HuangShiLab

Principal Investigator

Dr. HUANG Shi is an assistant professor in the Faculty of Dentistry, the University of Hong Kong. He has been engaged in microbiome research for over 10 years and made significant contributions in many frontiers in microbiome science. Firstly, he established a range of microbiome-based indices for the diagnosis and prediction of chronic diseases (such as dental caries, periodontal disease, gut health, skin health, aging, etc.). He first demonstrated that the onset of chronic diseases (e.g., dental caries) can be predicted by the human microbiome before the emergence of clinical symptoms. Secondly, he’s been focused on the basic metagenomics method development for years and is also an expert in benchmarking bioinformatic tools for metagenomics. To address the challenging low-biomass issue, he pioneered in developing a novel metagenomic sequencing strategy (i.e., 2bRAD-M), enabling the species-resolved, cost-effective microbiota profiling of challenging clinical samples (such as, FFPE tumor tissue, etc.). Last but not least, he has been actively exploiting the adaptive co-evolution between ingested probiotic bacteria and resident gut microbiota and developing personalized probiotic solutions that offer long-lasting efficacious probiotics for human health. In recent years, he published >40 research papers in peer-reviewed journals, including 20 first- or corresponding-authored papers published in Nature Methods, Cell Host Microbe, Microbiome, Genome Biology, ISMEJ, etc. His H-index has reached 37. His research has been funded by NSFC, HMRF, etc. He has five authorized microbiome-related patents (two international patents). He is also serving as a journal editor for iMeta, mSystems, Innovation, etc.

You can find more details here https://facdent.hku.hk/about/staff-profile.php?shortname=shihuang.

Contact us:

Address: Faculty of Dentistry, The University of Hong Kong, Room 2A10, Prince Philip Dental Hospital, 34 Hospital Road, Sai Ying Pun, Hong Kong

Email: shihuang@hku.hk

Whatsapp:

Research Interests

• Metagenomics method development
• Human microbiome association with chronic diseases
• Adaptive co-evolution of probiotics and native gut microbiome
• Machine learning applications in microbiome data

Current Members

Yufeng Zhang, PhD Student

Yufeng majored in Computer Science during her undergraduate and master’s studies and is currently focusing on bioinformatics, particularly in software development and data analysis for microbiome data. Her current work involves strain-level profiling and functional prediction of microbiota in low-microbial-biomass samples. In her free time, she enjoys hiking and cooking.

Yuesong Jiang, PhD Student

Yuesong completed his undergraduate studies majoring in Pharmacy at Nankai University. Currently, his research focuses on benchmarking bioinformatic tools for metagenomics and microbiome analysis under high host contamination. In his leisure time, he enjoys watching movies and exploring new restaurants.

Shuwen Hou, PhD Student

Shuwen obtained her BSc in biochemistry at HKU in 2023. Her current projects focus on low-biomass human microbiome analysis. In her free time, Shuwen enjoys hiking and watching TV series.

Enoch Kao, MPhil Student

Enoch was a Biochemistry major in his undergraduate years and worked on RNA aptamers as his final year project. His current focuses are Helicobacter pylori and the oral-stomach axis. Other than science, Enoch finds his passion in music, linguistics, and fitness.

Gang Wang, PhD Student

He majored in Oral Medicine during his undergraduate and master’s studies, developing a strong interest in oral microbiota. In the fall of 2024, he will begin his doctoral degree in this field. Currently, his research focuses on the interplay between oral microbiota and neurodegenerative diseases, such as Alzheimer’s Disease. In his free time, he enjoys reading and cycling.

Caihao Sun, PhD Student

He received the B.S. degree in Aerospace Science and Technology from Xidian University, Xi’an, China in 2021 and the M.S. degree in Electronic and Information Engineering (AI Direction). He majored in deep learning, computer vision, and hyperspectral image classification and published journals on RS and IEEE JSTARS as first author. He is currently working toward the Ph.D. under the guidance of Prof. Huang. His research interests include deep learning, LLM, and Bioinformation. Please feel free to contact Sun via email address: blinksch778@gmail.com.

Xinyue Zhang, PhD Student

She majored in Dentistry during her undergraduate studies and researched microbiology during her master’s program. Currently, her research focuses on the antimicrobial resistance mechanisms of bacterial microbiota in saliva. In her spare time, she enjoys sports, especially squash and Pilates.

