Our laboratory is interested in understanding the physiology of industrial fermentation from the molecular level and improving the performance of industrial microorganisms using systems biotechnology approach.

In our laboratory, solvent-producing bacteria and lactic acid bacteria are selected as research models. Insights into the molecular basis and the regulatory mechanism for the production of bulk chemicals by these microorganisms will be gained using genomics tools. By integrating the data generated from genomics, novel metabolic engineering strategies will be developed to improve the functionality of industrial microorganisms.

We are also interested in developing novel methodologies to support the development of systems biotechnology. This includes high-throughput screening method for obtaining microorganisms with industrial potential for producing bio-based chemicals; novel genetic tools for prokaryotes and genome-wide random mutagenesis strategy; methodology for integrating data generated from genome, transcriptome, proteome, metabolome, and fluxome studies; and development of genome-scale metabolic models by which the biological behavior of microorganisms can be predicted and simulated.

1995-2000 PhD, Wuxi University of Light Industry, Wuxi, China

1991-1995 Bsc, Wuxi University of Light Industry, Wuxi, China

​2013.06-Present Director, CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, Institute of Microbiology, Chinese Academy of Sciences

2013.01-Present Director, CAS-TWAS Centre of Excellence for Biotechnology, Institute of Microbiology, Chinese Academy of Sciences

2008.6-2009.6 Deputy Director-General, Tianjin Institute of Industrial Biotechnology, Chinese Academy ofSciences

2007.6-2008.6 Director, Center for Bioenergy and Industrial Biotechnology, Institute of Microbiology, Chinese Academy of Sciences 

2006-Present Professor and Principal Investigator, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China 

2004-2006 Research Officer, University College Cork, Cork, Ireland 

2003-2004 Associate Professor, Southern Yangtze University, Wuxi, China 

2001-2002 Postdoctoral Research Associate, Wageningen Centre for Food Sciences and NIZO Food Research, Ede, The Netherlands 

2000-2001 Lecturer, Southern Yangtze University, Wuxi, China

​

2010 SCOPUS Young Researcher Award 

2010 Young Affiliate Fellow, Third World Academy of Sciences (TWAS) 

2006 Chinese Academy of Sciences, Hundred Talent 

2006 National Science and Technology Progress Award, 2nd Prize 

2004 Ministry of Education Science and Technology Progress Award, 2nd Prize 

2003 China Petroleum and Chemical Industry Technology Invention Award, 1st Prize 

2003 Jiangsu Province Science and Technology Progress Award, 2nd Prize 

2000 “Ten Outstanding Young Persons” in Wuxi

   

Industrial Biotechnology: efficient production of commodity and specialty chemicals

Bao G, Wang R, Zhu Y, Dong H, Mao S, Zhang Y, Chen Z, Li Y*, Ma Y. Complete genome sequence of Clostridium acetobutylicum DSM 1731, a solvent producing strain with multi-replicon genome architecture. J. Bacteriol., 2011, in press

Zhu L, Dong H, Zhang Y*, Li Y*. Engineering the robustness of Clostridium acetobutylicum by introducing glutathione biosynthetic capability. Metab. Eng., 2011, 2011, 13(4): 426-434

Mao S, Luo Y, Bao G, Zhang Y, Li Y*, Ma Y. Comparative analysis on the membrane proteome of Clostridium acetobutylicum wild type strain and its butanol-tolerant mutant. Mol. Biosys. 2011, 7(5): 1660-1677

Wang S, Zhang Y, Dong H, Mao S, Zhu Y, Wang R, Luan G, Li Y*. Formic acid triggers the “acid crash” of acetone-butanol-ethanol fermentation of Clostridium acetobutylicum. Appl. Environ. Microbiol., 2011, 77(5): 1674-1680.

Jia K, Zhu Y, Zhang Y, Li Y*. Group II intron-anchored gene deletion in Clostridium. PLoS ONE, 2011, 6(1): e16693.

Jia K, Zhang Y, Li Y*. Systematic engineering of microorganisms to improve alcohol tolerance. Eng. Life Sciences, 2010, 10(5): 422-429.

