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黃適

Professor Huang, Shi

PhD (University of Chinese Academy of Sciences)

Profile

Title
  • Assistant Professor in Microbiology
    微生物學助理教授
Division
Applied Oral Sciences & Community Dental Care
E-mail
shihuang@hku.hk
Phone
+852 2859 0572
Research Theme
Microbiome Innovation
Areas of Research Expertise
  • Metagenomics method development
  • Human microbiome association with chronic diseases
  • Adaptive co-evolution of probiotics and native gut microbiome
  • Machine learning applications in microbiome data
Research Profile
Publication & Awards
Publications

    Article

  • Jiang Shuaiming, Du Lingwei, Zhao Qian, Su Shunyong, Huang Shi, Zhang Jiachao. Tropical postbiotics alleviate the disorders in the gut microbiota and kidney damage induced by ochratoxin A exposure, Food and Function 2024; 15(8): 3980-3992 doi:10.1039/d3fo05213c
  • Myers Tyler, Bouslimani Amina, Huang Shi, Hansen Shalisa T, Clavaud Cécile, Azouaoui Anissa, Ott Alban, Gueniche Audrey, Bouez Charbel, Zheng Qian, Aguilar Luc, Knight Rob, Moreau Magali, Song Se Jin. A multi-study analysis enables identification of potential microbial features associated with skin aging signs, Frontiers in Aging 2024; 4 doi:10.3389/fragi.2023.1304705
  • Liu Yingqiao, Lin Haitao, Zhong Weijun, Zeng Yudi, Zhou Guihai, Chen Zhifeng, Huang Shi, Zhang Leitao, Liu Xiqiang. Multi-omics analysis of immune-related microbiome and prognostic model in head and neck squamous cell carcinoma, Clinical Oral Investigations 2024; 28(5) doi:10.1007/s00784-024-05645-y
  • Jiang Ting, Zhang Meng, Hao Shaoyu, Huang Shi, Zheng Xin, Sun Zheng. Revealing the role of the gut microbiota in enhancing targeted therapy efficacy for lung adenocarcinoma, Experimental Hematology and Oncology 2024; 13(1) doi:10.1186/s40164-024-00478-7
  • Ren Lihui, Liu Shuang, Huang Shi, Wang Qi, Lu Yuan, Song Jiaojian, Guo Jinjia. Identification of microplastics using a convolutional neural network based on micro-Raman spectroscopy, Talanta 2023; 260 doi:10.1016/j.talanta.2023.124611
  • 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
  • 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
  • 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
  • Zhang Josie Shizhen, Huang Shi, Chen Zigui, Chu Chun-Hung, Takahashi Nobuhiro, Yu Ollie Yiru. Application of omics technologies in cariology research: A critical review with bibliometric analysis, Journal of Dentistry 2023; 141 doi:10.1016/j.jdent.2023.104801
  • Huang Shi, He Chengyong, Li Jiufeng, Gao Yi Zhou, Wang Zuoyun, Wei Yongjun. Emerging paradigms in exploring the interactions among diet, probiotics, and cancer immunotherapeutic response, The Innovation 2023; 4(4) doi:10.1016/j.xinn.2023.100456
  • Sun Zheng, Liu Jiang, Zhang Meng, Wang Tong, Huang Shi, Weiss Scott T, Liu Yang Yu. Removal of false positives in metagenomics-based taxonomy profiling via targeting Type IIB restriction sites, Nature Communications 2023; 14(1) doi:10.1038/s41467-023-41099-8
  • Wu Shunyao, Li Zhiruo, Chen Yuzhu, Zhang Mingqian, Sun Yangyang, Xing Jieqi, Zhao Fengyang, Huang Shi, Knight Rob, Su Xiaoquan. Host-Variable-Embedding Augmented Microbiome-Based Simultaneous Detection of Multiple Diseases by Deep Learning, Advanced Intelligent Systems 2023; 5(12) doi:10.1002/aisy.202300342
  • Gao Guangqi, Shen Siyuan, Zhang Tao, Zhang Jiachao, Huang Shi, Sun Zhihong, Zhang Heping. Lacticaseibacillus rhamnosus Probio-M9 enhanced the antitumor response to anti-PD-1 therapy by modulating intestinal metabolites, EBioMedicine 2023; 91 doi:10.1016/j.ebiom.2023.104533