Past Members

• Shuaiming Jiang (Hainan University, China)

Awards

• Outstanding Poster Award, 2024 Annual Academic Meeting of the Chinese Association of Microbial Ecology, 25-28 Nov 2024, Qingdao, China. Title: Strain2bFunc: strain-resolved profiling and functional prediction of microbiota in low-microbial-biomass samples using type IIB restriction sites. Presenter: Yufeng Zhang
• Best Poster Award, 2nd Frontiers Forum on Next-Generation Biomaterials in Dental Medicine, 2 June 2024, Hong Kong, China. Title: Strain-resolved taxonomic profiling and functional prediction of human microbiota using Strain2bFunc. Presenter: Yufeng Zhang
• HKU TEC MedTech Hackathon 2024 Finalist Award, HKU TEC MedTech Hackathon 2024, Hong Kong, China, Project title: Effective mining of Autologous Probiotics (ProbioMine Biotech.)
• Best Poster Award, SMART Symposium: Microbiota in Health and Disease, Shenzhen, China (13-14 Jan 2024). Title: A key genetic factor governing arabinan utilization in the gut microbiome alleviates constipation. Presenter: Dr. Shi Huang
• Poster of Distinction Award, International Digestive Disease Forum (IDDF), 10/06/2023-11/06/2023, Hong Kong, China. Title: Strain-resolved taxonomic profiling and functional prediction of human microbiota using Strain2bFunc; A120-A123 doi:10.1136/gutjnl-2023-IDDF.106. Presenter: Dr. Shi Huang
• Best Poster Award, TU-HKU-FJMU International Symposium, 17 November 2022, Hong Kong, China. Title: Strain-resolved taxonomic profiling and functional prediction of human microbiota using Strain2bFunc. Presenter: Dr. Shi Huang
• Qingdao Science and Technology Progress Second-class Award, 2021, “Mechanistic understanding of oral-microbiome-based diagnosis and prediction of diseases and its applications” (Co-I)
• Shandong Science and Technology Progress Third-class Award, 2022, “In-depth oral microbiome analysis based on next-generation sequencing technology for construction and application of the caries risk assessment model” (Co-I)
• International Postdoctoral Exchange Fellowship Program (China Postdoctoral Science Foundation), 2017-2018, Dr. Shi Huang
• China Postdoctoral Science Foundation-CAS Joint Fellowship for Excellent Postdoctoral Fellows (2016LH00036), 2016-2018, Dr. Shi Huang

Invited Speaker:

• 2024 中国工程院工程科技高层研讨会-精准营养与微生物生态暨第五届益生菌、肠道微生物与人体健康国际研讨会, Wuxi, China (3/12/2024)
• 2024 Annual Academic Meeting of the Chinese Association of Microbial Ecology, Qingdao, China (25-28/10/2024)
• 2024 NCCBB (The national computational biology and bioinformatic conference) (12-17/07/2024)
• Life & Health Technology Expo 2024, Hong Kong (27-29/06/2024)
• 2023 China Gut Conference, Beijing, China (20-22/5/2023)

• The Research and Transformation Platform for Maternal and Child Oral Health Prevention and Control in Guangdong-Hong Kong-Macao Bay Area (GBA) Conference (9-10/03/2023)

• China Medical University (2024)
• Sun Yat-sen University (2024)
• The First Bethune Hospital of Jilin University, Changchun (25-26/09/2024)
• The Affiliated Stomatological Hospital of Nanchang University, The First Affiliated Hospital of Nanchang University, and The Second Affiliated Hospital of Nanchang University, Jiangxi, China (7-9/08/2024)
• Fujian Cancer Hospital (09-11/04/2024)
• Nanchang University (2024)
• Jiangnan University (2022, 2023)
• Hainan University (2023)
• CAS-QIBEBT (2023)
• Southern Medical University (2023)
• Innermongolia Agricultural University (2023)

Selective Publications

Metagenomics Method Development

• Sun Z#, Huang S#*, Zhu P, Lam T, Zhao H, Lv J, Zhang R, Zhou L, Niu Q, Wang X, Zhang M, Jing G, Bao Z, Liu J, Wang S, Xu J. Species-resolved sequencing of low-biomass or degraded microbiomes using 2bRAD-M, Genome Biology 2022; 23: article no. 36-article no. 36 doi:10.1186/s13059-021-02576-9