Mao S, Luo Y, Zhang T, Li J, Bao G, Zhu Y, Chen Z, Zhang Y, Li Y*, Ma Y. Proteome reference map and comparative proteomic analysis between a wild type Clostridium acetobutylicum DSM 1731 and its mutant with enhanced butanol tolerance and butanol yield. J. Proteome Res., 2010, 9(6): 3046-3061.

Zhou J, Li Y*. Engineering cyanobacteria for fuels and chemicals production. Protein Cell, 2010, 1(3): 207-210

Dong H, Dai Z, Zhang Y, Li Y*. Engineering Clostridium strain to accept unmethylated DNA. PLoS ONE, 2010, 5(2): e9038.

Zhang Y, Zhu Y, Zhu Y, Li Y*. The importance of engineering physiological functionality into microbes. Trends Biotechnol., 2009, 27(12): 664-672.

Tian J, Sang P, Gao P, Fu R, Yang D, Zhang L, Wu S, Lu X, Li Y, Xu G. 2009. Optimization of a GC-MS metabolic fingerprint method and its application in characterizing engineered bacterial metabolic shift. J. Sep. Sci., 2009, 32(13): 2281-2288

Rao L, Zhao X, Pan F, Li Y, Xue Y, Ma Y, Lu JR. Solution behavior and activity of a halophilic esterase under high salt concentration. PLoS ONE. 2009, 4(9):e6980.

Zhang Y, Huang Z, Du C, Li Y*, Cao Z*. Introduction of an NADH regeneration system into Klebsiella oxytoca leads to an enhanced oxidative and reductive metabolism of glycerol. Metab. Eng., 2009, 11(2): 101-106

Zhang Y, Ju J, Peng H, Gao F, Zhou C, Zeng Y, Xue Y, Li Y, Henrissat B, Gao GF, Ma Y. Biochemical and structural characterization of the intracellular mannanase AaManA of Alicyclobacillus acidocaldarius reveals a novel glycoside hydrolase family belonging to clan GH-A. J. Biol. Chem., 2008, 283(46): 31551-31558.

Du C, Zhang Y, Li Y, Cao Z. A novel redox-potential-based screening strategy for rapid isolation of Klebsiella pneumoniae mutants with enhanced 1,3-propanediol producing capability. Appl. Environ. Microbiol., 2007, 73(14): 4515-4521

Liu L-M, Li Y, Zhu Y, Du G, Chen J. Redistribution of carbon flux in Torulopsis glabrata by altering vitamin and calcium level. Metab. Eng., 2007, 9(1): 21-29.

Zhang Y, Li Y, Du C, Liu M, Cao Z. Inactivation of aldehyde dehydrogenase: a key factor for engineering 1,3-propanediol production by Klebsiella pneumoniae. Metab. Eng., 2006, 8(6): 578-586.

Liu L-M, Li Y, Chen J. Redirection of the NADH oxidation pathway in Torulopsis glabrata leads to an enhanced pyruvate production. Appl. Microbiol. Biotechnol., 2006, 72(2): 377-385.

Du C, Yan H, Zhang Y, Li Y, Cao Z. Use oxidoreduction potential as an indicator to regulate 1,3- propanediol fermentation by Klebsiella pneumoniae. Appl. Microbiol. Biotechnol., 2006, 69(5): 554-563.

Li Y, Wei G, Chen J. Glutathione: a review on biotechnological production. Appl. Microbiol. Biotechnol., 2004, 66(3): 233-242 (Mini-review)

Li Y, He N, Guan H, Du G, Chen J. A novel poly-galacturonic acid bioflocculant REA-11 produced by Corynebacterium glutamicum: A proposed biosynthetic pathway and experimental confirmation. Appl. Microbiol. Biotechnol., 2003, 63(2): 200-206.

Li Y, Hugenholtz J, Chen J, Lun S. Enhancement of pyruvate production by Torulopsis glabrata using a two-stage oxygen supply control strategy. Appl. Microbiol. Biotechnol., 2002, 60(1-2): 101-106.

Li Y, Chen J, Lun S, Rui X. Efficient production of pyruvic acid by Torulopsis glabrata: the key role of vitamins and its’ optimization. Appl. Microbiol. Biotechnol., 2001, 55(6): 680-685.

