Recent advances in molecular biological techniques are broadening our understanding of bacterial diversity and the societal community interactions which occur between species within oral cavity. They led to tremendous advances in our understanding of oral microbiome and its involvement in health and disease, not only with oral infectious diseases, such as tooth decay and gum diseases, but also with systemic diseases.

Studies using culture-independent approaches have revealed sheer magnitude of the diverse microbes residing within oral cavity. The human mouth is estimated to harbor more than 700 different bacterial species, comprising one of the most complex microbial flora. The diversity of microorganisms that inhabit the oral cavity includes bacteria, archaea, spirochetes, protozoa, mycoplasma, yeasts, and fungi. The diversity of the microbial flora reflects a tremendous diversity of genetic information and immense bio-physiological potential. If we consider that an average bacterial species has 2,000 – 6,000 genes, then an oral bacterial population of some 700 individual species represents a pool of over 1 million genes, 10 times more than human host genes. This provides the oral microbial environment with a huge quantity of information related to unique metabolic pathways, the generation and secretion of various factors that can control and modify their ecological niche, and factors that may impact function of the human host.
 

Current Research Projects

The primary research interests of Drs. Wenyuan Shi and Xuesong He from UCLA School of Dentistry are focused on understanding the role of oral microbiota in host health and disease beyond the simple association and investigating actual cause-and-effect relationship. Meanwhile, they also actively study oral microbial ecology at individual species, inter-species as well as multispecies level. Their ultimate goal is to achieve a better understanding of the ecology of oral microbiome and the detailed characterization of oral bacterial species will become a gateway leading to more specific and practive preventative and therapeutic approaches in combating dental, periodontal, as well as oral microbiome-related systemic diseases.

Current oral microbiome projects in Dr. Huiying Li‘s group focus on understanding the role of the oral microbiota in periodontal health and disease. By comparing the metagenomes of the subgingival microbiome in healthy individuals and periodontitis patients, the Li lab aims to define the microbial community and metagenomic signatures that distinguish the subgingival microbiome of periodontal health and disease. Furthermore, type 2 diabetes is associated with an increase in the prevalence and progression of periodontitis. By comparing the periodontal microbiome between type 2 diabetics and non-diabetic subjects, the Li lab is investigating the impact of host factors, including immune response, on the oral microbiota in periodontal health and disease. The study addresses a fundamental gap in our knowledge of the periodontal microbiome in population at high risk for diabetes and periodontitis and may lead to further studies for the development of innovative clinical approaches to diagnose, prevent, and manage the disease in diabetics.

Representative Publications:

  • Guo, L., JS. McLean, Y.Yang, R. Eckert, C.W. Kaplan, P.Kyme, O. Sheikh, B. Varnum, R. Lux, W. Shi and X. He*. 2015 A precision guided antimicrobial peptide as a targeted modulator of human microbial ecology. Proc Natl Acad Sci USA 112(24): 7569-7574
  • He, X., JS. McLean, A. Edlund, S. Yooseph, A.P. Hall, SY. Liu, P. Dorrestein, E. Esquenazi, R. Hunter, G. Cheng, KE. Nelson, R. Lux and W. Shi. 2015. Domestication of a human-associated TM7 reveals a reduced genome and parasitic lifestyle. Proc Natl Acad Sci USA 112(1):244-9. PMCID:PMC4291631
  • Wu, T., L. Cen, C. Kaplan, X. Zhou, R. Lux, W. Shi and X. He*. 2015. Cellular components mediating co-aggregation of Candida albican and Fusobacterium nucleatum. Journal of Dental Research. DOI:10.1177/0022034515593706

 

Key Faculty

Photo of Xuesong He, DDS., PhD
Xuesong He, DDS., PhD
Assistant Adjunct Professor, UCLA School of Dentistry
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Address UCLA School of Dentistry 10833 Le Conte Avenue 20-118 CHS Los Angeles CA 90095-1668 Phone: (310) 825-9748

Dr. Xuesong He is an Adjunct Assistant Professor in School of Dentistry at UCLA. Dr. He received his D.D.S. from Peking University Health Science Center in 1999, and his PhD in Microbiology from Indiana University in USA in 2006. Dr. He’s research interest includes: 1) Interspecies interaction between oral microbes; 2) culturing and studying “yet-to-be” cultivated oral microbes; and 3) studying the oral microbial ecology and its impact on human oral health and diseases. He is currently the co-principle investigator of a NIH RO1 grant on studying the unique epibiotic parasitic relationship between two oral commensal bacteria that could be involved in oral mucosal infectious disease. The international impact of his research can be proved by his over 30 well-cited publications in peer-reviewed leading scientific journals including: PNAS, ISME Journal, Advance in Dental Research, Microbiology and Molecular Biology Reviews, Journal of dental research, Journal of Endodontics, Molecular Microbiology, Microbiome Journal, Scientific Reports, Frontiers in Microbiology, Molecular Oral Microbiology, Microbial Ecology, Plos One, International Journal of Oral Science, FEMS Microbiology Letter and Journal of Bacteriology, etc.

