Research
Microbial spatial assembly and functional emergence
Investigating the principles of microbial self-organization at interfaces and the mechanisms driving their ecological functions.
From phage therapy to ecological regulation
Exploring the mechanisms by which bacteriophages contribute to pathogen suppression, resistance-gene transmission control, and the restructuring of microbial community stability.
Computational simulation of microbial communities
Constructing a “microbial metaverse” through computational simulation to enable predictive analyses of community spatiotemporal dynamics.
01
Microbial spatial assembly and functional emergence
We focus on the mechanisms underlying the spatial self-organization and functional emergence of microorganisms attached to interfaces, with particular attention to how microbial interactions, including competition, cooperation, and chemical signaling, together with environmental factors such as nutrient gradients, shear forces, and surface properties, shape community spatial structure and maintain diversity. Through advanced microscopy, spatiotemporal dynamic tracking, and high-resolution quantitative image analysis, we systematically elucidate the spatial assembly patterns and structural evolutionary features of microbial communities at interfaces, thereby revealing the key processes that drive community stability and ecological function. This research direction aims to uncover the spatial coupling mechanisms linking individual microbial behaviors to emergent community-level functions. It not only helps explain the structural diversity and ecological resilience of natural biofilms and surface-associated microbial assemblages but also provides a theoretical framework and scientific foundation for the rational design of engineered interface microbiomes, ecological strategies for membrane-biofouling control, and the management of antibiotic resistance gene dissemination in surface environments.
02
From phage therapy to ecological regulation
We center our research on the ecological roles and molecular mechanisms of bacteriophages, expanding the traditional concept of “phage therapy” into a broader framework of “phage-based ecological regulation.” Our work examines the ecological niche distribution, host specificity, and system-level impacts of phages within multispecies microbial communities. The research objective extends beyond the suppression of pathogenic bacteria by lytic phages to include exploring their regulatory potential at the community level. By engineering phages carrying functional modules such as antimicrobial peptides, metabolic effectors, or gene regulatory elements, and by integrating community-scale assessments including community composition, biofilm mechanical properties, and host–phage interaction networks with fine-scale molecular analyses such as transcriptomic responses, we aim to elucidate the multilayered modes through which phages contribute to pathogen control, suppression of antibiotic-resistance gene dissemination, restructuring of microbial ecological stability, and environmental biocontrol. This research direction emphasizes redefining the functional attributes of phages from both microbial ecological and molecular biological perspectives, elevating them from single-purpose antibacterial tools to programmable microecological regulators. This work provides new theoretical foundations and engineering strategies for next-generation antimicrobial approaches and environmentally friendly biocontrol technologies, and also opens new pathways toward sustainable antimicrobial-resistance management.
03
Computational simulation of microbial communities
We employ the individual-based model (IBM) as a core methodological framework to construct a scalable “microbial metaverse,” a virtual ecosystem that reconstructs the spatiotemporal evolution of microbial communities within a computational environment. At the microscopic scale, IBM captures the behaviors and interactions of individual microorganisms, including competition, cooperation, chemotaxis, and signal transmission. At the macroscopic scale, it reveals how these local rules give rise to community-level spatial structures, dynamic steady states, and emergent functions. The introduction of the “metaverse” concept aims to establish a multi-agent, visual, and interactive simulation environment that allows researchers to immerse themselves in the microbial world, observe community dynamics in real time, test theoretical hypotheses, and predict system-level responses. This research direction provides quantitative and predictive tools for analyzing the complex behaviors of microbial communities and offers a computational framework for hypothesis testing and parameter optimization in experimental studies. In the longer term, the microbial metaverse is expected to serve as a digital bridge linking theory, experimentation, and engineering, supporting applications such as risk assessment of resistance dissemination, optimization of phage deployment strategies, and the design of engineered microecological systems. Furthermore, this direction may extend into broader and more creative domains, including the development of microbiology education software, interactive learning applications, and research-driven game-based innovations.