Li Y, Chen J, Lun S. Biotechnological production of pyruvic acid. Appl. Microbiol. Biotechnol., 2001, 57(4): 471-479 (Invited mini-review)

Lactic Acid Bacteria: genomics, genetics, physiology, and application

Zhang Y, Zhang Y, Zhu Y, Mao S, Li Y*. Proteomic analyses to reveal the protective role of glutathione in stress resistance of Lactococcus lactis. Appl. Environ. Microbiol., 2010, 76(10): 3177-3186.

Zhang J, Du GC, Zhang Y, Liao XY, Wang M, Li Y, Chen J. Glutathione protects Lactobacillus sanfranciscensis against freeze-thawing, freeze-drying, and cold treatment. Appl. Environ. Microbiol., 2010, 76(9): 2989-2996.

Fang F, Li Y, Bumann M, Raftis EJ, Casey PG, Cooney JC, Walsh MA, O’Toole PW.
Allelic variation of bile salt hydrolase genes contributes to, but is not the sole determinant of, bile resistance levels in Lactobacillus salivarius. J. Bacteriol., 2009, 191(18): 5743-5757.

Zhu Y, Zhang Y, Li Y*. Understanding the industrial application potential of lactic acid bacteria through genomics (Mini-review). Appl. Microbiol. Biotechnol., 2009, 83(4): 597-610.

Fang F, Flynn S, Li Y, Claesson MJ, van Pijkeren JP, Collins JK, van Sinderen D, O’Toole PW. Characterization of endogenous plasmids from Lactobacillus salivarius UCC118. Appl. Environ. Microbiol., 2008, 74(10): 3116-3128.

Ryan KA, Daly P, Li Y, Hooton C, O’Toole PW. Strain-specific inhibition of Helicobacter pylori by Lactobacillus salivarius and other lactobacilli. J. Antimicrobial. Chemotherapy, 2008, 61(4): 831-834.

Li Y, Canchaya C, Fang F, Raftis E, Ryan KA, van Pijkeren J-P, van Sinderen D, O’Toole PW. Distribution of megaplasmids in Lactobacillus salivarius and other lactobacilli. J. Bacteriol., 2007, 189(17): 6128-6139.

Zhang J, Fu R-Y, Hugenholtz J, Li Y* Chen J*. Glutathione protects Lactococcus lactis against acid stress. Appl. Environ. Microbiol., 2007, 73(16): 5268-5275.

Corr SC, Li Y, Riedel CU, O’Toole PW, Hill C, Gahan CGM. Bacteriocin production as a mechanism for the anti-infective activity of Lactobacillus salivarius UCC118. Proc. Natl. Acad. Sci. U. S. A., 2007, 104(18): 7617-7621. (cover article)

Claesson MJ*, Li Y*, Leahy S, Canchaya C, van Pijkeren JP, Cerdeño-Tárragad AM, Parkhill J, Flynn S, Collins JK, Higgins D, Shanahan F, Fitzgerald GF, van Sinderen D, O’Toole PW. Multi-replicon genome architecture of Lactobacillus salivarius. Proc. Natl. Acad. Sci. U. S. A., 2006, 103(17): 6718-6723. (cover article) (*equally contributed to this work).

Li Y, Raftis E, Canchaya C, Fitzgerald GF, van Sinderen D, O’Toole PW. Polyphasic analysis indicates that Lactobacillus salivarius subsp. salivarius and Lactobacillus salivarius subsp. salicinius do not merit separate subspecies status. Int. J. Syst. Evol. Microbiol., 2006, 56(10): 2397-2403.

van Pijkeren JP, Canchaya C, Ryan KA, Li Y, Claesson MJ, Sheil B, Steidler L, O’Mahony L, Fitzgerald GF, van Sinderen D, O’Toole PW. Comparative and functional analysis of sortase-dependent proteins in the predicted secretome of Lactobacillus salivarius. Appl. Environ. Microbiol., 2006, 72(6): 4143-4153.

