1、病原微生物耐药及持留机制的研究。本实验室在建立持留菌模型的基础上利用蛋白质组、转录组、筛选突变株等方法鉴定与持留菌相关基因和途径。了解不同微生物耐用和持留的机制，寻找相关的药物靶点。

2、病原微生物、寄生虫的药物筛选。开发新的高效、高通量、高灵敏度的微生物、寄生虫活性检测方法。针对耐药菌、持留菌，筛选并获得具有高效、低副作用、特异性好的药物、天然产物或先导化合物。用于抗菌新药的研发。

3、基因组系统进化研究。利用本实验室自主开发的supertree系统进化分析方法和程序对真核生物、原核生物、病毒开展基因组系统进化分析。

科研项目（课题）

1. 国家自然科学基金委员会，青年科学基金项目，81902099，莱姆病病原 B. garinii和 B. afzelii持留菌的形成机制和药物敏感性研究，2020-01至2022-12，主持

2. 国家自然科学基金委员会，面上项目，81671982，ArlS/ArlR和YycG/YycF协同调控表皮葡萄球菌生物膜形成的机制，2017.01至2020.12，参加

3. 国家自然科学基金委员会，面上项目，81573470，肠球菌属对利奈唑胺耐药新机制研究，2016.01至2019.12，参加

发表论文

1. Li, T., D. Liu, Y. Yang, J. Guo, Y. Feng, X. Zhang, S. Cheng and J. Feng (2020). "Phylogenetic supertree reveals detailed evolution of SARS-CoV-2." Scientific Reports 10(1): 22366.

2. Feng, J., J. Leone, S. Schweig, Y. Zhang (2020). Evaluation of natural and botanical medicines for activity against growing and non-growing forms of B. burgdorferi. Front Med 7, 6， DOI: 10.3389/fmed.2020.00006.

3. Feng, J., T. Li, R. Yee, Y. Yuan, C. Bai, M. Cai, W. Shi, M. Embers, C. Brayton, H. Saeki, K. Gabrielson and Y. Zhang (2019). Stationary phase persister/biofilm microcolony of Borrelia burgdorferi causes more severe disease in a mouse model of Lyme arthritis: implications for understanding persistence, Post-treatment Lyme Disease Syndrome (PTLDS), and treatment failure. Discov Med 27(148): 125-138.

4. Feng, J., Yee, R., Zhang, S., Tian, L., Shi, W., Zhang, W.-H., and Zhang, Y. (2018). A Rapid Growth-Independent Antibiotic Resistance Detection Test by SYBR Green/Propidium Iodide Viability Assay. Front Med 5, 127.

5. Feng, J., et al. (2017). Selective Essential Oils from Spice or Culinary Herbs Have High Activity against Stationary Phase and Biofilm Borrelia burgdorferi. Front Med 4: p. 169.

6. Feng, J., Zhang, S., Shi, W.L., and Zhang, Y. (2017). Activity of Sulfa Drugs and Their Combinations against Stationary Phase B. burgdorferi In Vitro. Antibiotics 6:10.

7. Feng, J., S. Zhang, W. Shi and Y. Zhang (2016). "Ceftriaxone Pulse Dosing Fails to Eradicate Biofilm-Like Microcolony B. burgdorferi Persisters Which Are Sterilized by Daptomycin/Doxycycline/Cefuroxime without Pulse Dosing." Front Microbiol 7:1744.

8. Feng, J., W. Shi, S. Zhang, D. Sullivan, P. G. Auwaerter and Y. Zhang (2016). "A Drug Combination Screen Identifies Drugs Active against Amoxicillin-Induced Round Bodies of In Vitro Borrelia burgdorferi Persisters from an FDA Drug Library." Front Microbiol 7: 743

9. Feng, J., Weitner, M., Shi, W., Zhang, S and Y. Zhang (2016). "Eradication of Biofilm-like Microcolony Structures of Borrelia burgdorferi by Daunomycin and Daptomycin but not Mitomycin C in Combination with Doxycycline and Cefuroxime" Front Microbiol 7:62.

