You Che
Ph.D
Research Assistant Professor
Division of Public Health Laboratory Sciences
Contact Information
Tel: +852 2831 5494
Email: youche@hku.hk
Address: 7/F Hong Kong Jockey Club Building for Interdisciplinary Research, 5 Sassoon Road, Hong Kong
Main Objectives and Strategy
Our lab focuses on understanding the human microbiome, antimicrobial resistance (AMR), and their interactions with pathogens. We employ a broad range of advanced techniques, including Next-Generation Sequencing (Nanopore technology), single-cell and spatial transcriptomics, bioinformatics, and molecular tools to investigate the multi-kingdom diversity, adaptation, and evolution of the skin microbiome in both health and disease. We are interested in investigating the microbiome of elderly individuals, with a focus on pathogen transmission and AMR development, and leveraging this knowledge to support overall health and promote healthy aging.
Our research also aims to reveal the resistome and associated mobile genetic elements (MGEs) through big data analysis, while experimentally investigating the mechanisms driving the spread of AMR among pathogens. Ultimately, we seek to develop innovative strategies, such as bacteriophage therapies, to combat the global AMR challenge.
Selected Publications
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Che, Y., Yang, Y., Xu, XQ., Břinda, K., Hanage, WP., Polz, MF., Hanage, WP., Zhang, T. Conjugative plasmids cooperate with insertion sequences to shape the horizontal transfer of antibiotic resistance genes. PNAS. 118, e2008731118 (2021, highly cited paper).
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Che, Y., Xia, Y., Liu, L., Li, AD., Yang, Yu., Zhang, T. Mobile antibiotic resistome in wastewater treatment plants revealed by Nanopore metagenomic sequencing. Microbiome. 7(1), 44 (2019, highly cited paper).
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Che, Y., Xu, XQ., Yang, Y., Břinda, K., Hanage, WP., Yang, C. Zhang, T. High-resolution genomic surveillance elucidates a multilayered hierarchical transfer of resistance between WWTP- and human/animal-associated bacteria. Microbiome. 10(1), 16 (2022).
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Huo, K., Liu, Y., Huang, R., Zhang, Y., Liu, H., Che, Y., Yang, C. Development of a novel promoter engineering‐based strategy for creating an efficient para‐nitrophenol‐mineralizing bacterium. Journal of Hazardous Materials. 424, 127672 (2022, corresponding author).
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Che, Y., Han, JM., Harkins, C., Conlan, S., Deming, C., Amirkhani, A., Bingham, MA., Holmes, C., Englander, H., Shen, ZY., NISC, Castelo-Soccio, L., Pittaluga, S., Zhao, C., Dell’Orso, S., Pai, SY., Hickstein, D., Holland, SM., Brownell, I., Nagao, K., Gonzalez, CE., Shah, NN., Freeman, AF., Su, HC., Segre, JA., Kong, HH. Restoration of the human skin microbiome following immune recovery after hematopoietic stem cell transplantation. (2024, submitted)
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Shen, ZY., Robert, L., Stolpman, M., Che, Y., Walsh, A., Saffery, R., Allen, KJ., Eckert, J., Young, A., Deming, K., Chen, Q., Conlan, S., Laky, K., Li, JM., Chatman, L., Kashaf, SS., NISC., Kong, HH., Frischmeyer-Guerrerio, PA., Perrett, KP., Segre, JA. A genome catalog of the early‐life human skin microbiome. Genome Biol. 24(1), 252. (2023).
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Yang, Y., Che, Y., Liu, L., Wang, CX., Yin, XL., Deng, Y., Yang, C., Zhang, T. Rapid absolute quantification of pathogens and ARGs by nanopore sequencing. Sci Total Environ. 809, 152190 (2022).
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Deng, Y., Huang, Y., Che, Y., Yang, Y., Yin, XL., Yan, AX., Dai, L., Liu, YY., Polz, MF., Zhang, T. Microbiome assembly for sulfonamide subsistence and the transfer of genetic determinants. ISME J. 15(10):2817‐2829 (2021).
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Liu, L., Wang, YL., Che, Y., Chen, YQ., Xia, Y., Luo, RB., Cheng, SH., Zheng, CM., Zhang, T. High‐quality bacterial genomes of a partial‐nitritation/anammox system by an iterative hybrid assembly method. Microbiome. 8(1), 155 (2020).
Biosketch
Before joining the School of Public Health, Dr. Che was a postdoctoral fellow at the National Institutes of Health (NIH), US, starting in 2021. His research focused on the skin microbiome, and in 2024, he was honored with the Annual NIAMS IPR Fellow’s Research Award. He completed his PhD in environmental microbiology at the University of Hong Kong, focusing on the environmental dimension of antimicrobial resistance and pathogens, and was recognized as the Outstanding Research Postgraduate Student in 2020. During his PhD, he also served as a visiting scholar at the Harvard School of Public Health, where he focused on antimicrobial resistance and pathogen transmission epidemiology.
Join Us!
The Che Lab is seeking talented and motivated graduate students with a passion for exploring the microbiome and antimicrobial resistance through cutting-edge technologies. For more details, please visit this link.
We are also hiring Research Assistant I/II positions to support various microbiome and antimicrobial resistance projects. This role offers a valuable opportunity for individuals interested in gaining both wet and dry lab experience while learning a range of advanced techniques. For more information, please visit this link.
For inquiries, please contact youche@hku.hk.