Ventura M, Canchaya C, Bernini V, Altermann E, Barrangou R, Mc Grath S, Claesson MJ, Li Y, Leahy S, Walker CD, Zink R, Neviani E, Steele J, Broadbent J, Klaenhammer TR, Fitzgerald GF, O’Toole PW, van Sinderen D. Comparative genomics and transcriptional analysis of prophages identified in the genomes of Lactobacillus gasseri, Lactobacillus salivarius and Lactobacillus casei. Appl. Environ. Microbiol., 2006, 72(5): 3130-3146.

Fu R-Y, Bongers BS, van Swam II, Chen J, Molenaar D, Kleerebezem M, Hugenholtz J, Li Y*. Introducing glutathione biosynthetic capability into Lactococcus lactis subsp. cremoris NZ9000 improves the oxidative-stress resistance of the host. Metab. Eng., 2006, 8(6): 662-671.

Fu R-Y, Chen J, Li Y*. Heterologous production of transglutaminase in Lactococcus lactis significantly enhances the growth performance of the host. Appl. Environ. Microbiol., 2005, 71(12): 8911-8919.

Li Y, Hugenholtz J, Sybesma W, Abee J, Molenaar D. Using Lactococcus lactis for glutathione overproduction. Appl. Microbiol. Biotechnol., 2005, 67(1): 83-90.

Li Y, Hugenholtz J, Abee J, Molenaar D. Glutathione protects Lactococcus lactis against oxidative stress. Appl. Environ. Microbiol., 2003, 69(10): 5739-5745.

董红军，戴宗杰，张延平，李寅 一种稳定联产异丙醇和丁醇的工程菌及其构建方法与应用 201110084263.1
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张延平，王少华，刘伟，李寅 自动调控氧化还原电位的装置及其应用 201010593474.3
张延平，王少华，刘伟，李寅 自动调控氧化还原电位的装置 201020667985.0
董红军，张延平，李寅 一种使产丁醇梭菌易于遗传操作的方法及其易于遗传操作的突变体 200910241532.3
李寅，朱泰承，游丽金 表达谷氨酰胺转氨酶的重组菌及其应用 200910091763
徐洪涛，朱林江，张延平，李寅 一种制备L-乳酸的方法及其专用菌株 200910089764.1
张天瑞，张延平，李寅 一种高通量检测溶剂产生菌溶剂产量的方法 200810240859.4
张天瑞，张延平，李寅 一种筛选解除葡萄糖代谢阻遏的丁醇产生菌突变株的方法 200810240858.x
朱林江，张延平，王少华，李寅 生产丁醇的菌剂及其应用 200810241011.3
王少华，张延平，董红军，李寅 重组丙酮丁醇梭菌及其构建方法与应用 200810239557.5 （已获授权）
朱林江，张延平，李寅 合成谷胱甘肽的梭菌及其构建方法与应用 200810239559.4 （已获授权）
周杰，解鹃，高成华，张延平，李寅 一种重组蓝藻产丁醇的方法 200810239558.X
董红军，张延平，李寅 重组梭菌及其构建方法与应用 200810239560.7 （已获授权）
张延平，张天瑞，李寅 一种获得丁醇产生菌突变株的方法 200810239556.0
贾开志，李寅，张延平 一种生物传感器及其应用 200810239476.5 （已获授权）
张延平，王鑫昕，李寅，王少华 一种生产丁醇的方法 200810239319.4
徐洪涛，张延平，李 寅 一种筛选乳酸生产率高的菌株的方法 200810116218.8
徐洪涛，张延平，李 寅 一种生产乳酸的方法及其专用植物乳杆菌 200810116194.6
张艳禾，张延平，李 寅 一种培育抗盐胁迫乳酸乳球菌的方法及其专用培养基 200810116193.1
张延平，郑文超，王少华，李 寅 一种发酵生产丁醇和丁二酸的方法 200810104083.3
王少华，张延平，李 寅 一株丙酮丁醇梭菌及其应用 200810102673.2 （已获授权）