  • 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
  • Chen Y, Li J, Zhang Y, Zhang M, Sun Z, Jing G, Huang S, Su X. Parallel-Meta Suite: Interactive and rapid microbiome data analysis on multiple platforms, iMeta 2022; 1(1): article no. e1-article no. e1 doi:10.1002/imt2.1
  • Zhu Qiyun, Hou Qiangchuan, Huang Shi, Ou Qianying, Huo Dongxue, Vázquez-Baeza Yoshiki, Cen Chaoping, Cantu Victor, Estaki Mehrbod, Chang Haibo, Belda-Ferre Pedro, Kim Ho Cheol, Chen Kaining, Knight Rob, Zhang Jiachao. Correction to: Compositional and genetic alterations in Graves’ disease gut microbiome reveal specific diagnostic biomarkers, ISME Journal 2022; 16(4): 1201-1201 doi:10.1038/s41396-021-01040-7
  • 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
  • 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
  • Hu Yichen, Amir Amnon, Huang Xiaochang, Li Yan, Huang Shi, Wolfe Elaine, Weiss Sophie, Knight Rob, Xu Zhenjiang Zech. Diurnal and eating-associated microbial patterns revealed via high-frequency saliva sampling, Genome Research 2022; 32(6): 1112-1123 doi:10.1101/gr.276482.121
  • Kuthyar Sahana, Watson Karli, Huang Shi, Brent Lauren JN, Platt Michael, Horvath Julie, Gonzalez-Martinez Janis, Martínez Melween, Godoy-Vitorino Filipa, Knight Rob, Dominguez-Bello Maria Gloria, Amato Katherine R. Limited microbiome differences in captive and semi-wild primate populations consuming similar diets, FEMS Microbiology Ecology 2022; 98(10) doi:10.1093/femsec/fiac098
  • 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
  • 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, 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
  • 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 Lingjing, Haiminen Niina, Carrieri Anna Paola, Huang Shi, Vázquez-Baeza Yoshiki, Parida Laxmi, Kim Ho Cheol, Swafford Austin D., Knight Rob, Natarajan Loki. Utilizing stability criteria in choosing feature selection methods yields reproducible results in microbiome data, Biometrics 2021; doi:10.1111/biom.13481
  • Zhu Qiyun, Hou Qiangchuan, Huang Shi, Ou Qianying, Huo Dongxue, Vázquez-Baeza Yoshiki, Cen Chaoping, Cantu Victor, Estaki Mehrbod, Chang Haibo, Belda-Ferre Pedro, Kim Ho Cheol, Chen Kaining, Knight Rob, Zhang Jiachao. Compositional and genetic alterations in Graves’ disease gut microbiome reveal specific diagnostic biomarkers, ISME Journal 2021; 15(11): 3399-3411 doi:10.1038/s41396-021-01016-7
  • Marotz Clarisse, Belda-Ferre Pedro, Ali Farhana, Das Promi, Huang Shi, Cantrell Kalen, Jiang Lingjing, Martino Cameron, Diner Rachel E., Rahman Gibraan, McDonald Daniel, Armstrong George, Kodera Sho, Donato Sonya, Ecklu-Mensah Gertrude, Gottel Neil, Salas Garcia Mariana C., Chiang Leslie Y., Salido Rodolfo A., Shaffer Justin P., Bryant Mac Kenzie, Sanders Karenina, Humphrey Greg, Ackermann Gail, Haiminen Niina, Beck Kristen L., Kim Ho Cheol, Carrieri Anna Paola, Parida Laxmi, Vázquez-Baeza Yoshiki, Torriani Francesca J., Knight Rob, Gilbert Jack, Sweeney Daniel A., Allard Sarah M.. SARS-CoV-2 detection status associates with bacterial community composition in patients and the hospital environment, Microbiome 2021; 9(1): article no. 132-article no. 132 doi:10.1186/s40168-021-01083-0
  • 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
  • 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
  • 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
