UCLA faculty members who have microbiome related funding (extra-or intramural)



Photo of Grace Aldrovandi, MD
Grace Aldrovandi, MD
Professor and Chief, Pediatrics – Infectious Diseases, UCLA


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 Bridget Callaghan, PhD
Bridget Callaghan, PhD
Assistant Professor, Department of Psychology, UCLA; Director, Brain and Body Lab, UCLA

Dr. Bridget Callaghan is an Assistant Professor in the Department of Psychology at UCLA where she directs the Brain and Body Lab. Her laboratory studies the impact of early adversity on the development of the brain, body, and behavior in humans, specifically focusing on limbic system function, learning and memory, the gastrointestinal microbiome, and how each of these systems interact. Her studies have shown that early adverse caregiving experiences are associated with changes at the level of the gastrointestinal microbiome and brain, and are related to mental health outcomes (e.g., anxiety). Building from these data, Dr. Callaghan is developing a health care app which uses gastrointestinal and somatic symptoms to predict anxiety risk in children, which she hopes to eventually deploy in primary healthcare settings. Funded through the National Institutes of Mental Health, Dr. Callaghan is currently running a 3-year longitudinal study examining mechanisms of change in the microbiome following caregiving adversity, and how such change is related to functional brain development. Through her work, Dr. Callaghan has received numerous honors, including the Association for Psychological Science’s Rising Star Award, a Young Investigator Award from the International Society for Developmental Psychobiology, fellowships from the American Australian Association, Sackler Institute for Developmental Psychobiology, Brain Behavior Research Foundation, and National Health and Medical Research Council of Australia, and is an elected board member of the International Society for Developmental Psychobiology.


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 Jennifer Fulcher, MD, PhD
Jennifer Fulcher, MD, PhD
Assistant Professor in Residence, Department of Medicine, Infectious Disease, UCLA


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 Nandita Garud, PhD
Nandita Garud, PhD
Assistant Professor, Department of Ecology and Evolutionary Biology, UCLA

Dr. Nandita Garud is an assistant professor in the department of Ecology and Evolutionary Biology at UCLA where she leads a computational group studying how bacteria in the human microbiome evolve. In recent work, Garud and her collaborators have quantified the evolutionary dynamics of roughly 40 prevalent species of gut bacteria. They have found that gut bacteria can evolve in healthy humans on six-month time scales, but that over our lifetimes, the bacteria inside us are completely replaced. These results suggest that gut bacteria can evolve on time scales relevant to our health, but that they do not become so personalized that they cannot be replaced. Inspired by this work, the Garud lab continues to probe the mode and tempo of evolution in the gut microbiome using a population genetics framework.

Relevant Recent Publications

  • Garud NR*, Good BH*, Hallatschek O, and Pollard KS. “Evolutionary dynamics of bacteria in the gut microbiome within and across hosts.” PLoS Biology (2019). *equal contributors.
  • Garud NR, Messer P, Buzbas E, and Petrov D. “Soft selective sweeps are the primary mode of adaptation in Drosophila.” PLoS Genetics 11: e1005004 (2015).
  • Garud NR and Petrov DA. “Elevated linkage disequilibrium and signatures of soft sweeps are common in Drosophila melanogaster.” Genetics (2016).
Photo of Arpana Gupta, PhD
Arpana Gupta, PhD
Adjunct Assistant Professor, Division of Digestive Diseases, David Geffen School of Medicine at UCLA; Oppenheimer Center for Neurobiology of Stress

Dr. Arpana (Annie) Gupta completed a PhD degree in Psychology from the University of Tennessee, Knoxville, followed by an APA accredited clinical internship at Massachusetts General Hospital/Harvard Medical Center. After coming to UCLA she joined the neuroimaging and psychophysiological cores at the Center for Neurobiology of Stress in 2012. She is currently Adjunct Assistant Professor, where she specializes in research that investigates the influence of environmental factors on shaping neurobiological phenotypes associated with stress and pain-based diseases such as obesity and functional gastroenterological disorders (FGIDs) [vuvlodynia, irritable bowel syndrome]. Her programmatic line of research broadly defined focuses on the bidirectional interactions between the brain and peripheral factors (in particular immune factors and gut microbiota-related metabolites) and how these interactions are modified by vulnerability (early adversity, race, adult stress, socioeconomic status [SES], diet) and protective (resilience, exercise) factors in contributing to the underlying pathophysiology of these disorders. She is dedicated to using advanced automated and mathematical analytic techniques, which allows her to integrate information from multiple data sources, while accounting for sex and race differences. Her goal is to develop a comprehensive model that provides a powerful and sensitive biomarker that will increase biological readouts of these stress and pain-based disorders, thus bringing to the forefront those individuals who are at increased risk as a result of disadvantaged backgrounds.

