Research Systems

Research Overview

 Over the four-billion-year history of life, organisms have radiated into diverse environments through adaptive evolution. Throughout this history, symbioses with other species have repeatedly driven biological innovation, often triggering explosive diversification and the emergence of new ecological opportunities.

Our laboratory aims to uncover the mechanisms that generate biological diversity, focusing on species interactions—particularly symbiosis—as a key process. By integrating fieldwork in natural ecosystems with genomic and computational approaches, we seek to elucidate the principles governing living systems across hierarchical levels, from molecular and cellular processes to populations, communities, and ecosystems.

We mainly study plant–microbe and fish–microbe symbiotic systems, while also exploring a wide variety of organisms in the field to pursue bold, curiosity-driven research that reveals novel biological phenomena. By combining cutting-edge methods in molecular biology and information science, we examine the history of life from new and integrative perspectives.

Research System 1: Plant–Microbe Symbiosis

We take for granted the green terrestrial ecosystems around us today. Yet, if the ancestors of land plants had not formed symbioses with fungi roughly 450 million years ago, neither modern terrestrial ecosystems nor humans would exist. The key event was the establishment of mycorrhizal symbiosis.

For early land plants derived from algal ancestors, acquiring water and nutrients in terrestrial environments was extremely challenging. Fungi, having colonized land earlier, developed extensive underground hyphal networks capable of absorbing water, nitrogen, and phosphorus. When land plants began to utilize these fungal networks as “infrastructure,” explosive diversification became possible, ultimately giving rise to Earth’s verdant landscapes.

Recent studies have shown that, beyond classical mycorrhizal fungi, diverse endophytic fungi inhabiting the plant root zone also play pivotal roles in nutrient acquisition and resistance to environmental or biotic stress. The sophisticated symbiotic machinery plants use to interact with fungi is deeply encoded in their genomes.

Our research integrates extensive fieldwork in forests, grasslands, and agricultural ecosystems with molecular approaches, including inoculation assays using our laboratory’s fungal culture libraries and gene expression analyses. In natural environments, a single plant interacts with hundreds to thousands of fungal and bacterial species. We aim to identify key symbiotic microbes from these complex networks and build a scientific foundation for predicting and controlling the behavior of multi-species symbiotic systems.

Research System 2: Fish–Microbe Symbiosis

It is now well recognized that diverse gut microbes inhabit the human intestine and strongly influence host physiology. By contrast, interactions between microbial communities and non-mammalian hosts remain poorly understood, representing a vast frontier in biological research.

Our lab investigates how microbial community dynamics influence the performance of fish, our primary model. Like humans and mice, fish harbor complex gut microbiomes. Moreover, because fish live in aquatic environments, their physiology is also shaped by the structure and dynamics of environmental microbial communities.

Our research has revealed dramatic fluctuations in the species composition of aquatic microbiomes. These systems exhibit multiple stable states: microbial configurations that promote host health, and alternative configurations that impair it. Abrupt regime shifts between these states can profoundly impact fish physiology and ecology.

We focus on the possibility that stable and functional fish microbiomes emerge through “consortia” of microbes involved in nutrient (e.g., vitamin) provisioning and immune activation. Using high-throughput DNA sequencing integrated with theoretical frameworks from statistical physics, machine learning, and network science, we aim to uncover the physical principles underlying such multi-species stability.

These insights may reveal fundamental rules governing the multi-stability of biological systems. Similar regime-shift phenomena, such as dysbiosis in the human gut, likely share common underlying dynamics. We aim to build theoretical and experimental foundations for predicting and controlling microbiome regime shifts.

Research System X: New Model Systems You Will Develop

Our laboratory actively welcomes the development of new research systems.

If you are fascinated by a particular group of organisms but cannot find a suitable lab, or if traditional approaches are insufficient to answer your questions, or if there is simply a species you are eager to study—we will do our best to support you.

By combining field observations with molecular biology, imaging, DNA sequencing, and multifaceted computational analysis, entirely new research avenues can emerge.

In the study of interspecies interactions—the core theme of our lab—current knowledge represents only the tip of the iceberg. Join us in exploring the frontiers of biological complexity.