  • He Tao, Huang Shi, Yue Feng, Wang Lijiang, Liu Jiquan, Xu Jian. A randomized, controlled comparison of a stannous-containing dentifrice for reducing gingival bleeding and balancing the oral microbiome relative to a positive control, American journal of dentistry 2021; 34(4): 222-227
  • He Yuehui, Huang Shi, Zhang Peng, Ji Yuetong, Xu Jian. Intra-ramanome correlation analysis unveils metabolite conversion network from an isogenic population of cells, mBio 2021; 12(4): article no. e01470-21-article no. e01470-21 doi:10.1128/mBio.01470-21
  • Armstrong George, Cantrell Kalen, Huang Shi, McDonald Daniel, Haiminen Niina, Carrieri Anna Paola, Zhu Qiyun, Gonzalez Antonio, McGrath Imran, Beck Kristen L., Hakim Daniel, Havulinna Aki S., Méric Guillaume, Niiranen Teemu, Lahti Leo, Salomaa Veikko, Jain Mohit, Inouye Michael, Swafford Austin D., Kim Ho Cheol, Parida Laxmi, Vázquez-Baeza Yoshiki, Knight Rob. Efficient computation of Faith's phylogenetic diversity with applications in characterizing microbiomes, Genome research 2021; 31(11): 2131-2137 doi:10.1101/gr.275777.121
  • 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
  • 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
  • Su Xiaoquan, Jing Gongchao, Sun Zheng, Liu Lu, Xu Zhenjiang, McDonald Daniel, Wang Zengbin, Wang Honglei, Gonzalez Antonio, Zhang Yufeng, Huang Shi, Huttley Gavin, Knight Rob, Xu Jian. Multiple-disease detection and classification across cohorts via microbiome search, mSystems 2020; 5(2): article no. e00150-20-article no. e00150-20 doi:10.1128/mSystems.00150-20
  • Ma Chenchen, Guo Hongyang, Chang Haibo, Huang Shi, Jiang Shuaiming, Huo Dongxue, Zhang Jiachao, Zhu Xiaopeng. The effects of exopolysaccharides and exopolysaccharide-producing Lactobacillus on the intestinal microbiome of zebrafish (Danio rerio), BMC Microbiology 2020; 20(1): article no. 300-article no. 300 doi:10.1186/s12866-020-01990-6
  • 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
  • Xu Zhenjiang Zech, Amir Amnon, Sanders Jon, Zhu Qiyun, Morton James T., Bletz Molly C., Tripathi Anupriya, Huang Shi, McDonald Daniel, Jiang Lingjing, Knight Rob. Calour: an Interactive, Microbe-Centric Analysis Tool, mSystems 2019; 4(1): article no. e00269-18-article no. e00269-18 doi:10.1128/MSYSTEMS.00269-18
  • 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
  • Xiaoquan Su, Jing Gongchao, McDonald Daniel, Wang Honglei, Wang Zengbin, Gonzalez Antonio, Sun Zheng, Huang Shi, Navas Jose, Knight Rob, Xu Jian. Reply to Sun et al., “Identifying composition novelty in microbiome studies: Improvement of prediction accuracy”, mBio 2019; 10(4): article no. e01234-19-article no. e01234-19 doi:10.1128/mBio.01234-19
  • Zhu Qiyun, Mai Uyen, Pfeiffer Wayne, Janssen Stefan, Asnicar Francesco, Sanders Jon G., Belda-Ferre Pedro, Al-Ghalith Gabriel A., Kopylova Evguenia, McDonald Daniel, Kosciolek Tomasz, Yin John B., Huang Shi, Salam Nimaichand, Jiao Jian Yu, Wu Zijun, Xu Zhenjiang Z., Cantrell Kalen, Yang Yimeng, Sayyari Erfan, Rabiee Maryam, Morton James T., Podell Sheila, Knights Dan, Li Wen Jun, Huttenhower Curtis, Segata Nicola, Smarr Larry, Mirarab Siavash, Knight Rob. Phylogenomics of 10,575 genomes reveals evolutionary proximity between domains Bacteria and Archaea, Nature Communications 2019; 10(1): article no. 5477-article no. 5477 doi:10.1038/s41467-019-13443-4
  • 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
  • Teng Fei, Darveekaran Nair Sree Sankar, Zhu Pengfei, Li Shanshan, Huang Shi, Li Xiaolan, Xu Jian, Yang Fang. Impact of DNA extraction method and targeted 16S-rRNA hypervariable region on oral microbiota profiling, Scientific Reports 2018; 8(1): article no. 16321-article no. 16321 doi:10.1038/s41598-018-34294-x
