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

Huiying Li, PhD

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

Biographical Info

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”
Categories: Faculty, Member, Oral Biology, Skin Diseases

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