Research Environment

Fieldwork

We undertake research expeditions to forests, grasslands, oceans, and lakes in search of our target ecosystems and organisms. In the real environments where organisms have evolved, we explore novel biological phenomena.

International Activities

When countries and fields of expertise differ, so do ways of thinking. As international collaborative networks expand, creative and original research naturally flourishes.

Open, Barrier-Free Discussions

Our laboratory values open and unrestricted dialogue. In front of the 4-meter whiteboard, there is always someone engaged in discussion, and anyone is welcome to jump in at any time. These everyday conversations often give rise to new research approaches.

Microscopes

Direct observation of organisms is the essential first step in research. For everyday use, we keep a variety of microscopes as well as field guides and reference books. In addition, we have access to a wide range of shared research instruments provided by the Graduate School of BioStudies.

High-throughput sequencing

We maintain an Illumina MiSeq in our laboratory and perform sequencing on a routine basis. Questions such as “What kinds of symbionts does this organism collected in the field harbor?” can quickly be transformed into data. We have established a high-throughput workflow capable of processing thousands of samples. A 96-channel micropipette enables efficient large-scale experiments, and we have four PCR machines that can handle 384 samples each. High-throughput library purification is also available.

When larger sequencing output is required, we use the NextSeq 500 located in the shared instrumentation facility on the same floor or outsource sequencing to services that provide platforms such as NovaSeq. For long-read sequencing, we also have an Oxford Nanopore system, and we anticipate increasing opportunities to conduct analyses using PacBio’s Revio platform through collaborations.

Robots

Robotic systems are indispensable for high-throughput sample processing. Automation enables precise experiments with a greatly reduced risk of contamination.

Other Equipment

We also maintain equipment for nucleic acid extraction from biological samples, as well as plate readers for chemical analyses. When necessary, we even build our own cultivation setups for organisms through DIY approaches.

A wide range of additional shared instruments is also available through Innovative Support Alliance for Life Sciences (iSAL).

Data Analysis (Dry Lab)

Our laboratory’s core approach is to advance new research areas by continuously feeding insights back and forth between experimental (wet) work and data analysis (dry) work. Using our in-house workstations, we analyze shotgun metagenomic data and perform various simulations, and when necessary, we also make use of the supercomputer at Kyoto University’s Institute for Chemical Research.

Programming can feel intimidating at first, but once you obtain next-generation sequencing data for your own research project, the strong motivation to “understand what’s going on” greatly accelerates the learning process. A particularly effective path is to first collect large amounts of wet-lab data from your own perspective, and then dive into dry-lab analysis—this enables highly efficient research progress.

Current members of the lab also struggled with dry-lab analyses at the beginning, but they have leveraged those experiences to build a culture of sharing know-how and helping one another. Through this collaborative support system, we work together to solve challenges and improve our analytical skills.

Microbial Libraries

We isolate bacteria and fungi for various experiments and genomic analyses. In the future, we also plan to isolate hard-to-culture strains using microfluidic devices and related techniques.