Expanding New Medical Possibilities From Microbial Research
Daiki Kumakura
(Junior Research Associate, iTHEMS / Student Trainee, iTHEMS / Ph.D. Student, Graduate School of Life Science, Hokkaido University)
Daiki Kumakura, is a Ph.D. student at the Graduate School of Life Science, Hokkaido University. He is also a Junior Research Associate (JRA) at RIKEN iTHEMS, where he conducts his research. We asked him about the advantages of conducting research at iTHEMS as a student and his aspirations for the future.
Keywords: Precision Medicine, Personalized and Stratified Medicine, Microbiology, Mathematical Biology, Bioinformatics, Outreach Activities
Affiliation and position are as of the interview date: September 2024
(Written by Naoko Shinozaki (Freelance Announcer / Mathematics Communicator) / Photo by Makoto Oikawa (Photographer))
Researching Microbiology Using Mathematical Biology and Bioinformatics
Kumakura specializes in microbiology, studying bacteria, archaea, and viruses through approaches that combine mathematical biology and bioinformatics. His research in microbiology and mathematical biology explores mathematical models that explain theoretical conditions for treatments of bacterial infections, such as tuberculosis and cholera, and models microbial growth. Bioinformatics is a field that bridges life sciences and information sciences. He collects microorganism and virus genomes from hot springs to study new genomes, genetic resources, and the formation of microbial ecosystems in such environments.
For Kumakura, the appeal of research lies in the idea of achieving something not as an individual but as part of a collective. He explains that microorganisms do not act alone; they thrive in groups, cooperating with both their kind and other species. Through mathematical and data-driven analysis, he enjoys visualizing how even the smallest organisms achieve significant results collectively. "The ability to quantify the collaborative actions of microorganisms is what makes this research fascinating," he says.
Discovering Mathematical Biology and Advancing to a Doctoral Program
From an early age, Kumakura had an interest in biology and mathematics. His fascination with biology was sparked by windsurfing, which he began as a child. His instructor, a doctoral student at the time, introduced him to various scientific phenomena through the lens of the ocean. His interest in mathematics stemmed from his father, who taught him how to approach math problems logically, translating real-world issues into equations during his elementary school years.
In high school, he aspired to study plankton and microbial research at the Faculty of Fisheries at Hokkaido University. This aspiration was influenced by his grandfather, a fisherman in Esashi Town in Hokkaido, and by the stories his grandfather shared with him during his high school years about university students conducting fieldwork there. And then, witnessing marine phenomena like red and blue tides, which cause fish to die or jellyfish to proliferate, further motivated him to study marine environments and contribute to society.
He eventually enrolled in Hokkaido University’s Faculty of Fisheries, joining a marine microbiology laboratory to conduct research on the metabolic analysis of novel bacteria. During his university years, he was also a member of the equestrian club, where his experiences with horse care, injuries, and treatments led him to recognize the importance of personalized medicine. He also learned about zoonotic pathogens, such as drug-resistant bacteria, which further deepened his interest in the medical applications of microbiology.
A pivotal moment came when he discovered the book Introduction to Mathematical Biology (Senior Advisor Yoh Iwasa) at the university library. Combining his love for biology and mathematics, he decided to apply mathematical biology to microbial research. This realization prompted him to pursue graduate studies in the Mathematical Biology Laboratory at Hokkaido University's Graduate School of Life Sciences under the guidance of Dr. Shinji Nakaoka.
A Supportive and Interdisciplinary Research Environment at iTHEMS
“The research environment at iTHEMS is outstanding,” says Kumakura. He appreciates the freedom to pursue his research interests and the support system, including Program Director Tetsuo Hatsuda and the iTHEMS staff, who help find alternative solutions when challenges arise.
Engaging with researchers at iTHEMS provides valuable feedback that sharpens his work. The diversity of expertise at iTHEMS has also taught him how to tailor his communication to different audiences. For instance, discussions with biologists involve technical terms, whereas conversations with mathematicians require more foundational explanations about biology. “This environment naturally hones my skill to adjust how I convey ideas depending on the audience,” he explains.
During his time at iTHEMS, Kumakura has achieved significant milestones, including publishing a paper during the second year of his doctoral studies. He is currently finalizing a mathematical analysis project with Deputy Program Director Catherine Beauchemin and a hot spring microbiology project with Senior Research Scientist Jeffrey Fawcett.
Advocating for Personalized and Stratified Medicine
Kumakura actively engages in outreach activities, such as founding the Young Researchers’ Association for Theoretical Biology and organizing the Summer School on Theoretical Biology. His efforts aim to provide equal opportunities for students and researchers to learn and network, given the limited number of mathematical biology laboratories in Japan.
He has also created study materials such as, a One S&T poster for Household Connecting Mathematics to the World, contributing to RIKEN Open Labs, and has participated in university events. His goal is to introduce the public to the interdisciplinary field of combining mathematics and biology.
After completing his doctoral studies, Kumakura plans to work in the pharmaceutical industry while continuing his research at iTHEMS. He is passionate about advancing personalized and stratified medicine, aiming to optimize treatments tailored to individual patient profiles. By utilizing his knowledge and methodologies in practical settings, he hopes to provide treatments that maximize effectiveness for patients, ultimately contributing to the broader adoption of personalized healthcare.