Dr. Wang Rui

Researcher
Biogas Institute Ministry of Agriculture and Rural affairs
Key Member,Anaerobic Microbial Technology Innovation Team at the Chinese Academy of Agricultural Sciences
Address: No.13, Section 4, South Renmin Road, Wuhou District, Chengdu, Sichuan 610041, China
Email:wangrui05@caas.cn

Education

l Ph.D. in Genetics, Institute of Microbiology, Chinese Academy of Sciences, September 2010- January 2017

Supervisor: Researcher Xiang Hua

l B.Sc. in Biological Science and Technology,University of Science and Technology Beijing, September 2006-June 2010

 

Work Experience

l Researcher, Anaerobic Microbial Technology Innovation Team, Biogas Institute, Ministry of Agriculture and Rural Affairs, December 2025-Present

l Associate Researcher, Key Laboratory of Microbial Physiology and Metabolic Engineering, Institute of Microbiology, Chinese Academy of Sciences, November 2023- November 2025

l Postdoctoral Fellow, Key Laboratory of Microbial Physiology and Metabolic Engineering, Institute of Microbiology, Chinese Academy of Sciences, October 2021-December 2024

Cooperative Supervisor: Researcher Li Ming

l Assistant Researcher, Key Laboratory of Microbial Physiology and Metabolic Engineering, Institute of Microbiology, Chinese Academy of Sciences, October 2021-October 2023

l Lecturer, Science Research Experimental Center, Chengdu Medical College, September 2016-September 2021

 

Research Work

   Dr. Wang Rui investigates the molecular interplay between bacteria/archaea and phages/Viruses, focusing on CRISPR-Cas adaptive immunity and novel innate defense systems, and explores applications in gene editing and antimicrobial therapy. He elucidated the functional transition of CRISPR-Cas from adaptive defense to endogenous gene regulation via sequence complementarity, with key findings published in Nucleic Acids Research (2014 co-first, 2016 co-first, 2021 co-first) and Cell Host & Microbe (2023 co-first). He first uncovered that CRISPR systems modulate CreTA toxin-antitoxin modules to coordinate innate herd immunity with adaptive immunity, reported in  Nature Chemical Biology (2025 co-first & co-corresponding, featured in News & Views). By integrating CRISPR immunity with guard RNA dual-killing circuits, he developed the ATTACK technology for precision elimination of multidrug-resistant bacteria (Nature Communications, 2023 co-first; highlighted as an editor's choice). Collectively, his work advances mechanistic understanding of microbe–phage interactions and provides original genetic elements and tools for microbiome editing, in situ gene modulation, and targeted clearance of drug-resistant pathogens.

 

Current Research Interests

1. Molecular interaction mechanisms between anaerobic archaea/bacteria and viruses/phages; discovery of novel elements and functional mechanisms of specific antiviral defense systems.

2. Development of customized and high-efficiency gene editing technologies and genetic manipulation platforms for systematic modification of key anaerobic chassis strains.

3. Construction of microbiome editing and gene drive technologies for precise regulation of intestinal flora and anaerobic microbial communities, supporting applications in methane emission reduction and intestinal health.

 

Research Projects Led & Participated

1. National Key R&D Program of China (Synthetic Biology Special Project) Topic 2: Construction and Application of Living Biologics Based on Synthetic Microbiome (2024YFA0918502) Sub-project Leader, RMB 800,000, Dec 2024-Nov 2029

2. National Key R&D Program of China (Frontier Biotechnology Special Project) Topic 4: Development and Clinical Research of Safe and Efficient Engineered Phage Therapy Technology (2025YFC3408404) Sub-project Leader, RMB 700,000, Jun 2025-May 2028. 

3. National Natural Science Foundation of China General Program Project: Mechanism and Function of Novel CRISPR Guard RNA in Acinetobacter (32270092) Principal Investigator, RMB 540,000, Jan 2023-Dec 2026

4. National Natural Science Foundation of China Youth Scientists Fund Project: Site-specific Integration Mechanism of Exogenous Spacer Acquisition in I-F Type CRISPR-Cas System of Acinetobacter baumannii (31701078) Principal Investigator, RMB 250,000, Jan 2018-Dec 2020

Representative Academic Papers

1. Shu Xian^#; Wang Rui^#; Li Zhihua^#; Xue Qiong^#; Wang Jiajun; Liu Jingfang; Cheng Feiyue; Liu Chao; Zhao Huiwei; Hu Chunyi; Li Jie; Ouyang Songying*; Li Ming*. CRISPR-repressed toxin-antitoxin provides herd immunity against anti-CRISPR elements. Nature Chemical Biology, 2025, 21(3): 337–347.

2. Wang Rui^#; Shu Xian^#; Zhao Huiwei^#; Xue Qiong; Liu Chao; Wu Aici; Cheng Feiyue; Wang Lingyun; Zhang Yihan; Feng Jie; Wu Nannan; Li Ming*. Associate toxin-antitoxin with CRISPR-Cas to kill multidrug-resistant pathogens. Nature Communications, 2023, 14(1): 2078.

3. Liu Chao^#; Wang Rui^#; Li Jie^#; Cheng Feiyue^#; Shu Xian^#; Zhao Huiwei; Xue Qiong; Yu Haiying; Wu Aici; Wang Lingyun; Hu Sushu; Zhang Yihan; Yang Jun; Xiang Hua*; Li Ming*. Widespread RNA-based cas regulation monitors crRNA abundance and anti-CRISPR proteins. Cell Host & Microbe, 2023, 31(9): 1481–1493.

4. Cheng Feiyue^#; Wang Rui^#; Yu Haiying^#; Liu Chao; Yang Jun; Xiang Hua*; Li Ming*. Divergent degeneration of creA antitoxin genes from minimal CRISPRs and the convergent strategy of tRNA-sequestering CreT toxins. Nucleic Acids Research, 2021, 49(18): 10677–10688.

5. Wu Shuqi^#; Xu Run^#; Su Mengjiao^#; Gao Can; Liu Yang; Chen Yujia; Luan Guangxin; Jia Xu*; Wang Rui*. A pyrF-Based Efficient Genetic Manipulation Platform in Acinetobacter baumannii To Explore the Vital DNA Components of Adaptive Immunity for I-F CRISPR-Cas. Microbiology Spectrum, 2022, 10(5): e0195722.

6. Wang Rui^#; Li Ming^#; Gong Luyao; Hu Songnian; Xiang Hua*. DNA motifs determining the accuracy of repeat duplication during CRISPR adaptation in Haloarcula hispanica. Nucleic Acids Research, 2016, 44(9): 4266–4277.

7. Li Ming^#; Wang Rui^#; Zhao Dahe; Xiang Hua*. Adaptation of the Haloarcula hispanica CRISPR-Cas system to a purified virus strictly requires a priming process. Nucleic Acids Research, 2014, 42(4): 2483–2492.