• Zhu Q#, Huang S#, Gonzalez A, McGrath I, McDonald D, Haiminen N, Armstrong G, Vazquez-Baeza Y, Yu J, Kuczynski J, Sepich-Poore GD, Swafford AD, Das P, Shaffer JP, Lejzerowicz F, Belda-Ferre P, Havulinna AS, Meric G, Niiranen T, Lahti L, Salomaa V, Kim HC, Jain M, Inouye M, Gilbert JA, Knight R. Phylogeny-Aware Analysis of Metagenome Community Ecology Based on Matched Reference Genomes while Bypassing Taxonomy, mSystems 2022; e0016722-e0016722 doi:10.1128/msystems.00167-22

• Sun Zheng#, Huang Shi#, Zhang Meng, Zhu Qiyun, Haiminen Niina, Carrieri Anna Paola, Vázquez-Baeza Yoshiki, Parida Laxmi, Kim Ho Cheol, Knight Rob, Liu Yang Yu. Challenges in benchmarking metagenomic profilers, Nature Methods 2021; 18(6): 618-626 doi:10.1038/s41592-021-01141-3

Human Microbiome Association with Chronic Diseases

• Huang S, He T, Yue F, Xu X, Wang L, Zhu P, Teng F, Sun Z, Liu X, Jing G, Su X, Jin L, Liu J, Xu J*. Longitudinal Multi-omics and Microbiome Meta-analysis Identify an Asymptomatic Gingival State That Links Gingivitis, Periodontitis, and Aging, mBio 2021; 12(2): article no. e03281-20-article no. e03281-20 doi:10.1128/mBio.03281-20

• Huang Shi, Haiminen Niina, Carrieri Anna Paola, Hu Rebecca, Jiang Lingjing, Parida Laxmi, Russell Baylee, Allaband Celeste, Zarrinpar Amir, Vázquez-Baeza Yoshiki, Belda-Ferre Pedro, Zhou Hongwei, Kim Ho Cheol, Swafford Austin D., Knight Rob, Xu Zhenjiang Zech#. Human skin, oral, and gut microbiomes predict chronological age, mSystems 2020; 5(1): article no. e00630-19-article no. e00630-19 doi:10.1128/mSystems.00630-19

• Huang Shi, Li Rui, Zeng Xiaowei, He Tao, Zhao Helen, Chang Alice, Bo Cunpei, Chen Jie, Yang Fang, Knight Rob, Liu Jiquan, Davis Catherine, Xu Jian*. Predictive modeling of gingivitis severity and susceptibility via oral microbiota, ISME Journal 2014; 8(9): 1768-1780 doi:10.1038/ismej.2014.32

• Huang Shi, Yang Fang, Zeng Xiaowei, Chen Jie, Li Rui, Wen Ting, Li Chun, Wei Wei, Liu Jiquan, Chen Lan, Davis Catherine, Xu Jian. Preliminary characterization of the oral microbiota of Chinese adults with and without gingivitis, BMC Oral Health 2011; 11(1): article no. 33-article no. 33 doi:10.1186/1472-6831-11-33

• Teng Fei#, Yang Fang#, Huang Shi#, Bo Cunpei, Xu Zhenjiang Zech, Amir Amnon, Knight Rob, Ling Junqi, Xu Jian. Prediction of Early Childhood Caries via Spatial-Temporal Variations of Oral Microbiota, Cell Host and Microbe 2015; 18(3): 296-306 doi:10.1016/j.chom.2015.08.005

• Huang Shi, Li Zhen, He Tao, Bo Cunpei, Chang Jinlan, Li Lin, He Yanyan, Liu Jiquan, Charbonneau Duane, Li Rui, Xu Jian*. Microbiota-based Signature of Gingivitis Treatments: A Randomized Study, Scientific Reports 2016; 6: article no. 24705-article no. 24705 doi:10.1038/srep24705

• Ma Chenchen, Zhang Yufeng, Jiang Shuaiming, Teng Fei, Huang Shi, Zhang Jiachao. Cross-cohort single-nucleotide-variant profiling of gut microbiota suggests a novel gut-health assessment approach, mSystems 2023; 8(6) doi:10.1128/msystems.00828-23

• Jiang S, Chen D, Ma C, Liu H, Huang S, Zhang J. Establishing a novel inflammatory bowel disease prediction model based on gene markers identified from single nucleotide variants of the intestinal microbiota, iMeta 2022; e40-e40 doi:10.1002/imt2.40

• Qiyun Zhu#, Qiangchuan Hou#, Shi Huang#, Qianying Ou, Dongxue Huo, Yoshiki Vázquez-Baeza, Chaoping Cen, Victor Cantu, Mehrbod Estaki, Haibo Chang, Pedro Belda-Ferre, Ho-Cheol Kim, Kaining Chen, Rob Knight, Jiachao Zhang, Compositional and genetic alterations in Graves’ disease gut microbiome reveal specific diagnostic biomarkers, The ISME Journal, Volume 15, Issue 11, November 2021, Pages 3399–3411, https://doi.org/10.1038/s41396-021-01016-7

