Actinomycete Systematics, Ecology, and Resource Exploitation

The phylum Actinomycetota encompasses a large group of Gram-positive bacteria with high genomic G+C contents. The phylum currently consists of 6 recognized classes, 36 orders, over 80 families and 400 genera. Actinomycetes are ubiquitous in nature and play important roles in biodegradation and bioremediation. These microorganisms are also well-known producers of bioactive compounds, notably antibiotics, making ~40% of the known antibiotics derived from microbial sources. Notwithstanding these findings, it is predicted that less than 10% of actinobacterial bioactive metabolites have been discovered so far. An integrated understanding of their genetic diversity, species diversity, and functional diversity is essential to the resource exploitation, but also a big challenge. By applying and developing methods and theories of actinomycete systematics and ecology, our group focuses on elucidating the diversity and functions of actinomycetes, exploring the pathways and mechanisms of their species and functional evolution, and promoting the development and utilization of actinomycete resources. The overall goal of our studies is to improve and apply actinomycete systematics to unravel their natural biodiversity and evolutionary history and to facilitate the exploitation and ecological research of these organisms.

The following projects are currently ongoing in our lab:

1. Speciation and evolution of actinomycetes

2. Diversity and ecological functions of actinomycetes in special habitats

3. Natural products exploitation and functional evolution of actinomycetes

4. Biological effects of outer space conditions on actinomycetes

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

1994-1996   Research Assistant of Microbial Engineering, Sichuan University, Chengdu
1999-2001   Research Associate of Microbiology, Institute of Microbiology, CAS
2002-2003   Visiting scholar of Actinomycete Systematics, Ghent University and Newcastle University
2002-2007   Associate Professor and Principal Investigator of Microbiology, IMCAS.
2007-present  Professor and Principal Investigator of Microbiology, IMCAS

1. Wang J, Liu N, Liu M, Huang Y^*. 2026. Eco-evolutionary dynamics sustain a potent yet rare antibiotic gene cluster in Streptomyces. ISME J, 20: wrag060, https://doi.org/10.1093/ismejo/wrag060
2. Ali M, Liu M^*, Liu N, Zhang L, Huang J, Zhong N, Zhao P, Huang Y^*. 2026. Diversity of Streptomyces species associated with potato common scab and genomic insights into their pathogenicity. Plant Soil, https://doi.org/10.1007/s11104-026-08454-2
3. Yu Q-Y, Liu X, Yao H, Lü P-P, Yang G-J, Lü X-T, Han X-G, Guo L-D, Huang Y*. 2025. The adaptability of grassland soil microbiomes to resource and stress shifts is mainly accomplished by niche conservatism under nitrogen deposition. ISME Commun, 5: ycaf215.
4. Huang J, Zheng X, Yu T, Ali M, Wiese J, Hu S, Huang L, Huang Y*. 2025. Diverse lifestyles and adaptive evolution of uncultured UBA5794 actinobacteria, a sister order of "Candidatus Actinomarinales". Environ Microbiome, 20: 39.
5. Wang K, Liu N, Liu M*, Zhao P, Zhong N, Challis GL, Huang Y*. 2024. Discovery and biosynthesis of streptolateritic acids A–D: acyclic pentacarboxylic acids from Streptomyces sp. FXJ1.172 with promising activity against potato common scab. J Agr Food Chem, 72: 14760-14768.
6. Lu L, Liu N, Fan Z, Liu M, Zhang X, Tian J, Yu Y, Lin H*, Huang Y*, Kong Z*. 2024. A novel PGPR strain, Streptomyces lasalocidi JCM 3373T, alleviates salt stress and shapes root architecture in soybean by secreting indole-3-carboxaldehyde. Plant Cell Environ, 47: 1941-1956.
7. Du X, Liu N, Yan B, Li Y, Liu M*, Huang Y*. 2024. Proximity-based defensive mutualism between Streptomyces and Mesorhizobium by sharing and sequestering iron. ISME J, 18: wrad041.
8. Bai B, Zhang L*, Dong H, Huang Y*. 2023. Coupled Fe(III) reduction and phenanthrene degradation by marine-derived Kocuria oceani FXJ8.057 under aerobic condition. J Hazard Mater, 459: 132237.
9. Liu M#, Wang K#, Wei J#, Liu N, Niu G, Tan H, Huang Y*. 2023. Comparative and functional analyses reveal conserved and variable regulatory systems that control lasalocid biosynthesis in different Streptomyces species. Microbiol Spectr, 11: e0385222
10. Wang J, Li Y, Pinto-Tomás AA, Cheng K, Huang Y*. 2022. Habitat adaptation drives speciation of a Streptomyces species with distinct habitats and disparate geographic origins. mBio. 13: e02781-21.
11. Li Y, Huang Y*. 2022. Distribution and evolutionary history of sialic acid catabolism in the phylum Actinobacteria. Microbiol Spectr. 10: e02380-21.
12. Yan B, Liu N, Liu M, Du X, Shang F, Huang Y*. 2021. Soil actinobacteria tend to have neutral interactions with other co-occurring microorganisms, especially under oligotrophic conditions. Environ Microbiol, 23: 4126–4140.
13. Yan B, Guo X, Liu M, Huang Y*. 2020. Ktedonosporobacter rubrisoli gen. nov., sp. nov., a novel representative of the class Ktedonobacteria, isolated from red soil, and proposal of Ktedonosporobacteraceae fam. nov. Int J Syst Evol Microbiol, 70: 1015-1025.
14. Zhang L, Zeng Q, Liu X, Chen P, Guo X, Ma LZ, Dong H*, Huang Y*. 2019. Iron reduction by diverse actinobacteria under oxic and pH-neutral conditions and the formation of secondary minerals. Chem Geol, 525: 390-399.
15. Li Y, Pinto-Tomás AA, Rong X, Cheng K, Liu M, Huang Y*. 2019. Population genomics insights into adaptive evolution and ecological differentiation in streptomycetes. Appl Environ Microbiol, 85: e02555-18.
16. Huang B, Li DG, Huang Y^*, Liu CT^*. 2018. Effects of spaceflight and simulated microgravity on microbial growth and secondary metabolism. Military Med Res, 5: 18.
17. Song F, Liu N, Liu M, Chen Y, Huang Y*. 2018. Identification and characterization of mycemycin biosynthetic gene clusters in Streptomyces olivaceus FXJ8.012 and Streptomyces sp. FXJ1.235. Mar Drugs, 16: 98.
18. Zhang L, Dong H*, Liu Y, Bian L, Wang X, Zhou Z, Huang Y*. 2018. Bioleaching of rare earth elements from bastnaesite-bearing rock by actinobacteria. Chem Geol, 483: 544-557.
19. Zhang L, Xi L, Ruan J, Huang Y*. 2017. Kocuria oceani sp. nov, isolated from a deep-sea hydrothermal plume. Int J Syst Evol Microbiol, 67: 164-169.
20. Cheng K, Rong X*, Huang Y*. 2016. Widespread interspecies homologous recombination reveals reticulate evolution within the genus Streptomyces. Mol Phylogenet Evol, 102: 246-254.
21. Liu N#, Song L#, Liu M#, Shang F, Anderson Z, Fox DJ, Challis GL*, Huang Y*. 2016. Unique post-translational oxime formation in the biosynthesis of the azolemycin complex of novel ribosomal peptides from Streptomyces sp. FXJ1.264. Chem Sci, 7: 482-488.
22. Liu N#, Song F#, Shang F, Huang Y*. 2015. Mycemycins A-E, new dibenzoxazepinones isolated from two different streptomycetes. Mar Drugs, 13: 6247-6258.
23. Huang B, Liu N, Rong X, Ruan J, Huang Y*. 2015. Effects of simulated microgravity and spaceflight on morphological differentiation and secondary metabolism of Streptomyces coelicolor A3(2). Appl Microbiol Biotechnol, 99: 4409-4422.
24. Guo X#, Liu N#, Li X, Ding Y, Shang F, Gao Y, Ruan J, Huang Y*. 2015. Red soils harbour diverse culturable actinomycetes that are promising sources of novel secondary metabolites. Appl Environ Microbiol, 81: 3086-3103.
25. Cheng K#, Rong X#, Pinto-Tomás A, Fernández-Villalobos M, Murillo-Cruz C, Huang Y*. 2015. Population genetic analysis of Streptomyces albidoflavus reveals habitat barriers to homologous recombination in the diversification of streptomycetes. Appl Environ Microbiol, 81: 966-975.
26. Rong X, Doroghazi JR, Cheng K, Zhang L. Buckley DH, 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: 401-407.
27. Liu N, Shang F, Xi L, Huang Y*. 2013. Tetroazolemycins A and B, two new oxazole-thiazole siderophores from deep-sea Streptomyces olivaceus FXJ8.012. Mar Drugs, 11: 1524-1533.
28. Rong X, 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.
29. Wang H#, Liu N#, Xi L, Rong X. Ruan J, Huang Y*. 2011. Genetic screening strategy for rapid access to polyether ionophore producers and products in actinomycetes. Appl Environ Microbiol, 77: 3433-3442.
30. Gao P, 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.
31. Rong X, Guo Y, 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.
32. Qiu D, Ruan J, Huang Y.* 2008. Selective isolation and rapid identification of members of the genus Micromonospora. Appl Environ Microbiol, 74: 5593-5597.
33. Guo Y, Zheng W, Rong X, 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.