Relevant Recent Publications

  1. Guo, L., JS. McLean, Y.Yang, R. Eckert, C.W. Kaplan, P.Kyme, O. Sheikh, B. Varnum, R. Lux, W. Shi and X. He*. 2015 A precision guided antimicrobial peptide as a targeted modulator of human microbial ecology. Proc Natl Acad Sci USA 112(24): 7569-7574
  2. He, X., JS. McLean, A. Edlund, S. Yooseph, A.P. Hall, SY. Liu, P. Dorrestein, E. Esquenazi, R. Hunter, G. Cheng, KE. Nelson, R. Lux and W. Shi. 2015. Domestication of a human-associated TM7 reveals a reduced genome and parasitic lifestyle. Proc Natl Acad Sci USA 112(1):244-9. PMCID:PMC4291631
  3. Wu, T., L. Cen, C. Kaplan, X. Zhou, R. Lux, W. Shi and X. He*. 2015. Cellular components mediating co-aggregation of Candida albican and Fusobacterium nucleatum. Journal of Dental Research. DOI:10.1177/0022034515593706

Active Funding in Microbiome-Related Research

Funding Agency/Grant Number:NIH NIDCR 1R01DE023810
Title:“Domestication and characterization of TM7-the most elusive oral phylum”

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Photo of Huiying Li, PhD
Huiying Li, PhD
Assistant Professor, Department of Molecular & Medical Pharmacology; Faculty, Crump Institute for Molecular Imaging, UCLA
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Address 4339 CNSI 570 Westwood Plaza, Building 114 Los Angeles CA 90095-1770 Phone: (310) 206-5585Lab Phone: (310) 983-3212Website: Li Lab

My interest in the microbiome research began from The Sorcerer II Global Ocean Sampling Expedition led by the J Craig Venter Institute several years ago, where I applied bioinformatics to study microbial protein families in the ocean microbiome. The current research in my lab focuses on understanding the human microbiome, the collective genome of trillions of microorganisms residing in the human body, and its interactions with the host in relation to human health and diseases. Using multi-disciplinary approaches, including genomics, metagenomics, bioinformatics, high-throughput sequencing, microbiology, and biochemistry, we aim to identify the molecular mechanism of the human microbiome in health and disease pathogenesis and to develop diagnostic markers and therapeutics for microorganism-related human diseases. By combining computational and experimental approaches, the ultimate goal of my research is to understand the human-microbiota symbiotic system at both molecular level and systems level.

My research group is highly experienced in high-throughput sequencing and data analysis with expertise in bioinformatics, 16S rDNA sequence analysis, metagenomic shotgun sequence analysis, RNA-Seq data analysis, and genome assembly, annotation and comparison. I was funded by the Human Microbiome Project (HMP) among the 15 Demonstration Projects to study the role of the human skin microbiome in acne. I am currently funded by the NIGMS and NIDCR to study the human skin microbiome and oral microbiome and their associations with diseases.

Relevant Recent Publications

  1. Kang D, Shi B, Erfe MC, Craft N, Li H. Vitamin B12 modulates the transcriptome of the skin microbiota in acne pathogenesis. Science Translational Medicine. 2015; 293(7): 293ra103.
  2. Liu J, Yan R, Zhong Q, Ngo S, Bangayan NJ, Nguyen L, Lui T, Liu M, Erfe MC, Craft N, Tomida S, Li H. The Diversity and Host Interactions of Propionibacterium acnes Bacteriophages on Human Skin. The ISME Journal. 2015; 9: 2078-2093.
  3. Shi B, Chang M, Martin J, Mitreva M, Lux R, Klokkevold P, Sodergren E, Weinstock GM, Haake SK, Li H. Dynamic Changes in the Subgingival Microbiome and Their Potential for Diagnosis and Prognosis of Periodontitis. mBio. 2015; 6(1): e01926-14.
  4. Liu J, Cheng A, Bangayan NJ, Barnard E, Curd E, Craft N, Li H. Draft Genome Sequences of Propionibacterium acnes Type Strain ATCC6919 and Antibiotic-Resistant Strain HL411PA1. Genome Announcements. 2014; 2(4): e00740-14.
  5. Kasimatis G, Fitz-Gibbon S, Tomida S, Wong M, Li H. Analysis of Complete Genomes of Propionibacterium acnes Reveals a Novel Plasmid and Increased Pseudogenes in an Acne Associated Strain. BioMed Research International. 2013; 2013: 918320.
  6. Tomida S, Nguyen L, Chiu BH, Liu J, Sodergren E, Weinstock GM, Li H. Pan-Genome and Comparative Genome Analyses of Propionibacterium acnes Reveal Its Genomic Diversity in the Healthy and Diseased Human Skin Microbiome. mBio. 2013; 4(3): e00003-13.
  7. Fitz-Gibbon S, Tomida S, Chiu BH, Nguyen L, Du C, Liu M, Elashoff D, Erfe MC, Loncaric A, Kim J, Modlin RL, Miller JF, Sodergren E, Craft N, Weinstock GM, Li H. Propionibacterium acnes Strain Populations in the Human Skin Microbiome Associated with Acne. Journal of Investigative Dermatology. 2013; 133: 2152-2160.