10. Feng, J., W. Shi, S. Zhang and Y. Zhang (2015). "Identification of new compounds with high activity against stationary phase Borrelia burgdorferi from the NCI compound collection." Emerg Microbes Infect 4: e31.

11. Feng, J., P. G. Auwaerter and Y. Zhang (2015). "Drug combinations against Borrelia burgdorferi persisters in vitro: eradication achieved by using daptomycin, cefoperazone and doxycycline." PLoS One 10(3): e0117207.

12. Feng, J., W. Shi, S. Zhang and Y. Zhang (2015). "Persister mechanisms in Borrelia burgdorferi: implications for improved intervention." Emerg Microbes Infect 4(8): e51.

13. Feng, J., Weitner, M., Shi, W., Zhang, S., Sullivan, D., et al. (2015) Identification of Additional Anti-Persister Activity against Borrelia burgdorferi from an FDA Drug Library. Antibiotics 4: 397.

14. Feng, J., J. Wang, Y. Zhang, X. Du, Z. Xu, Y. Wu, W. Tang, M. Li, B. Tang and X. F. Tang (2014). "Proteomic analysis of the secretome of haloarchaeon Natrinema sp. J7-2." J Proteome Res 13(3): 1248-1258.

15. Feng, J., T. Wang, S. Zhang, W. Shi and Y. Zhang (2014). "An Optimized SYBR Green I/PI Assay for Rapid Viability Assessment and Antibiotic Susceptibility Testing for Borrelia burgdorferi." PLoS One 9(11): e111809.

16. Feng, J., T. Wang, W. Shi, S. Zhang, D. Sullivan, P. G. Auwaerter and Y. Zhang (2014). "Identification of novel activity against Borrelia burgdorferi persisters using an FDA approved drug library." Emerg Microbes Infect 3: e49.

17. Feng, J., B. Liu, Z. Zhang, Y. Ren, Y. Li, F. Gan, Y. Huang, X. Chen, P. Shen, L. Wang, B. Tang and X. F. Tang (2012). "The complete genome sequence of Natrinema sp. J7-2, a haloarchaeon capable of growth on synthetic media without amino acid supplements." PLoS One 7(7): e41621.

18. Li, T., M. Gargouri, Feng, J., J.-J. Park, D. Gao, C. Miao, T. Dong, D. R. Gang and S. Chen (2015). "Regulation of Starch and Lipid Accumulation in a Microalga Chlorella sorokiniana." Bioresource Technology 108: 250.

19. Shi, W., J. Chen, Feng, J., P. Cui, S. Zhang, X. Weng, W. Zhang and Y. Zhang (2014). "Aspartate decarboxylase (PanD) as a new target of pyrazinamide in Mycobacterium tuberculosis." Emerg Microbes Infect 3: e58.

20. Yee R, Cui P, Shi W, Feng, J., Zhang Y. Genetic Screen Reveals the Role of Purine Metabolism in Staphylococcus aureus Persistence to Rifampicin. Antibiotics 2015; 4(4): 627.

21. Niu, H., P. Cui, W. Shi, S. Zhang, Feng, J., Y. Wang, D. Sullivan, W. Zhang, B. Zhu and Y. Zhang (2015). "Identification of Anti-Persister Activity against Uropathogenic Escherichia coli from a Clinical Drug Library." Antibiotics 4(2): 179.

22. Niu, H., P. Cui, R. Yee, W. Shi, S. Zhang, J. Feng, D. Sullivan, W. Zhang, B. Zhu and Y. Zhang (2015). "A Clinical Drug Library Screen Identifies Tosufloxacin as Being Highly Active against Staphylococcus aureus Persisters." Antibiotics (Basel) 4(3): 329-336.