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Actinomycete Systematics and Resources

Principal Investigator
Dr.Prof. Ying Huang
Deputy Director of SKLMR, IMCAS




Research Area

Systematics, evolution, ecology and bioprospecting of actinomycetes

Research Interests

Actinomycetes encompass a large group of Gram-positive bacteria with high genome GC content. The phylum Actinobacteria currently consists of 6 classes, 22 orders, >50 families and >300 genera. Actinomycetes are ubiquitous in nature, and well-known producers of bioactive compounds, notably antibiotics, making nearly half of the known antibiotics derived from microbial sources, and playing important roles in biodegradation and bioremediation. Notwithstanding these findings, it is predicted that less than 10% of actinomycete bioactive metabolites have been discovered. To establish the relationships between the species and genetic diversity and the functional diversity is essential to the resource exploitation, but also a big challenge. Our group is engaged in molecular systematics and ecology of actinomycetes, as well as in evaluation and bioprospecting of actinomycetes of potential commercial significance. The overall goal of our studies is to improve and apply actinomycete systematics to unravel their natural diversity and evolutionary history for facilitating exploitation and ecological research of these organisms.

The following projects are currently ongoing in our lab:

  • Molecular systematics and speciation of actinomycetes
  • Community structures and ecological functions of marine actinomycetes
  • Diversity and biosynthetic potential of acidophilic actinomycetes
  • Bioprospecting and functional evolution of actinomycetes


Lab Members

Principal Investigator

Ying Huang, Ph.D. Professor

1987-1991   B.E. Department of Biotechnology, East China University of Science and Technology, Shanghai, China
1991-1994   M.Sc. Department of Bioengineering, Sichuan University, Chengdu, China
1996-1999   Ph.D. Department of Biochemistry and Molecular Biology, Health Science Center, Peking University, Beijing, China

Professional Experience
1994-1996   Teaching Assistant of Microbial Engineering, Sichuan University, Chengdu, China
1999-2001   Research Associate of Microbial Systematics, Institute of Microbiology, Chinese Academy of Sciences
2002-2003   Visiting Scholar of Actinomycete Systematics, Ghent University and Newcastle University
2002-2007   Associate Professor and Principal Investigator, Institute of Microbiology, Chinese Academy of Sciences
2007-present   Professor and Principal Investigator, Institute of Microbiology, Chinese Academy of Sciences
2011-present   Deputy director, State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences

Permanent staff

Xiaoying Rong
PhD, Assistant Professor

Jian Wang
PhD, Assistant Professor

Ning Liu
MS, Engineer

Limin Zhang
MS, Assistant Professor

Jisheng Ruan
PhD, Professor (consultant)

Limin Zhang
MS, Assistant Professor

Graduate Students  
Bing Huang (Ph.D student)          
Xiaoxuan Guo (Ph.D student)               
Minghao Liu (Ph.D student)           
Kun Cheng (Ph.D student)              
Ping Chen  (Ph.D student)            
Fangying Song (Ph.D student)  
Yisong Li  (M.Sc student)            

Former Graduate Students

Qingfeng Cui (2004, M.Sc) 
Chunguang Xu (2005, M.Sc)
Hongli Luo (2006, M.Sc)
Qiang Gu (2006, M.Sc)
Yinping Guo (2007, M.Sc)
Ning Liu (2007, M.Sc)
Danheng Qiu (2008, M.Sc)
Xiaoying Rong (2009, Ph.D)
Peng Gao (2009, M.Sc)
Hao Wang (2010, M.Sc)
Lijun Xi (2012, Ph.D)

Representative pictures

Phylogenetic NJ tree and Structure analyses of S. albidoflavus multi-locus sequence data.
(Appl Environ Microbiol, 2015, doi:10.1128/AEM.02925-14)


Recent Publications (*Corresponding author)

