Our research focuses on the gut microbiome as a dynamic biological ecosystem shaped by microbial interaction networks, host regulatory mechanisms, and environmental perturbations. Central to our work is the interplay between bacteria, bacteriophages, and host immunity. By integrating immune-informed metrics with ecological and quantitative approaches, we seek to understand how microbiome–host systems respond to challenges such as antibiotic exposure or immune alteration, why recovery trajectories differ between individuals, and how ecosystem balance can be restored. Through the combination of microbiology, viromics, immunology, and quantitative ecology, we aim to link microbial ecosystem dynamics to human health. Our goal is to move beyond descriptive microbiome profiling toward a mechanistic and predictive understanding of microbiome–host interactions, with relevance across diverse clinical contexts.
Scientific Axis 1 — Virome
We study bacteriophages as key, yet largely unexplored, regulators of microbiome–host ecosystems. This axis focuses on how phages structure bacterial communities, drive microbial evolution, and interface with host immune surveillance. Particular attention is given to the viral “dark matter” of the gut, whose ecological and immunological roles remain poorly characterized despite consistent host engagement. By integrating viromics, immune-informed approaches, and ecological modeling, we aim to establish phages as active components of microbiome regulation rather than passive by-products of bacterial dynamics.
Scientific Axis 2 — Immune Surveillance and Microbiome Ecology
This axis examines how host immune surveillance functions as a governing ecological force structuring microbial communities. We focus on mucosal immune mechanisms, particularly antibody-mediated interactions, to understand how immune pressure organizes microbiome composition, stabilizes host–microbe coexistence, and contributes to inflammatory or immune-mediated dysregulation. Through immune-informed metrics and systems-level analyses, we seek functional definitions of microbiome–host homeostasis that go beyond descriptive taxonomic approaches.
Scientific Axis 3 — Perturbations, Resilience, and Ecosystem Recovery
We investigate how microbiome ecosystems respond to perturbations such as antibiotics, infection, and immune dysfunction, and why recovery trajectories differ between individuals. This axis integrates ecological theory, experimental models, and longitudinal analyses to identify determinants of resilience, dysregulation, and long-term remodeling of microbiome–host interactions. A central objective is to define principles enabling restoration of ecosystem balance and to inform microbiome- and immune-guided intervention strategies in inflammatory and disease contexts.