已指导学生

郭银平  硕士研究生  071005-微生物学  

刘宁  硕士研究生  071005-微生物学  

古强  硕士研究生  071005-微生物学  

邱旦恒  硕士研究生  071005-微生物学  

高鹏  硕士研究生  071005-微生物学  

王浩  硕士研究生  071005-微生物学  

郗丽君  博士研究生  071005-微生物学  

荣晓莹  博士研究生  071005-微生物学  

岳昌武  博士研究生  071005-微生物学  

黄兵  博士研究生  071005-微生物学  

郭晓璇  博士研究生  071005-微生物学  

刘明皓  博士研究生  071005-微生物学  

程坤  博士研究生  071005-微生物学  

陈萍  博士研究生  071005-微生物学  

张超波  博士研究生  071005-微生物学  

黄娇  硕士研究生  071005-微生物学  

宋方英  博士研究生  071005-微生物学  

李一凇  博士研究生  071005-微生物学  

闫兵法  博士研究生  071005-微生物学  

王开锐  硕士研究生  085238-生物工程  

黄娇  博士研究生  071005-微生物学  

王姣  博士研究生  071005-微生物学  

黄静  硕士研究生  071005-微生物学  

独学渊  博士研究生  071005-微生物学  

白冰冰  博士研究生  071005-微生物学  

孔啸鸣  硕士研究生  071005-微生物学  

王开锐  博士研究生  071005-微生物学  

李元媛  硕士研究生  071005-微生物学  

黄静  博士研究生  071005-微生物学  

现指导学生

于清弋  博士研究生  071005-微生物学  

谭寿生  硕士研究生  071005-微生物学  

闫堃  博士研究生  071005-微生物学  

周欣蕊  博士研究生  071005-微生物学  

倪进榆  硕士研究生  086000-生物与医药  

王梦然  硕士研究生  071005-微生物学