  1. Kun Cheng#, Xiaoying Rong#, Adrián A. Pinto-Tomás, Marcela Fernández- Villalobos, Catalina Murillo-Cruz and  Ying Huang*. 2015. Population genetic analysis of Streptomyces albidoflavus reveals habitat barriers to homologous recombination in the diversification of streptomycetes. Appl Environ Microbiol, doi:10.1128/AEM.02925-14.
  2. Xiaoying Rong and Ying Huang*. 2014.  Multi-locus sequence analysis: taking prokaryotic systematics to the next level. In Michael Goodfellow, Iain Sutcliffe and Jongsik Chun. Method Microbiol, 41: 221-251.
  3. Fei Ren#, Limin Zhang#, Lei Song, Shiyao Xu, Lijun Xi, Li Huang, Ying Huang* and Xin Dai*. 2014. Fulvimarina manganoxydans sp. nov., isolated from a deep-sea hydrothermal plume in the south-west Indian Ocean. Int J Syst Evol Microbiol,64(8):2920-2925.
  4. Haiyan Chen, Ning Liu, Ying Huang* and Yihua Chen*. 2014. Isolation of an anthrabenzoxocinone 1.264-C from Streptomyces sp. FXJ1.264 and absolute configuration determination of the anthrabenzoxocinones. Tetrahedron: Asymmetry, 25(2): 113-116.
  5. Rong X., Doroghazi J.R., Cheng K., Zhang L., Buckley D.H. and Huang Y.* 2013. Classification of Streptomyces phylogroup pratensis (Doroghazi and Buckley, 2010) based on genetic and phenotypic evidence, and proposal of Streptomyces pratensis sp. nov. Syst Appl Microbiol, 36(6): 401-407.
  6. Liu N., Shang F., Xi L. and Huang Y.* 2013. Tetroazolemycins A and B, two new oxazole-thiazole siderophores from deep-sea Streptomyces olivaceus FXJ8.012. Mar Drugs, 11(5): 1524-1533.
  7. Wang P., Xi L., Liu P., Wang Y., Wang W., Huang Y.* and Zhu W.* 2013. Diketopiperazine derivatives from the marine-derived actinomycete Streptomyces sp. FXJ7.328. Mar Drugs, 11(4): 1035-1049.
  8. Rong X. and Huang Y.* 2012. Taxonomic evaluation of the Streptomyces hygroscopicus clade using multilocus sequence analysis and DNA-DNA hybridization, validating the MLSA scheme for systematics of the whole genus. Syst Appl Microbiol, 35: 7-18.
  9. Xi L., Ruan J. and Huang Y.* 2012. Diversity and biosynthetic potential of culturable actinomycetes associated with marine sponges in the China seas. Int J Mol Sci, 13: 5917-5932.
  10. Zhang L., Xi L., Ruan J. and Huang Y.* 2012. Microbacterium marinum sp. nov., isolated from deep-sea water. Syst Appl Microbiol, 35: 81-85.
  11. Zhang L., Xi L., Ruan J. and Huang Y.* 2012. Micromonospora yangpuensissp. nov., isolated from a sponge in South China Sea. Int J Syst Evol Microbiol, 62: 272–278. 
  12. Li X., Zhang L., Ding Y., Gao Y., Ruan J. and Huang Y.* 2012. Lentzea jiangxiensis sp. nov., isolated from acidic soil in south-east China. Int J Syst Evol Microbiol, 62: 2342-2346.
  13. Wang H., Liu N., Xi L., Rong X., Ruan J. and Huang Y.* 2011. Genetic screening strategy for rapid access to polyether ionophore producers and products in actinomycetes. Appl Environ Microbiol, 77: 3433-3442.
  14. Rong X., Liu N., Ruan J. and Huang Y.* 2010. Multilocus sequence analysis of Streptomyces griseusisolates delineating intraspecific diversity in terms of both taxonomy and biosynthetic potential. Antonie van Leeuwenhoek, 98: 237-248.
  15. Rong X. and Huang Y.* 2010. Taxonomic evaluation of the Streptomyces griseus clade using multilocus sequence analysis and DNA-DNA hybridization, with proposal to combine 29 species and three subspecies as 11 genomic species. Int J Syst Evol Microbiol, 60: 696-703.
  16. Gao P. and Huang Y.* 2009. Detection, distribution, and organohalogen compound discovery implications of the reduced flavin adenine dinucleotide-dependent halogenase gene in major filamentous actinomycete taxonomic groups. Appl Environ Microbiol, 75: 4813-4820.
  17. Rong X., Guo Y. and Huang Y.* 2009. Proposal to reclassify the Streptomyces albidoflavus clade on the basis of multilocus sequence analysis and DNA-DNA hybridization, and taxonomic elucidation of Streptomyces griseus subsp. solvifaciens. Syst Appl Microbiol, 32: 314-322.
  18. Liu N., Wang H., Liu M., Gu Q., Zheng W., and Huang Y.* 2009. Streptomyces alni sp. nov., a daidzein-producing endophyte isolated from a root of Alnus nepalensis D. Don. Int J Syst Evol Microbiol, 59: 254-258.
  19. Qiu D., Ruan J. and Huang Y.* 2008. Selective isolation and rapid identification of members of the genus Micromonospora. Appl Environ Microbiol, 74: 5593-5597.
  20. Guo Y. Zheng W., Rong X. and Huang Y.* 2008. A multilocus phylogeny of Streptomyces griseus 16S rRNA gene clade: use of multilocus sequence analysis for streptomycete systematics. Int J Syst Evol Microbiol, 58: 149-159.