• Liu Wenjun#, Sun Zheng#, Ma Chen, Zhang Jiachao, Ma Chen Chen, Zhao Yinqi, Wei Hong, Huang Shi#, Zhang Heping#. Exposure to soil environments during earlier life stages is distinguishable in the gut microbiome of adult mice, Gut Microbes 2021; 13(1): article no. 1830699-article no. 1830699 doi:10.1080/19490976.2020.1830699

• Sun Zheng#, Huang Shi#, Zhu Pengfei, Yue Feng, Zhao Helen, Yang Ming, Niu Yueqing, Jing Gongchao, Su Xiaoquan, Li Huiying, Callewaert Chris, Knight Rob, Liu Jiquan, Smith Ed, Wei Karl, Xu Jian. A microbiome-based index for assessing skin health and treatment effects for atopic dermatitis in children, mSystems 2019; 4(4): article no. e00293-19-article no. e00293-19 doi:10.1128/mSystems.00293-19

• de la Cuesta-Zuluaga Jacobo, Kelley Scott T., Chen Yingfeng, Escobar Juan S., Mueller Noel T., Ley Ruth E., McDonald Daniel, Huang Shi, Swafford Austin D., Knight Rob, Thackray Varykina G.. Age- And sex-dependent patterns of gut microbial diversity in human adults, mSystems 2019; 4(4): article no. e00261-19-article no. e00261-19 doi:10.1128/mSystems.00261-19.

• Ji Wenyan#, Jiang Ting#, Sun Zheng#, Teng Fei, Ma Chenchen, Huang Shi, Yan Suhua. The Enhanced Pharmacological Effects of Modified Traditional Chinese Medicine in Attenuation of Atherosclerosis Is Driven by Modulation of Gut Microbiota, Frontiers in Pharmacology 2020; 11: article no. 546589-article no. 546589 doi:10.3389/fphar.2020.546589

• Li Shanshan#, Huang Shi#, Guo Yi, Zhang Ying, Zhang Lijuan, Li Fan, Tan Kaixuan, Lu Jie, Chen Zhenggang, Guo Qingyuan, Tang Yongping, Teng Fei, Yang Fang. Geographic Variation Did Not Affect the Predictive Power of Salivary Microbiota for Caries in Children With Mixed Dentition, Frontiers in Cellular and Infection Microbiology 2021; 11: article no. 680288-article no. 680288 doi:10.3389/fcimb.2021.680288

• Zhang Ying#, Huang Shi#, Jia Songbo, Sun Zheng, Li Shanshan, Li Fan, Zhang Lijuan, Lu Jie, Tan Kaixuan, Teng Fei, Yang Fang. The predictive power of saliva electrolytes exceeds that of saliva microbiomes in diagnosing early childhood caries, Journal of Oral Microbiology 2021; 13(1): article no. 1921486-article no. 1921486 doi:10.1080/20002297.2021.1921486

• Jiang T, Zhang M, Hao S, Huang S, Zheng X, Sun Z*. Revealing the role of the gut microbiota in enhancing targeted therapy efficacy for lung adenocarcinoma. Exp Hematol Oncol. 2024 Feb 9;13(1):15. doi: 10.1186/s40164-024-00478-7. PMID: 38336927; PMCID: PMC10854116.

• Yang Fang#, Teng Fei#*, Zhang Yufeng#, Sun Yanfei, Xu Jian, Huang Shi. Single-tooth resolved, whole-mouth prediction of early childhood caries via spatiotemporal variations of plaque microbiota, Cell Host and Microbe, 2025, doi: 10.1016/j.chom.2025.05.006.

Probiotics and Human Microbiome

• Jiang Shuaiming#, Huang Shi#, Zhang Zeng, Ma Wenyao, Han Zhe, Song Yuan, Huo Dongxue, Cui Weipeng, Zhang Jiachao. (2025). Gut microbiota drives structural variation of exogenous probiotics to enhance colonization. Gut Microbes, 17(1). doi:10.1080/19490976.2025.2503371