  • Ma Chen, Sun Zheng, Zeng Benhua, Huang Shi, Zhao Jie, Zhang Yong, Su Xiaoquan, Xu Jian, Wei Hong, Zhang Heping. Cow-to-mouse fecal transplantations suggest intestinal microbiome as one cause of mastitis, Microbiome 2018; 6(1): article no. 200-article no. 200 doi:10.1186/s40168-018-0578-1
  • Su Xiaoquan, Jing Gongchao, McDonald Daniel, Wang Honglei, Wang Zengbin, Gonzalez Antonio, Sun Zheng, Huang Shi, Navas Jose, Knight Rob, Xu Jian. Identifying and predicting novelty in microbiome studies, mBio 2018; 9(6): article no. e02099-18-article no. e02099-18 doi:10.1128/mBio.02099-18
  • Xian Peng, Xuedong Zhou, Xin Xu, Yuqing Li, Yan Li, Jiyao Li, Xiaoquan Su, Shi Huang, Jian Xu, Ga Liao. The Oral Microbiome Bank of China, International Journal of Oral Science 2018; 10(2): article no. 16-article no. 16 doi:10.1038/s41368-018-0018-x
  • Sun Tong Zheng, Teng Fei, Jia Song Bo, Tang Yong Ping, Jiang Ming, Huang Shi, Yuan Xiao, Li Xiao Lan, Yang Fang. 与重症低龄儿童龋病相关的唾液微生物群落研究, 华西口腔医学杂志 2018; 36(2): 150-155 doi:10.7518/hxkq.2018.02.007
  • Su Lijuan, Yang Lele, Huang Shi, Li Yan, Su Xiaoquan, Wang Fengqin, Bo Cunpei, Wang En Tao, Song Andong. Variation in the Gut Microbiota of Termites (Tsaitermes ampliceps) Against Different Diets, Applied Biochemistry and Biotechnology 2017; 181(1): 32-47 doi:10.1007/s12010-016-2197-2
  • Jing Gongchao, Sun Zheng, Wang Honglei, Gong Yanhai, Huang Shi, Ning Kang, Xu Jian, Su Xiaoquan. Parallel-META 3: Comprehensive taxonomical and functional analysis platform for efficient comparison of microbial communities, Scientific Reports 2017; 7: article no. 40371-article no. 40371 doi:10.1038/srep40371
  • Tao Yifan, Wang Yun, Huang Shi, Zhu Pengfei, Huang Wei E., Ling Junqi, Xu Jian. Metabolic-Activity-Based Assessment of Antimicrobial Effects by D2O-Labeled Single-Cell Raman Microspectroscopy, Analytical Chemistry 2017; 89(7): 4108-4115 doi:10.1021/acs.analchem.6b05051
  • Zheng Xin, He Jinzhi, Wang Lin, Zhou Shuangshuang, Peng Xian, Huang Shi, Zheng Liwei, Cheng Lei, Hao Yuqing, Li Jiyao, Xu Jian, Xu Xin, Zhou Xuedong. Ecological Effect of Arginine on Oral Microbiota, Scientific Reports 2017; 7(1): article no. 7206-article no. 7206 doi:10.1038/s41598-017-07042-w
  • He Yuehui, Zhang Peng, Huang Shi, Wang Tingting, Ji Yuetong, Xu Jian. Label-free, simultaneous quantification of starch, protein and triacylglycerol in single microalgal cells, Biotechnology for Biofuels 2017; 10(1): article no. 275-article no. 275 doi:10.1186/s13068-017-0967-x
  • Gao Pengfei, Ma Chen, Sun Zheng, Wang Lifeng, Huang Shi, Su Xiaoquan, Xu Jian, Zhang Heping. Feed-additive probiotics accelerate yet antibiotics delay intestinal microbiota maturation in broiler chicken, Microbiome 2017; 5(1): article no. 91-article no. 91 doi:10.1186/s40168-017-0315-1
  • Xu Jian, Ma Bo, Su Xiaoquan, Huang Shi, Xu Xin, Zhou Xuedong, Huang Wei E., Knight Rob. Emerging Trends for Microbiome Analysis: From Single-Cell Functional Imaging to Microbiome Big Data, Engineering 2017; 3(1): 66-70 doi:10.1016/J.ENG.2017.01.020
  • Guo Zhuang, Zhang Jiachao, Wang Zhanli, Ang Kay Ying, Huang Shi, Hou Qiangchuan, Su Xiaoquan, Qiao Jianmin, Zheng Yi, Wang Lifeng, Koh Eileen, Danliang Ho, Xu Jian, Lee Yuan Kun, Zhang Heping. Intestinal Microbiota Distinguish Gout Patients from Healthy Humans, Scientific Reports 2016; 6: article no. 20602-article no. 20602 doi:10.1038/srep20602
  • 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