2010.12.10 The 3rd International Symposium for contribution of lactic acid bacteria to preventive and pre-symptomatic medicine, Hiroshima University, Japan
2010.08.22 International Conference on Biomass Energy Technologies, Beijing, China
2010.04.14 The Second International Congress EurasiaBIO’2008, Moscow, Russia
2010.01.14 OECD workshop “industrial biotechnology“, Vienna, Austria
2009.10.02 Synthetic Biology Ethics Workshop, Delft, The Netherlands
2009.09.26 12th Annual Chinese-American Kavli Frontiers of Science Symposium, Kunming, China
2009.09.25 BBSRC China Partnering Award Workshop on improving biobutanol production by solventogenic Clostridia, Shanghai, China
2009.07.22 World Congress Industrial Biotechnology and Bioprocessing, Montreal, Canada
2008.10.31 Kluyver Centre Expert Workshop on Biofuel Development, Vlaardingen, The Netherlands
2008.10.13 International Biotechnology Symposium, Dalian, China
2008.09.02 9th Symposium on Lactic Acid Bacteria, Egmond aan Zee, The Netherlands
2008.08.30 The first symposium on glutathione and related thiols, Nancy, France
2008.04.24 The First International Congress EurasiaBIO’2008, Moscow, Russia

Collaboration with Shell Research Limited (UK): Novel biofuels (2008-2011)

Collaboration with DSM White Biotechnology B.V. (The Netherlands): Novel bio-based chemicals (2008-2010) 

Collaboration with Nestec Ltd. (Switzerland) : Novel cultivation process for lactic acid bacteria (2011)

已指导学生

解鹃  硕士研究生  071005-微生物学  

王润江  硕士研究生  071005-微生物学  

毛绍名  博士研究生  071005-微生物学  

董红军  博士研究生  071005-微生物学  

王少华  博士研究生  071005-微生物学  

朱林江  博士研究生  071005-微生物学  

朱岩  博士研究生  071005-微生物学  

杨列健  硕士研究生  430139-生物工程


现指导学生

陶文文  硕士研究生  071005-微生物学  

巩伏雨  硕士研究生  071005-微生物学  

栾国栋  博士研究生  071005-微生物学  

鲍冠辉  博士研究生  071005-微生物学  

邓思颖  硕士研究生  071005-微生物学  

   

张延平 博士  副研究员  zhangyp@im.ac.cn
朱泰承 博士 副研究员 zhutc@im.ac.cn
蔡    真  博士  助理研究员 caiz@im.ac.cn
周    杰  博士 助理研究员 jiezhouw@im.ac.cn
董红军 博士 助理研究员 redarmy305@gmail.com
王瑞妍 博士 助理研究员 rywang07@gmail.com
赵秋伟 硕士 工程师  zhaoqiuwei@im.ac.cn
张天瑞 硕士  技术人员 myparadise365@yahoo.com.cn
孙红兵 硕士  技术人员 bbmm0412@sina.com  
张君丽 硕士 技术人员 18211097021@163.com
  

张艳禾 （已出站）
贾开志  （已出站）
朱泰承  （已出站）
李兴华 clarke1110@163.com
柳国霞 KLDS.moml@gmail.com

National High Technology Program (863) “Key technologies for the biotechnological production of long-chain alcohols and systems integration” (2011-2015) 

National Basic Research Program (973): “Synthetic Cell Factories” (2011-2015)

National High Technology Program (863) “Key Technology for Bio-butanol Production” (2006-2008)

National Basic Research Program (973): Cell Factories for Biorefinery (2007-2011) 

Knowledge Innovation Program of the Chinese Academy of Sciences: Key Technology for the Production of L-Lactic Acid (2006-2009)

Knowledge Innovation Program of the Chinese Academy of Sciences (Major Project): Biorefinery and Production of Cellulosic Ethanol by Thermophilic Bacteria (2008-2012)

Equipment Program of the Chinese Academy of Sciences: A novel equipment for anaerobic bioprocess monitor and control (2009-2011). 

E-Science Program of the Chinese Academy of Sciences: The knowledge environment of Industrial Biotechnology and it’s E-Science demonstration (2009-2011)

National Science Foundation of China (NSFC): The physiological role of glutathione in adapting different environmental niches (2009-2011)

National Science Foundation of China (NSFC): Molecular mechanism of the redox potential in the production of 1,3-propandiol (coordinated by Dr. Yanping Zhang) (2010-2012) 

National Science Foundation of China (NSFC): Novel algae biofuels (coordinated by Dr. Jie Zhou) (2010-2012)