The skin is the largest organ in the human body and provides the first line of defense against environmental attack and pathogen invasion. The skin is also a host for hundreds of microorganisms, including bacteria, fungi, eukaryotic mites, and viruses. Immediately after birth, diverse microbial communities at different skin sites with unique physiological and immunological niches colonize the skin. They play important roles in sensing the environment, protecting against colonization and infection of pathogens, and guiding the host immune system in response to foreign invasions. The resident microorganisms sequester nutrients from skin secretions and form a dynamic ecological system with the host skin through complex interactions within the microbial communities and with the host. The composition, dynamics, and function of the skin microbiota have significant impact on skin health and function.

Current Research Projects

Li Lab

The skin microbiome projects in Dr. Huiying Li‘s group focus on understanding the molecular function of the skin microbiota in health and disease. By studying the genomes and the transcriptomes of the microbes living on the human skin, the Li lab investigates how skin microorganisms interact among themselves and with the host and play a role in skin diseases. The microbiome in two most common skin diseases, acne vulgaris and atopic dermatitis, is currently being investigated, particularly at the bacterial strain level and at the functional level. These studies will provide molecular insights on the role of the commensal skin microbiota in health and disease, and will improve our understanding of disease mechanisms involved with the microbiota and potential future manipulations of the microbiota in disease therapeutics and skin health maintenance.


Key People

Photo of Laurent Bentolila, PhD
Laurent Bentolila, PhD
Scientific Director, Advanced Light Microscopy/Spectroscopy Lab; Scientific Director, Macro-Scale Imaging Lab; Researcher, California NanoSystems Institute, UCLA

Dr. Bentolila is a senior researcher at the California NanoSystems Institute (CNSI) at the University of California, Los Angeles (UCLA). He is also the Scientific Director of the Advanced Light Microscopy/Spectroscopy Laboratory (ALMS) and the Macro-Scale Imaging Laboratory (MSI) at CNSI. Dr. Bentolila earned his B.S. in Biochemistry and M.S. in Genetics from Paris-XI University, Orsay and Ph.D. in Molecular Genetics and Immunology from the Pasteur Institute, Paris, France. He was a European Molecular Biology Organization Postdoctoral fellow at the University of California, Berkeley before joining the Department of Chemistry and Biochemistry at UCLA in 2002.

Dr. Bentolila’s long-standing research interest focuses on the application of novel fluorescent probes and advanced microscopy techniques to biology and medicine. Towards this goal, Dr. Bentolila has developed and assembled a unique collection of custom-made and commercial light microscopes for the application of novel spectroscopic methods and advanced microscopy techniques used for the study of macromolecules, cellular dynamics and nano-scale characterization of biomaterials. His most recent research projects include developing new experimental tools for visualizing and tracking cells, bacteria and parasites within a host.

Dr. Bentolila is the recipient of several awards from the Burroughs Wellcome Fund, the European Molecular Biology Organization and the Roux Foundation.

Relevant Recent Publications

  1. Bentolila LA, Prakash R, Mihic-Probst D, Wadehra M, Kleinman HK, Carmichael TS, Péault B, Barnhill RL and Lugassy C. Imaging of Angiotropism/Vascular Co-Option in a Murine Model of Brain Melanoma. Implications for Melanoma Progression along Extravascular Pathways. 2016. Scientific Reports. In press.
  2. Chen AL, Kim EW, Toh JY, Vashisht AA, Rashoff AQ, Van C, Huang AS, Moon AS, Bell HN, Bentolila LA, Wohlschlegel JA and Bradley PJ. Novel components of the Toxoplasma inner membrane complex revealed by BioID. 2015. mBio 6(1) e02357-14.
  3. Kisalu NK, Langousis GD, Bentolila LA, Ralston KS, Hill KL. Mouse infection and pathogenesis by Trypanosoma brucei motility mutants. Cellular Microbiology. 2014. 16(6):912-924.
  4. Mitchell-Jordan S, Chen H, Franklin S, Stefani E, Bentolila LA and Vondriska TM. Features of endogenous cardiomyocyte chromatin revealed by super resolution STED microscopy. J Mol Cell Cardiol. 2012. 53(4):552-8.
Photo of Dino Di Carlo, PhD
Dino Di Carlo, PhD
Professor, Department of Bioengineering; Member, California NanoSystems Institute, Jonsson Comprehensive Cancer Center