  • Teng Fei, He Tao, Huang Shi, Bo Cun Pei, Li Zhen, Chang Jin Lan, Liu Ji Quan, Charbonneau Duane, Xu Jian, Li Rui, Ling Jun Qi. Cetylpyridinium Chloride Mouth Rinses Alleviate Experimental Gingivitis by Inhibiting Dental Plaque Maturation, International Journal of Oral Science 2016; 8(3): 182-190 doi:10.1038/ijos.2016.18
  • Wang Ying, Su Lijuan, Huang Shi, Bo Cunpei, Yang Sen, Li Yan, Wang Fengqin, Xie Hui, Xu Jian, Song Andong. Diversity and resilience of the wood-feeding higher termite Mironasutitermes shangchengensis gut microbiota in response to temporal and diet variations, Ecology and Evolution 2016; 6(22): 8235-8242 doi:10.1002/ece3.2497
  • Su Li Juan, Yang Le Le, Huang Shi, Su Xiao Quan, Li Yan, Wang Feng Qin, Wang En Tao, Kang Ning, Xu Jian, Song An Dong. Comparative gut microbiomes of four species representing the higher and the lower termites, Journal of Insect Science 2016; 16(1): article no. 97-article no. 97 doi:10.1093/jisesa/iew081
  • Wang Qintao, Lu Yandu, Xin Yi, Wei Li, Huang Shi, Xu Jian. Genome editing of model oleaginous microalgae Nannochloropsis spp. by CRISPR/Cas9, Plant Journal 2016; 88(6): 1071-1081 doi:10.1111/tpj.13307
  • Zhang Dayi, Berry James P., Zhu Di, Wang Yun, Chen Yin, Jiang Bo, Huang Shi, Langford Harry, Li Guanghe, Davison Paul A., Xu Jian, Aries Eric, Huang Wei E.. Magnetic nanoparticle-mediated isolation of functional bacteria in a complex microbial community, ISME Journal 2015; 9(3): 603-614 doi:10.1038/ismej.2014.161
  • Sheng Rong, Qin Hongling, O’Donnell Anthony G., Huang Shi, Wu Jinshui, Wei Wenxue. Bacterial succession in paddy soils derived from different parent materials, Journal of Soils and Sediments 2015; 15(4): 982-992 doi:10.1007/s11368-014-1058-2
  • 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
  • Fan Jianhua, Ning Kang, Zeng Xiaowei, Luo Yuanchan, Wang Dongmei, Hu Jianqiang, Li Jing, Xu Hui, Huang Jianke, Wan Minxi, Wang Weiliang, Zhang Daojing, Shen Guomin, Run Conglin, Liao Junjie, Fang Lei, Huang Shi, Jing Xiaoyan, Su Xiaoquan, Wang Anhui, Bai Lili, Hu Zanmin, Xu Jian, Li Yuanguang. Genomic foundation of starch-to-lipid switch in oleaginous chlorella spp., Plant Physiology 2015; 169(4): 2444-2461 doi:10.1104/pp.15.01174
  • Su Xiaoquan, Wang Xiaojun, Jing Gongchao, Huang Shi, Xu Jian, Ning Kang. Application of Meta-Mesh on the analysis of microbial communities from human associated-habitats, Quantitative Biology 2015; 3(1): 4-18 doi:10.1007/s40484-015-0040-3
  • Xu Yuan, Teng Fei, Huang Shi, Lin Zhengmei, Yuan Xiao, Zeng Xiaowei, Yang Fang. Changes of saliva microbiota in nasopharyngeal carcinoma patients under chemoradiation therapy, Archives of Oral Biology 2014; 59(2): 176-186 doi:10.1016/j.archoralbio.2013.10.011
  • Wang Tingting, Ji Yuetong, Wang Yun, Jia Jing, Li Jing, Huang Shi, Han Danxiang, Hu Qiang, Huang Wei E., Xu Jian. Quantitative dynamics of triacylglycerol accumulation in microalgae populations at single-cell resolution revealed by Raman microspectroscopy, Biotechnology for Biofuels 2014; 7(1): article no. 58-article no. 58 doi:10.1186/1754-6834-7-58
  • Li Jing, Han Danxiang, Wang Dongmei, Ning Kang, Jia Jing, Wei Li, Jing Xiaoyan, Huang Shi, Chen Jie, Li Yantao, Hu Qiang, Xu Jian. Choreography of transcriptomes and lipidomes of Nannochloropsis reveals the mechanisms of oil synthesis in microalgae, Plant Cell 2014; 26(4): 1645-1665 doi:10.1105/tpc.113.121418
  • 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
  • Su Xiaoquan, Hu Jianqiang, Huang Shi, Ning Kang. Rapid comparison and correlation analysis among massive number of microbial community samples based on MDV data model, Scientific Reports 2014; 4: article no. 6393-article no. 6393 doi:10.1038/srep06393
