineages and measurements of growth rates”
Molecular Microbiology, 119(6), 659-676 (2023). *equally contributed, doi: 10.1111/mmi.15064
– cover of issue, editor’s choice

Takuya Ohmura*, Yukinori Nishigami*, Atsushi Taniguchi, Shigenori Nonaka, Takuji Ishikawa, Masatoshi Ichikawa: “Near-wall rheotaxis of the ciliate Tetrahymena induced by the kinesthetic sensing of cilia”
Science Advances, 7(43), eabi5878 (2021). *equally contributed, doi: 10.1126/sciadv.abi5878

Saori Suda, Tomoharu Suda, Takuya Ohmura, Masatoshi Ichikawa: “Straight-to-Curvilinear Motion Transition of a Swimming Droplet Caused by the Susceptibility to Fluctuations”
Physical Review Letters, 127(8), 088005 (2021). doi: 10.1103/PhysRevLett.127.088005
– cover of issue

Takuya Ohmura*, Yukinori Nishigami*, Atsushi Taniguchi, Shigenori Nonaka, Junichi Manabe, Takuji Ishikawa, Masatoshi Ichikawa: “Simple mechanosense and response of cilia motion reveal the intrinsic habits of ciliates”
Proceedings of the National Academy of Sciences USA, 115(13), 3231-3236 (2018). *equally contributed, doi: 10.1073/pnas.1718294115

Full publication list in researchmap
（https://researchmap.jp/takuyaohmura?lang=en）

Note

<Office Hour>
– Time: Anytime during the lecture period
– Place:Research Institute for Electronic Science (RIES) Building, #02-107
Please contact in advance by E-mail.
E-mail: takuya.ohmura[at]es.hokudai.ac.jp

Affiliation