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Name: LI Yin
Title: Professor
Dept.: CAS Key Laboratory of Microbial Physiological and Metabolic Engineering
Tel: +86-10-64807485
E-mail: yli@im.ac.cn
Add.: NO.1 Beichen West Road, Chaoyang District, Beijing 100101, P.R.China
Prof. Yin Li received his Ph.D degree at Jiangnan University in 2000. He then went to the Netherlands and worked in Wageningen Centre for Food Sciences as a post-doctoral researcher. He was later recruited as Research Officer by Science Foundation of Ireland and worked in University College Cork. In 2006 he was recruited as Principle Investigator by Institute of Microbiology, Chinese Academy of Sciences (IMCAS), under the support of the Hundred Talents Program of CAS. Currently, he is serving as the Associate Editor of Chinese Journal of Biotechnology, and Member of the Editorial Board of Biotechnology Journal. In 2010 he was selected as the Young Affiliate of the Third-World Academy of Sciences.

Research interests:

Dr. Li’s major research interest is to improve the functionality of industrial microorganisms. He has published more than 60 papers in international peer-reviewed journals. The research of his group is supported by the Knowledge Innovation Program of CAS, National High-Technology Program, National Basic Research Program, and National Science Foundation of China. His group has also established extensive collaborations with industry partners including Shell and DSM.


His 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 his laboratory, lactic acid bacteria and extremophiles with acid-, alkali-, and solvent-tolerance 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.


They 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.

Awards & Honors:

Selected Publications and Books:

[1] ZHU Yan, SONG Jiangning, XU Zixiang, SUN Jibin, ZHANG Yanping, LI Yin*, MA Yanhe. 2012. Development of thermodynamic optimum searching (TOS) to improve the prediction accuracy of flux balance analysis. Biotechnology Bioengineering. doi: 10.1002/bit.24739.

[2] ZHANG Yanping, LI Yin*. 2012, Engineering the antioxidative properties of lactic acid bacteria for improving its robustness. Current Opinion in Biotechnology, DOI: 10.1016/j.copbio.2012.08.013.

[3] JIA Kaizhi, ZHANG Yanping, LI Yin*. 2012. Identification and characterization of two functionally unknown genes involved in butanol tolerance of Clostridium acetobutylicum. PLoS ONE. 7(6): e38815.

[4] DAI Zongjie, DONG Hongjun, ZHU Yan, ZHANG Yanping, LI Yin*, MA Yanhe. 2012. Introducing a single secondary alcohol dehydrogenase into butanol-tolerant Clostridium acetobutylicum Rh8 switches ABE fermentation to high level IBE fermentation. Biotechnology for Biofuels. 5: 44.

[5] GE Shaolin, ZHU Taicheng*, LI Yin. 2012. Expressing bacterial GshF in Pichia pastoris for glutathione production. Applied and Environmental Microbiology. doi: 10.1128/​AEM.00509-12.

[6]  ZHOU Jie, ZHANG Haifeng, ZHANG Yanping, LI Yin*, MA Yanhe. 2012. Designing and creating a modularized synthetic pathway in cyanobacterium Synechocystis enables production of acetone from carbon dioxide. Metabolic Engineering. 14(4): 394-400.

[7] DONG Hongjun, TAO Wenwen, DAI Zongjie, YANG Liejian, GONG Fuyu, ZHANG Yanping, LI Yin*. 2012. Biobutanol. Advances in Biochemical Engineering-Biotechnology. 128: 85-100.

[8] ZHU Linjiang#, ZHU Yan#, ZHANG Yanping, LI Yin*. 2012. Engineering the robustness of industrial microbes through synthetic biology. Trends in Microbiology. 20(2): 94-101 (#equal contribution)

[9]  DONG Hongjun#, TAO Wenwen#, ZHANG Yanping, LI Yin*. 2012. Development of an anhydrotetracycline-inducible gene expression system for solvent-producing Clostridium acetobutylicum: A useful tool for strain engineering. Metabolic Engineering. 14(1): 59-67 ( #equal contribution)

[10] WANG Shaohua, ZHU Yan, ZHANG Yanping*, LI Yin*. 2012. Controlling the oxidoreduction potential of the culture of Clostridium acetobutylicum leads to an earlier initiation of solventogenesis, thus increasing solvent productivity. Applied Microbiology and Biotechnology. 93(3): 1021-1030.

[11]  ZHU Linjiang, DONG Hongjun, ZHANG Yanping*, LI Yin*. 2011. Engineering the robustness of Clostridium acetobutylicum by introducing glutathione biosynthetic capability. Metabolic Engineering 13(4):426-34

[12]  JIA Kaizhi, ZHU Yan, ZHANG Yanping, LI Yin*. 2011. Group II intron-anchored gene deletion in Clostridium. PLoS ONE. 6(1): e16693.

[13] WANG Shaohua, ZHANG Yanping, DONG Hongjun, MAO Shaoming, ZHU Yan, WANG Runjiang, LUAN Guodong, LI Yin*. 2011. Formic acid triggers the “acid crash” of acetone-butanol-ethanol fermentation of Clostridium acetobutylicum. Applied and Environmental Microbiology. 77(5):1674-1680.

[14] MAO Shaoming, LUO Yuanming, BAO Guanhui, ZHANG Yanping, LI Yin*, MA Yanhe. 2011. Comparative analysis on the membrane proteome of Clostridium acetobutylicum wild type strain and its butanol-tolerant mutant. Molecular BioSystems 7(5): 1660-1677.

[15] BAO Guanhui, WANG Runjiang, ZHU Yan, DONG Hongjun, MAO Shaoming, ZHANG Yanping, CHEN Zugen, LI Yin*, MA Yanhe. 2011. Complete genome sequence of Clostridium acetobutylicum DSM 1731, a solvent producing strain with multi-replicon genome architecture. Journal of Bacteriology. 193(18): 5007-5008.

[16] ZHU Taicheng, YOU Lijin, GONG Fuyu, XIE Minfeng, XUE Yanfen, LI Yin*, MA Yanhe*. 2011. Combinatorial strategy of sorbitol feeding and low-temperature induction leads to high-level production of alkaline beta-mannanase in Pichia pastoris. Enzyme and Microbial Technology 49: 407-412.

[17] DONG Hongjun#, TAO Wenwen#, ZHU Linjiang, ZHANG Yanping, LI Yin*. 2011. CAC2634-disrupted mutant of Clostridium acetobutylicum can be electrotransformed in air. Letters in Applied Microbiology. 53(3): 379-382. (#equal contribution)

[18] Zhang YH,Zhang YP, 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 (cover article).

[19] 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.

[20] 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.

[21] 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.

[22] 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.

[23] 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.

[24] 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.

[25] 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.

[26] 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)

[27] 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).

[28] 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.

[29] 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.

[30] 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.

[31] 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.

[32] 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.

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

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

[35] 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.

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

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

[38] 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

[39] 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.

[40] 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

[41] 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.

[42] 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

[43] 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.

[44] 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.

[45] 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.

[46] 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.

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

[48] 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.

[49] 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.

[50] 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.

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

Institute Of Microbiology Chinese Academy of Sciences
NO.1 West Beichen Road, Chaoyang District, Beijing 100101, China Phone: 0086-10-64807462 Fax: 0086-10-64807468 Email: office@im.ac.cn