Relevant Recent Publications

  1. Gupta A, Mayer EA, Sanmiguel CP, Van Horn JD, Woodworth D, Ellingson BM, Fling C, Love A, Tillisch K, Labus JS. Patterns of Brain Structural Connectivity Differentiate Lean from Overweight Subjects. Neuroimage-Clinical, 2015. 13(7): 506-17. doi:10.1016/j.nicl.2015.01.005 [Epub Ahead of Print]. PMCID: PMC4338207.
  2. Mayer EA, Tillisch K, Gupta A. Gut-Brain Axis and the Microbiota. Journal of Clinical Investigation. 2015; 125(3): 926-38. doi: 10.1172/JCI76304. [Epub ahead of Print]. PMID: 25689247.
  3. Sanmiguel CP, Gupta A, Mayer EA. Gut Microbiome and Obesity: A Plausible Explanation for Obesity. Current Obesity Reports. 2015. In press.

Active Funding in Microbiome-Related Research

Funding Agency/Grant Number:American Psychological Fellowship – Visionary Grant
Title:“Mind Altering Microorganisms: Sex and Race Differences in the Influence of Gut Microbiota on Brain Signatures in Obese Healthy Control Subjects”
Goals:The goal of the proposed study is to assess sex (males versus females) and race (African Americans versus non-Hispanic White Americans) differences in the influence of gut-microbiota on brain signatures in obese subjects


Photo of Eran Halperin, PhD
Eran Halperin, PhD
Professor, Departments of Computer Science, Computational Medicine, Anesthesiology, Human Genetics, UCLA; Associate Director of Informatics, Institute of Precision Health, UCLA; Co-Director, Computation Genomics Summer Institute, UCLA

Dr. Eran Halperin is a professor in the departments of Computer Science, Computational Medicine, Anesthesiology, and Human Genetics. He is also the associate director of informatics in the Institute of Precision Health at UCLA and the co-director of the Computation Genomics Summer Institute at UCLA. Dr. Halperin received his Ph.D. in computer science from Tel-Aviv University. Prior to his current position, he held research and postdoctoral positions at the University of California, Berkeley, the International Computer Science Institute in Berkeley, Princeton University, and Tel-Aviv University. Dr. Halperin is a computational biologist who develops statistical and computational methods for the analysis of genomic and medical data in the context of human diseases. His group has developed methods and software that have been used by hundreds of researchers worldwide in a range of genomic applications including genetics, epigenetics, and microbiome. He has published over 100 peer-reviewed articles across different disciplines such as human genetics, computational biology, and theoretical computer science. He received various honors for academic achievements, including the Rothschild Fellowship, the Technion-Juludan prize, and the Krill prize.

Relevant Recent Publications

  1. Sankararaman, S., Sridhar, S., Kimmel, G., & Halperin, E. (2008). Estimating local ancestry in admixed populations. The American Journal of Human Genetics, 82(2), 290-303.
  2. Sankararaman, S., Obozinski, G., Jordan, M. I., & Halperin, E. (2009). Genomic privacy and limits of individual detection in a pool. Nature genetics, 41(9), 965
  3. Yang, W. Y., Novembre, J., Eskin, E., & Halperin, E. (2012). A model-based approach for analysis of spatial structure in genetic data. Nature genetics, 44(6), 725.
  4. Rahmani, Elior, et al. “Sparse PCA corrects for cell type heterogeneity in epigenome-wide association studies.” Nature methods 13.5 (2016): 443
  5. Shenhav, L., Furman, O., Briscoe, L., Thompson, M., Silverman, J. D., Mizrahi, I., & Halperin, E. (2019). Modeling the temporal dynamics of the gut microbial community in adults and infants. PLOS Computational Biology, 15(6), e1006960
  6. Shenhav, L., Thompson, M., Joseph, T. A., Briscoe, L., Furman, O., Bogumil, D., … & Halperin, E. (2019). FEAST: fast expectation-maximization for microbial source tracking. Nature methods, 1
  7. Baran, Yael, and Eran Halperin. “Joint analysis of multiple metagenomic samples.” PLoS computational biology 8.2 (2012): e1002373.
Photo of Xuesong He, DDS., PhD
Xuesong He, DDS., PhD
Assistant Adjunct Professor, UCLA School of Dentistry