  • Yang F., Huang S., he T., Catrenich C., Teng F., bo C., Chen J., Liu J., li J., Song Y., Li R., Xu J.. Microbial Basis of Oral Malodor Development in Humans, Journal of Dental Research 2013; 92(12): 1106-1112 doi:10.1177/0022034513507065
  • Wang Yun, Chen Yin, Zhou Qian, Huang Shi, Ning Kang, Xu Jian, Kalin Robert M., Rolfe Stephen, Huang Wei E.. A Culture-Independent Approach to Unravel Uncultured Bacteria and Functional Genes in a Complex Microbial Community, PLoS ONE 2012; 7(10): article no. e47530-article no. e47530 doi:10.1371/journal.pone.0047530
  • 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

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    Conference Paper

  • Huang Shi, Zhang Yufeng, Liu Jiang, Wang Xiuping, Zhou Lisa, Wang Shi. IDDF2023-ABS-0267 Strain-resolved taxonomic profiling and functional prediction of human microbiota using Strain2bFunc, International Digestive Disease Forum (10/06/2023-11/06/2023, Hong Kong) 2023; A120-A123 doi:10.1136/gutjnl-2023-IDDF.106
  • Li Xiaoxu, Huang Shi, Yu Jun, Wang Quanxi, Wu Shuangxiu. Improvement of hydrogen production of Chlamydomonas reinhardtii by co-cultivation with isolated bacteria, International Journal of Hydrogen Energy 2013; 38(25): 10779-10787 doi:10.1016/j.ijhydene.2013.02.102
Knowledge Exchange
  • 15 November 2023: Huang Shi. Seminar: In situ metabolic function targeted single-cell multi-omics of microbiomes via the Ramanomics Platform.
  • 10 July 2023: Huang Shi. Seminar: "The spatiotemporal dynamics of oral microbiome and its impact on oral and gastrointestinal diseases" delivered by Prof. Xu, Zech Zhenjiang from Nanchang Univ, China .
  • 22 February 2023: Huang Shi. Seminar: "Small molecules from the oral microbiome" delivered by Dr. Tang Xiaoyu from Shenzhen Bay Lab, China.
Grants
  • Project Title: Effectiveness of a Home Care Ultrasonic Cleaner Combined with Immersion in Peroxide-based Cleanser in the Mitigation of Respiratory Pathogens on Dentures of Institutionalised Elderly: A Randomised Controlled Clinical Trial
    Grant Type: General Research Fund (GRF) 2024/25
    Funding Year: 2024
    Amount: HK$974,145
    Principal Investigator: Professor Lim, Tong Wah
    Co-investigator(s): Professor Huang Shi, Professor Burrow Michael Francis, Professor Kwok Wang Chun, Mohd Dom Tuti Ningseh, Professor McGrath Colman
  • Project Title: Roles of oral microbiome bacteria in modulating pathogenicity of Helicobacter pylori in infected population
    Grant Type: Seed Fund for PI Research – Basic Research
    Funding Year: 2023
    Amount: HK$70,533
    Principal Investigator: Professor Huang, Shi
    Co-investigator(s): Professor Hung Fan Ngai Ivan
  • Project Title: ASM Microbe 2023
    Grant Type: Conference Support for Teaching Staff
    Funding Year: 2022
    Amount: HK$16,500
    Principal Investigator: Dr Huang, Shi
  • Project Title: Discovering Microbial Features for Oral Cancer Diagnosis and Prediction
    Grant Type: Seed Fund for Basic Research for New Staff
    Funding Year: 2021
    Amount: HK$150,000
    Principal Investigator: Professor Huang, Shi
    Co-investigator(s): Dr Koohi-Moghadam Hongzhe, Professor Su Yuxiong, Dr Liu Pei, Professor Khoo Ui Soon
HKU Committee Appointments
  • 12 January 2022-Present: Faculty of Dentistry, Board of the. The teachers who are members of the Faculty and who are full-time employees of the University

Note

  • All publication and awards data are automatically fetched periodically from the HKU Scholars Hub.