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Takeyama Lab
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The lab reads microbial genomes from just a single cell, connecting the environment and life.
AboutAbout the lab
Reading microbes and tissues with single-cell analysis technology.
The Takeyama Lab studies microorganisms found everywhere, from the sea and soil to human skin and the gut.
Because many of them are difficult to culture, the lab developed a method that confines microbes one cell at a time in microdevices and reads their genomes with high accuracy.
It also combines Raman spectroscopy, which can examine molecules without staining or destroying cells, to search for molecules inside a single cell.
The lab also builds its own information technology to analyze the large amounts of data collected, and has extended it to the analysis of not only microbes but also animal cells and tissues.
Key terms
- Single-cell genome analysis
- A method of isolating one cell and reading the genome sequence of that cell alone
- Metagenome
- Data from environmental samples in which the genomes of many different organisms remain mixed together
- Raman spectroscopy
- A method of identifying the type of molecule from scattered light whose wavelength shifts slightly when light is shone on a sample
NewsLab news
A doctoral student received the Gtex Poster Award at IBS2026
A doctoral student received the Outstanding Student Poster Award at IBS2026
A doctoral student received the Student Outstanding Oral Presentation Award at the 26th Annual Meeting of the Japan Society for Marine Biotechnology
A result of collaborative research co-authored by Prof. Takeyama was published in Nature Microbiology
A master's student received the Outstanding Presentation Award at the 20th Annual Meeting of the Japanese Society for Genome Microbiology
ResearchResearch themes
The Takeyama Lab uses single-cell technologies it has developed in-house to analyze environmental microbes and biological tissues digitally, with the aim of putting them to use. Its research is divided into two parts: "technology," which creates the analysis technologies themselves, and "projects," which put those technologies to work.
*Illustrative imageReading Microbes with Single-Cell Genomics
Most microbes in the environment cannot be cultured, and it has been difficult to extract the genome of a target microbe from a metagenome, in which many different genomes are mixed together. With the single-cell genome analysis method the lab developed, microbes are confined one cell at a time in picoliter-scale droplets and analyzed, yielding high-accuracy genome information from just a single cell.
*Illustrative imageIntegrated Cell-Level Analysis of Tissues
To understand biological phenomena, information on where in the tissue each cell was located is essential, in addition to the gene expression of each individual cell. The lab is developing technologies to collect very small regions from tissue sections, technologies to analyze DNA and RNA from a small number of cells in frozen or paraffin-embedded tissue, and analysis technologies that link sequence information with tissue structure.
*Illustrative imageFinding Molecules Inside Cells with Raman Spectroscopy
Raman spectroscopy is a method that can examine molecules without labels and without damaging cells. By developing instruments and devices suited to measuring biomolecules and building its own analysis algorithms, the lab is creating technology to find molecules in biological tissues, cells, and microbes. It is building libraries of various Raman spectra, aiming at analysis and screening at the level of a single microbial cell.
*Illustrative imageSoil Microbes and Future Agriculture
This is a project under the Moonshot Research and Development Program. Using technologies such as single-cell genome analysis, microscopic Raman spectroscopy, and spatial omics analysis, the lab collects and analyzes genome information on microbes living in diverse soils and is building a soil microbiome atlas. It aims to realize circular synecoculture by accurately grasping the three elements of soil, plants, and environment, and understanding and controlling their interactions.
MembersFaculty
The Takeyama Lab's members consist of faculty, researchers, research assistants, secretaries, visiting faculty, doctoral, master's, and undergraduate students, and collaborating members.As of 2026
- ProfessorHaruko Takeyama
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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: “Petri dish 2” Drhx / CC BY-SA 4.0 (cropped)
- Reading Microbes with Single-Cell Genomics: “Variety of Gram positive and Negative bacteria in Gram stain of Sewage” Ajay Kumar Chaurasiya / CC BY-SA 4.0 (cropped)
- Integrated Cell-Level Analysis of Tissues: “Histology of liver tissue from a gallbladder resection” Mikael Häggström / CC0 (cropped)
- Finding Molecules Inside Cells with Raman Spectroscopy: “Optical elements and green laser beem” Dasha Butova / CC BY-SA 4.0 (cropped)
- Soil Microbes and Future Agriculture: “Soybean field in Boone County, Indiana - Norm” Norm / Public domain (cropped)
- Related lab (細川研究室): “Single cell sequencing （MDA） (cropped)” Qianli Ma / Public domain (cropped)
- Related lab (常田研究室): “E-coli (Escherichia coli)” Nurgul D / CC BY-SA 4.0 (cropped)
- Related lab (由良研究室): “Myoglobin” AzaToth / Public domain (cropped)
- Related lab (西田研究室): “Macs killing cancer cell” Susan Arnold (photographer) / Public domain (cropped)
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