Dino Di Carlo is a Professor in the Department of Bioengineering at UCLA. Over the last 8 years he pioneered using inertial fluid dynamic effects for the control, separation, and analysis of cells in microfluidic devices. His work now extends into numerous fields of biomedicine and biotechnology including directed cellular evolution of microbes, cell and microbial analysis for rapid diagnostics, new amplified molecular assays, next generation biomaterials, and phenotypic drug screening. He also serves as Director of the Cancer Nanotechnology Program of the Jonsson Comprehensive Cancer Center at UCLA and holds a visiting Professorship at the University of Tokyo. He co-founded and currently advises four companies that are commercializing intellectual property developed in his lab over the last six years (CytoVale, Vortex Biosciences, Tempo Therapeutics, and Ferrologix). He has received numerous honors and awards including the Pioneers of Miniaturization Prize in 2015, Analytical Chemistry Young Innovator Award in 2014, the National Science Foundation (NSF) CAREER award, the U.S. Office of Naval Research (ONR) Young Investigator Award, the Packard Fellowship, the Defense Advanced Research Projects Agency (DARPA) Young Faculty Award, the National Institutes of Health (NIH) Director’s New Innovator Award and the Coulter Translational Research Award.

Weaver WM, Milisavljevic V, Miller JF, Di Carlo D., “Fluid flow induces biofilm formation in Staphylococcus epidermidis polysaccharide intracellular adhesin-positive clinical isolates,” Appl Environ Microbiol. 2012 Aug;78(16):5890-6. doi: 10.1128/AEM.01139-12. Epub 2012 Jun 15.

Weaver WM, Dharmaraja S, Milisavljevic V, Di Carlo D., “The effects of shear stress on isolated receptor-ligand interactions of Staphylococcus epidermidis and human plasma fibrinogen using molecularly patterned microfluidics,” Lab Chip. 2011 Mar 7;11(5):883-9. doi: 10.1039/c0lc00414f. Epub 2011 Jan 20.

Photo of Omai Garner, PhD
Omai Garner, PhD
Assistant Professor, Pathology & Laboratory Medicine, UCLA

Dr. Omai Garner is a Health Sciences Assistant Clinical Professor and Associate Director of Clinical Microbiology in the UCLA Health System. He received his PhD from UC San Diego in Biomedical Sciences. He was a Postdoctoral Clinical Microbiology CPEP Fellow in the Department of Pathology at UCLA, and a former McNair Scholar. Dr. Garner is Board Certified by the American Board of Medical Microbiology. Dr. Garner’s research focuses on novel Point of Care Devices for infectious disease diagnosis in the developing world. Dr. Garner was always taught that science, at its best, is a collaborative process. “It is collaboration, and not competition, which produces the most significant advances in biomedical research.” He also serves as the Chairman of the Board for the Social Justice Learning Institute of Inglewood, California.

Relevant Recent Publications

  1. Cellphone-Based Hand-Held Microplate Reader for Point-of-Care Testing of Enzyme-Linked Immunosorbent Assays.
    Berg B, Cortazar B, Tseng D, Ozkan H, Feng S, Wei Q, Chan RY, Burbano J, Farooqui Q, Lewinski M, Di Carlo D, Garner OB, Ozcan A.
    ACS Nano. 2015 Aug 25;9(8):7857-66
  2. Comparison of the Vitek MS and Bruker Microflex LT MALDI-TOF MS platforms for routine identification of commonly isolated bacteria and yeast in the clinical microbiology laboratory.
    Deak E, Charlton CL, Bobenchik AM, Miller SA, Pollett S, McHardy IH, Wu MT, Garner OB.
    Diagn Microbiol Infect Dis. 2015 Jan;81(1):27-33.
  3. Detection of human viral pathogens: conventional versus molecular approaches.
    Wu MT, Garner OB.
    MLO Med Lab Obs. 2014 Jul;46(7):8, 10-2; quiz 14
Photo of Huiying Li, PhD
Huiying Li, PhD
Assistant Professor, Department of Molecular & Medical Pharmacology; Faculty, Crump Institute for Molecular Imaging, UCLA

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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