Active Funding in Microbiome-Related Research

Funding Agency/Grant Number:NIH R01 GM099530
Title:“Population Dynamics of P. acnes and Their Phages in the Human Skin Microbiome”
Funding Agency/Grant Number:NIH R01 DE021574
Title:“Metagenomic Study of the Periodontal Microbiome in Healthy and Diabetic Subjects”

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Photo of Wenyuan Shi, PhD
Wenyuan Shi, PhD
Professor and Chairman, Oral Biology, UCLA School of Dentistry Professor, Microbiology and Molecular Genetics, UCLA School of Medicine Founding scientist and chief science officer, C3 Jian Inc.
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Home 10833 Le Conte Avenue Los Angeles CA 90095-1668 Phone: (310) 825-8356Fax: (310) 794-7109

Dr. Wenyuan Shi is a chairman and professor of Oral Biology at UCLA Schools of Dentistry. Dr. Shi’s laboratory has been using multidisciplinary approaches to study oral microbial pathogenesis with a specific focus on microbial biofilm, inter-species interaction and signal transduction. In addition, Dr. Shi’s laboratory is actively involved in the development of next generation of diagnostic and therapeutic tools against oral microbial infections, including instant chairside detection of oral pathogens and peptide based targeted antimicrobial therapeutics. These translational research efforts have resulted in novel technologies that are licensed and developed by major pharmaceutical, dental and biotech companies. Dr. Shi is also the founding scientist, chief science officer, and chairman of the scientific advisory board of C3 Jian Inc. (www.c3-jian.com).

Dr. Shi obtained his BS degree from Fudan University (Shanghai) in 1984, acquired his Ph.D degree from University of Wisconsin-Madison in 1991 and fulfilled his postdoctoral training at University of California-Berkeley during 1992-1995. He is co-author and co-inventor of over 200 scientific articles and patents.

Relevant Recent Publications

  1. He, X., T. Yan, L. Guo, R. Lux, D. R. Zusman and W. Shi. 2010. In vitro communities derived from oral and gut microbial floras inhibit the growth of bacteria of foreign origins. Microbial Ecology. 60(3):665-76 PMCID: PMC2954289
  2. He, X., T. Yan, L. Guo, R. Lux, D. R. Zusman and W. Shi. 2010. Oral-derived bacterial flora defends its domain by recognizing and killing intruders—a molecular analysis using Escherichia coli as a model intestinal bacterium. Microbial Ecology. 60(3):655-64 PMCID: PMC2954290
  3. He, X., W. Hu, J. He, H. Guo, R. Lux and W. Shi. 2011 Community-based interference against of human integration of Pseudomonas aeruginosa into human salivary microbial biofilm. Molecular Oral Microbiology. 26: 1-16. PMCID:PMC3327514
  4. He, X., J. McLean, L. Guo, R. Lux and W. Shi 2013. The social structure of microbial community involved in colonization resistance. The ISME Journal 8(3):564-74. PMCID:PMC3930314

Active Funding in Microbiome-Related Research

Funding Agency/Grant Number:NIH NIDCR 1R01DE023810
Title:“Domestication and characterization of TM7-the most elusive oral phylum”
Funding Agency/Grant Number:NIH NIDCR 1-R01-DE020102
Title:“Making a quantum leap in plaque research with modern sciences”
Funding Agency/Grant Number:NIH NIDCR 1-R01-DE021108
Title:“Molecular analysis of F. nucleatum interspecies interactions in biofilms”
Funding Agency/Grant Number:NIH NIGMS 1 R01 GM095373
Title:“Moving beyond diversity by revealing biological functions of uncultured bacteria”

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