• Huang Shi, Jiang Shuaiming, Huo Dongxue, Allaband Celeste, Estaki Mehrbod, Cantu Victor, Belda-Ferre Pedro, Vázquez-Baeza Yoshiki, Zhu Qiyun, Ma Chenchen, Li Congfa, Zarrinpar Amir, Liu Yang Yu, Knight Rob, Zhang Jiachao. Candidate probiotic Lactiplantibacillus plantarum HNU082 rapidly and convergently evolves within human, mice, and zebrafish gut but differentially influences the resident microbiome, Microbiome 2021; 9(1): article no. 151-article no. 151 doi:10.1186/s40168-021-01102-0

• Zhang CC, Yu LL, Ma CC, Jiang SM, Zhang YF, Wang SH, Tian FW, Xue YZ, Zhao JX, Zhang H, Liu LM, Chen W, Huang S, Zhang JC, Zhai QX*. A key genetic factor governing arabinan utilization in the gut microbiome alleviates constipation, Cell Host & Microbe 2023; 31(12): 1989-2006 doi:10.1016/j.chom.2023.10.011

• Jiang Shuaiming#, Zhang Chengcheng#, Han Zhe, Ma Wenyao, Wang Shunhe, Huo Dongxue, Cui Weipeng, Zhai Qixiao, Huang Shi, Zhang Jiachao*. Native microbiome dominates over host factors in shaping the probiotic genetic evolution in the gut, npj Biofilms and Microbiomes 2023; 9(1) doi:10.1038/s41522-023-00447-8

• Ma Chenchen#, Wasti Sanjeev#, Huang Shi#, Zhang Zeng, Mishra Rajeev, Jiang Shuaiming, You Zhengkai, Wu Yixuan, Chang Haibo, Wang Yuanyuan, Huo Dongxue, Li Congfa, Sun Zhihong, Sun Zheng, Zhang Jiachao. The gut microbiome stability is altered by probiotic ingestion and improved by the continuous supplementation of galactooligosaccharide, Gut Microbes 2020; 12(1): article no. 1785252-article no. 1785252 doi:10.1080/19490976.2020.1785252

• Ma Chenchen#, Zhang Chengcheng#, Chen Denghui#, Jiang Shuaiming, Shen Siyuan, Huo Dongxue, Huang Shi, Zhai Qixiao, Zhang Jiachao*. Probiotic consumption influences universal adaptive mutations in indigenous human and mouse gut microbiota, Communications Biology 2021; 4(1): article no. 1198-article no. 1198 doi:10.1038/s42003-021-02724-8

Overview of single-cell Raman Facilities

Flow-mode Raman-activated Cell Sorter, FlowRACS

Function / Capability

• Acquisition of single-cell Raman spectra with high-quality
• Label-free, automated high-throughput single-cell sorting
• Allows metabolic phenome-based profiling and sorting of cells at high speed (up to 2000 events/min)
• Maximal preservation of cell vitality and viability
• Intelligent data analysis

Raman-activated Single-cell Sorting and Sequencing, RACS-Seq

Function / Capability

• The world’s first instrument system for Raman-activated cell sorting and sequencing
• Rapid profiling of metabolic phenome in a label-free and multi-dimensional manner
• Precisely and readily acquiring target cells with their in situ activity preserved
• Single-cell DNA/RNA extraction and amplification with low bias and high sequence coverage

Single-cell Microdroplet Sorting System, EasySort Compact

Function / Capability

• AI-assisted identification and automatic sorting while preserving the in situ state of cells
• Built-in bright-field and fluorescence modules enable maximal flexibility in identifying target cells
• Rapidly wrapping target single cells (diameter > 0.5 μm) into microdroplets
• Fully integrated design of the system with a user-friendly interface

Access Log for Raman Facilities

• On 2024/04/23, the Qingdao government delegation led by Wang Bo, Vice Mayor of Qingdao, visited Raman facilities.
• On 2024/08/16, Prof. Tsoi James Kit Hon’s HKU Faculty of Dentistry group utilized the RACS-Seq.
• On 2024/08/23, Prof. Liu Fang’s HKU Faculty of Medicine team utilized the FlowRACS.
• On 2024/09/04, Prof. Ye Zhou’s HKU Faculty of Dentistry group utilized the RACS-Seq.
• On 2024/11/04, a government delegation led by Liu Luying, Minister of the Organization Department of Qingdao West Coast New Area, visited Raman facilities.
• On 2024/11/23, Prof. Wang Kailiang’s group from HKBU utilized the FlowRACS.
• On 2024/12/13, Prof. Ye Zhou’s HKU Faculty of Dentistry group utilized the FlowRACS.
• From 2025/01/08 to 2025/01/21, Prof. Tsoi James Kit Hon’s HKU Faculty of Dentistry group utilized the FlowRACS.