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Biochemical Engineering Lab
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Uncovering how microorganisms that live at 100°C work.
AboutAbout the lab
Getting to know archaea, the third domain of life.
The Biochemical Engineering Lab (Atomi Lab) studies microorganisms, especially archaea.
Archaea are organisms that are phylogenetically distinct from both bacteria and eukaryotes, and they include diverse groups such as methanogens, halophiles, and hyperthermophiles.
They have many features not found in other organisms, such as the structure of their membrane lipids and metabolic pathways found in neither bacteria nor eukaryotes.
Within archaeal physiology, the lab focuses in particular on the regulation of metabolism and transcription.
Key terms
- Archaea
- The third major group of living things, alongside bacteria and eukaryotes. Also called archaebacteria.
- Hyperthermophile
- A microorganism that grows well at high temperatures above 80°C.
- Homologous recombination
- A mechanism by which DNA molecules with similar sequences exchange segments. It can be used to disrupt or replace a targeted gene.
ResearchResearch themes
The lab's main subject is the hyperthermophilic archaeon Thermococcus kodakarensis KOD1, which was isolated from a hot spring on the coast of Takarajima Island in Kagoshima Prefecture. It grows at 60–100°C, with optimal growth at 85°C. It grows on a variety of organic substances such as amino acids and sugars, and produces hydrogen when grown on sugars.
*Illustrative imageExploring genes of unknown function
When the complete KOD1 genome was sequenced, about half of its roughly 2,300 genes turned out to have unknown functions. The lab built a system that can disrupt or replace genes through homologous recombination, and uses it to investigate gene functions, focusing on the regulation of metabolism and transcription.
*Illustrative imageDiverse microorganisms and applications
The lab also studies halophiles, methanogens, hyperthermophilic bacteria, and uncultured microorganisms found through metagenomics. It also explores applications, such as in vitro transcription and translation systems that make use of hyperthermophile enzymes, and hydrogen production from biomass.
MembersFaculty
The members of the Biochemical Engineering Lab are faculty, postdoctoral researchers, researchers, doctoral students, master's students, and undergraduate students.As of 2026
- ProfessorHaruyuki Atomi
- Associate ProfessorTakaaki Sato
- Assistant ProfessorYuta Michimori
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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: “Cathedral Hill Hydrothermal Vent of Guaymas Basin” Teske A, Wegener G, Chanton JP, White D, MacGregor B, Hoer D, de Beer D, Zhuang G, Saxton MA, Joye SB, Lizarralde D, Soule SA and Ruff SE / CC BY 4.0 (cropped)
- Exploring genes of unknown function: “Thermococcus gammatolerans” Angels Tapias. Microscopist: Jeril / CC BY 3.0 (cropped)
- Diverse microorganisms and applications: “Schematic diagram of a Thermococcus gammatolerans cell” Modified after Crion (Caption translated) / CC BY-SA 4.0 (cropped)
- Related lab (Interface Control Engineering Lab): “Zeolite Mordenite (with Al substitution)” Spacegroup143 / CC BY-SA 3.0 (cropped)
- Related lab (Solid State Chemistry Lab): “Copper-hydride-from-xtal-3D-SF” CCoil (talk) / CC BY 3.0 (cropped)
- Related lab (Organic Design Lab): “1-Undecanol molecular model” RandomKatze / CC0 (cropped)
- Related lab (Fundamental Glass Science Lab): “Electrostatic Levitation of a Titanium-Zirconium-Nickel Alloy” NASA/MSFC/Emmett Given / Public domain (cropped)
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