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Fujimoto Lab
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A lab exploring how the human microbiome is linked to disease.
AboutAbout the lab
Transforming the dimensions of microbial control, now
The Fujimoto Lab aims to understand the human microbiome in fine detail and to elucidate how various diseases, including immune diseases, develop.
Metagenomic analysis with next-generation sequencers is advancing, and it is becoming clear, one finding after another, that human diseases are closely linked to symbiotic pathogenic bacteria (pathobionts).
The lab also puts effort into training researchers versed in both experimental (wet) and computational (dry) approaches.
Going beyond the boundary between basic and clinical research, the lab pursues its work from both immunology and microbiology.
Key terms
- Metagenomic analysis
- Analysis that uses next-generation sequencers to examine the whole community of microbes in the human body at once
- Pathobiont
- A bacterium that lives symbiotically in humans and contributes to the onset and progression of disease
- Gnotobiotic animals
- Germ-free animals into which only specific microbes have been introduced
- Endolysin
- A type of phage-derived lytic enzyme. It targets peptidoglycan, the main component of the cell wall of Gram-positive bacteria
NewsLab news
Prof. Fujimoto won the Japan Medical Association Medical Research Encouragement Prize
Review article published in Frontiers in Immunology
Prof. Fujimoto won the 2025 Kao Science Prize
Project Assistant Professor Mizuno won the Young Investigator's Award at the Japanese Society for Clinical Immunology
Prof. Fujimoto and Project Assistant Professor Mizuno won the JSCI-FOCIS Emerging Investigator Recognition Award 2026
ResearchResearch themes
The Fujimoto Lab investigates how the commensal microbiota and pathobionts in humans contribute to the onset and progression of disease. Using metagenomic analysis and gnotobiotic animal models to study pathobiont functions, the lab is also developing methods to control disease with phage-derived lytic enzymes and working to put phage therapy into practical use.
*Illustrative imageIdentifying key microbes involved in disease
The lab has reported pathobionts involved in obesity, diabetes, graft-versus-host disease, and axillary osmidrosis (underarm body odor). By combining metagenomic analysis with gnotobiotic animal models, it aims to clarify the functions of these bacteria and to control disease by targeting the microbiota.
*Illustrative imageDeveloping phage-derived lytic enzymes
The lab is developing therapies that use phage-derived lytic enzymes, which are highly specific to particular bacteria. It has shown the effectiveness of endolysins against Gram-positive bacteria, and for Gram-negative bacteria it is searching metagenomic data for enzymes that can break down and penetrate the lipopolysaccharide (LPS) layer of the outer membrane.
*Illustrative imagePutting phage therapy into practical use
Phage therapy is not yet approved in Japan, but it is attracting attention as a promising option against drug-resistant bacteria. In April 2024, the lab started the first clinical trial of its kind in Japan, and it aims to build a system that carries out the work consistently from basic research through clinical trials.
MembersFaculty
The Fujimoto Lab's members consist of a professor, an assistant professor, a project assistant professor, and research assistants.As of 2026
- ProfessorKosuke Fujimoto
- Assistant Professor (Concurrent Appointment with the Graduate School of Medicine)Yuichi Maeda
- Assistant ProfessorKentaro Kuzuya
- Assistant ProfessorKenji Funakoshi
- Project Assistant ProfessorYumiko Mizuno
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Report an errorAbout the images
The top and research theme images are illustrative and were not taken at the lab. They are cropped from Wikimedia Commons images. Cropped CC BY-SA images are provided under the same CC BY-SA license as the original (version shown on each line).
- Top image: “Phosphate solubilizing bacteria cultured in petri dish” Joydeep / CC BY-SA 3.0 (cropped)
- Identifying key microbes involved in disease: “Overview of metagenomic methods” Puhijun / CC BY-SA 3.0 (cropped)
- Developing phage-derived lytic enzymes: “Bacteriophage T4 Infection” DavidGoodsell / CC BY 4.0 (cropped)
- Putting phage therapy into practical use: “Enterobacteria phage T2 transmission electron micrograph” SnaxMikn / CC BY-SA 4.0 (cropped)
- Related lab (分子細菌学分野 児玉研究室): “E. coli Bacteria ( )” NIAID / CC BY 2.0 (cropped)
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- Related lab (感染病態分野 山本研究室): “T. gondii tachyzoites” Persian Microbiologist / CC BY-SA 4.0 (cropped)
- Related lab (感染症メタゲノム研究分野 中村研究室): “370A automated DNA sequencer” Giac83 / CC BY-SA 2.5 (cropped)
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