1. Our research expands the concept of phage therapy into a broader framework of phage-based ecological regulation, focusing on the ecological niches and molecular mechanisms of bacteriophages within multispecies microbial communities. Ultimately, we aim to harness lytic phages to combat pathogenic bacteria while exploring their potential as ecological modulators. We engineer phages carrying functional modules, such as antimicrobial peptides, effector proteins, or regulatory elements and integrate community-scale analyses (community composition, biofilm mechanics, host–phage interaction networks) with molecular-level readouts (transcriptional responses, receptor recognition, and infection mechanisms). This multi-scale approach enables us to reveal how phages contribute to controlling antibiotic resistance dissemination, reshaping ecological stability, and environmental biocontrol. By combining ecological and molecular perspectives, this research seeks to redefine the functional role of bacteriophages, transforming them from mere “antibacterial agents” into programmable regulators of microbial ecosystems. It establishes a new theoretical and technological foundation for developing next-generation antimicrobial strategies, eco-friendly biological control approaches, and sustainable resistance management frameworks.

2. We focus on the spatial self-organization and functional emergence of microorganisms at solid–liquid interfaces, with particular emphasis on how microbial interactions (including competition, cooperation, and signaling) and environmental factors (such as nutrient gradients, shear forces, and surface properties) jointly shape community spatial diversity and influence functional performance. By integrating confocal and fluorescence microscopy, spatiotemporal tracking, and quantitative image analysis, we aim to uncover the rules of spatial assembly and the mechanisms underlying structural evolution of microbial communities on surfaces, thereby elucidating the driving forces that govern the stability and functionality of microscale ecosystems. This research direction seeks to bridge the gap between individual microbial behaviors and community-level functions, offering new insights into the structural diversity and ecological resilience of natural biofilms. Moreover, it provides a theoretical foundation for the rational design of artificial surface-associated microbiomes, the ecological control of biofouling, and the management of resistance gene dissemination in surface environments.

3.  We employ individual-based modeling (IBM) as the core methodological framework to construct a scalable “microbial metaverse”—a virtual ecosystem that digitally reconstructs the spatiotemporal evolution of microbial communities. At the microscopic level, IBM captures the behaviors and interactions of individual microbes, including competition, cooperation, chemotaxis, and signaling. At the macroscopic level, it reveals how these local rules collectively give rise to community-level spatial organization, dynamic stability, and functional emergence. By introducing the concept of a microbial metaverse, we aim to develop an interactive, visual, and multi-agent simulation environment that allows researchers to “enter” microbial worlds, observe community dynamics in real time, test mechanistic hypotheses, and predict system-level responses. This research direction provides quantitative and predictive tools for understanding the complex behaviors of microbial ecosystems, while offering a computational framework for hypothesis validation and parameter optimization in experimental studies. In the long term, the construction of the microbial metaverse will serve as a digital bridge connecting theory, experimentation, and engineering, offering a new theoretical foundation and technological platform for resistance dissemination risk assessment, optimization of phage deployment strategies, and the rational design of artificial microbial ecosystems.