阮楚晋
博士
副教授
福建省厦门市厦门大学翔安校区周隆泉楼B1-316
Dr.
Chujin Ruan
Associate Professor
Room B1-316, Zhou Longquan Building, Xiang'an Campus, Xiamen University, Xiamen, Fujian
Tel:
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Fax:
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Email:
chujin.ruan@xmu.edu.cn
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个人履历
Brief CV
- 工作经历
- 2026.04–至今 厦门大学 副教授
- 2022.11–2026.03 瑞士联邦水科学与技术研究所 (EAWAG) 博士后
- 2022.08–2024.07 中国农业大学(期间外派至 EAWAG) 博士后
- 教育背景
- 2021.03-2022.01 瑞士联邦水科学与技术研究所 (EAWAG) 联合培养博士
- 2018.09-2022.06 中国农业大学 博士
- 2016.07-2018.06 中国科学院微生物研究所 联合培养硕士
- 2015.09 - 2018.06 广西师范大学 硕士
研究方向
Research Interests
- 1、从噬菌体治疗到噬菌体生态调控 From Phage Therapy to Phage-Based Ecological Regulation
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研究以噬菌体为核心研究对象,将传统的“噬菌体治疗”拓展至“噬菌体生态调控”的概念框架,重点关注噬菌体在多物种微生物群落中的生态位分布、宿主特异性及其系统性生态效应。通过构建携带特定功能模块的工程噬菌体,系统揭示噬菌体在病原防控、抗性基因传播抑制以及环境生物防控中的多层次作用模式。相关研究不仅为新型抗菌策略与环境友好型生物防控技术提供理论基础与工程思路,也为构建可持续的抗性治理体系开辟了创新路径。
- 2、表面附着微生物的空间组装与功能涌现 Spatial Assembly and Functional Emergence of Surface-Associated Microbial Communities
- 研究聚焦于附着于界面上的微生物空间自组织与功能涌现机制,重点关注微生物间相互作用以及环境因素如何塑造群落的空间结构。该研究方向旨在阐明微生态系统中从个体行为到群落功能的空间耦合机制,不仅有助于解释自然界中微生物群落的结构多样性和生态韧性,还为人工界面微生态的定向设计、膜污染的生态防控以及表面环境中抗性基因传播的管理提供新的理论框架与科学依据。
- 3、计算机仿真模拟微生物群落 Individual-based modeling
- 以 individual-based model(个体基础模型,IBM)为核心方法,构建一个可扩展的“微生物元宇宙”,即在计算机中重建微生物群落时空演化的虚拟生态系统。在微观尺度上,IBM 能捕捉单个微生物的行为及其相互作用;在宏观尺度上,则揭示这些局部规则如何汇聚形成群落的空间结构、动态稳态与功能涌现。该研究方向为解析微生物群落的复杂行为提供了定量化和可预测的工具,也为实验研究提供了假设检验与参数优化的计算框架。这一方向未来还可扩展至微生物科普教学软件开发、交互式教育应用以及科研驱动的游戏化创新等更广泛而富有想象力的领域。
代表性论文
Selected Publications
- [1] Ruan CJ, Vinod D, Johnson DR. Phage-mediated peripheral kill-the-winner facilitates the maintenance of costly antibiotic resistance. Nature Communications. 2025. 16, 5839.
- [2] Ruan CJ, Ramoneda J, Kan A, Rudge T, Wang G, Johnson DR. Phage predation accelerates the spread of plasmid-encoded antibiotic resistance. Nature Communications, 2024, 15, 53972024.
- [3] Ruan CJ, Borer B, Ramoneda J, Wang G, Johnson DR. Evaporation-induced hydrodynamics control plasmid transfer during surface-associated microbial growth. npj Biofilms and Microbiomes, 2023, 9, 58.
- [4] Ruan CJ, Ramoneda J, Gogia G, Wang G, Johnson DR. Fungal hyphae regulate bacterial diversity and plasmid-mediated functional novelty during range expansion. Current Biology, 2022, 32(24):5285-5294.e4.
- [5] Han M, Ruan CJ (Co first Author), Wang G, Johnson DR. Fungal hyphae promote bacterial contact-dependent killing during surface-associated growth. The ISME Journal. 2025. 1751-7362.
- [6] Lin ZJ, Ruan CJ (Co-first Author), Xia Rong, Liao JQ, Zhu L, Wang DS, Alvarez P, Yu PF. Bacterium-phage interactions enhance biofilm resilience during membrane filtration biofouling under oxidative and hydraulic stresses. Environmental Science & Technology, 2025. 59 (17), 8614-8628.
- [7] Ruan CJ, Ramoneda J, Chen GW, Johnson DR, Wang G. Evaporation-induced hydrodynamics promote conjugation-mediated plasmid transfer in microbial populations. ISME Communications. 2021. 1: 54.
- [8] Ruan CJ, Wang J, Zheng XW, Song L, Zhu YX, Huang Y, Lu ZJ, Du WB, Huang L, Dai X. Halovulum marinum sp. nov., isolated from deep-sea water of the Indian Ocean, and emended description of the genus Halovulum. International Journal of Systematic and Evolutionary Microbiology, 2020, 70(8):4523-4530.
- [9] Wang J, Ruan CJ (Co-first Author), Song L, Zhu YX, Li A, Zheng XW, Wang L, Lu ZJ, Huang Y, Du WB, Zhou YG, Huang L, Dai X. Gimesia benthica sp. nov., a novel planctomycete isolated from a deep-sea water sample of the Northwest Indian Ocean. International Journal of Systematic and Evolutionary Microbiology, 2020, 70(7): 4384-4389.
- [10] Han M, Ruan CJ (Co-first Author), Wang G, Johnson DR. Evaporation controls contact-dependent bacterial killing during surface-associated growth. ISME Communications. 2025, ycaf034.
- [11] Ruan CJ, Zheng X, Wang J, Song L, Zhu YX, Du WB, Lu ZJ, Huang Y, Huang L, Dai X. Hyphobacterium indicum sp. nov., isolated from deep seawater, and emended description of the genus Hyphobacterium. International Journal of Systematic and Evolutionary Microbiology, 2018, 68(12): 3760-3765.
- [12] 阮楚晋, 郑小伟, 王丽, 王铱, 朱雅新, 王剑, 董志扬, 黄英, 杜文斌, 黄力, 戴欣. 基于流式细胞仪高通量分选的深海微生物单细胞培养. 微生物学报, 2021, 61(3): 1-12.
学术任职
Affiliations/Service
- 1. 国际微生物生态学学会 (ISME) 早期职业科学家 (ECS) / 审稿人
- 2. mLife 青年编委
- 3.《微生物学通报》青年编委
- 4.《土壤学报》青年编委
- 5. Nature Communications, The ISME Journal (>10), Environmental Science & Technology, ISME Communications, Chemical Engineering Journal, Journal of hazardous materials, Bioresource Technology, Applied microbiology and biotechnology, 微生物学通报, 土壤学报 等期刊审稿人
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.
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