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”
Photo of Elaine Y. Hsiao, PhD
Elaine Y. Hsiao, PhD
Assistant Professor, Department of Integrative Biology and Physiology, De Logi Chair in Biological Sciences, Division of Digestive Diseases, Department of Medicine, David Geffen School of Medicine at UCLA

Dr. Elaine Y. Hsiao is an Assistant Professor in the Department of Integrative Biology & Physiology at UCLA, where she leads a laboratory studying fundamental interactions between the microbiome, brain and behavior, and their applications to neurological disorders. Her studies on the relationships between the microbiota, immune system and nervous system led her to discover that the microbiota can regulate behavioral, metabolic and gastrointestinal abnormalities relevant to autism spectrum disorder (ASD). Her work in this area, and on neuroimmune interactions in autism, has led to several honors, including the National Institutes of Health Director’s Early Independence Award, distinction as Forbes’ 30 Under 30 in Science and Healthcare, National Geographic’s Emerging Explorer Award and fellowships from the National Institute of Mental Health and Autism Speaks. Inspired by this interplay between the microbiota and nervous system, the Hsiao laboratory is mining the human microbiota for microbial modulators of host neuroactive molecules, investigating the impact of microbiota-immune system interactions on neurodevelopment and examining the microbiome as an interface between gene-environment interactions in neurological diseases.

Relevant Recent Publications

  1. Yano JM, Yu K, Donaldson G, Shastri G, Ma L, Ann P, Nagler C, Ismagilov RF, Mazmanian SK, Hsiao EY (2015) Indigenous bacteria from the gut microbiota regulate host serotonin biosynthesis. Cell, 161:264-76.
  2. Hsiao EY, McBride SW, Hsien S, Sharon G, Hyde ER, McCue T, Codelli JA, Chow J, Reisman SE, Petrosino JF, Patterson PH*, Mazmanian SK* (2013) The microbiota modulates behavioral and physiological abnormalities associated with neurodevelopmental disorders. Cell, 155:1451-1463.
  3. Hsiao EY, McBride SW, Chow J, Mazmanian SK, Patterson PH (2012) Modeling an autism risk factor in mice leads to permanent immune dysregulation. PNAS 109:12776-81
Photo of Yu Huang, PhD
Yu Huang, PhD
Associate Professor, Materials Science and Engineering; Member, California NanoSystems Institute, JCCC Cancer and Stem Cell Biology Program Area

Dr. Huang is a Professor in the department of Materials Science and Engineering at UCLA. She received her Ph.D. and M.A degrees in physical chemistry from Harvard University and her B.S. degree from University of Science and Technology of China. Following her Ph.D. studies, Dr. Huang received the Lawrence Postdoctoral Fellowship and conducted her postdoctoral research at MIT and Lawrence Livermore National Labs concurrently. Dr. Huang’s research interest focuses around two intertwined goals: creating complex materials structures with nanoscale precision using chemical and biological approaches; and studying the new physical properties (optical, magnetic, electrical, and even catalytic properties) that arise in these new nanoscale architectures. The overall goal is to create functional nanostructures through rational design, and to systematically determine the fundamental structure-property relationship at the nanometer scale; and in doing so, to understand and to explore the new dimension of applications that these well-defined nanostructures can bring. In order to achieve this goal, we set out to tackle the most challenging and critical problem of understanding the fundamental mechanism governing material/molecular assembly process, and apply the knowledge gleaned from these studies in biomimetic materials, quantum electronics and biomedical applications.


Photo of Jonathan Jacobs, MD, PhD
Jonathan Jacobs, MD, PhD
Assistant Professor-in-Residence, Division of Digestive Diseases, David Geffen School of Medicine at UCLA

Dr. Jonathan Jacobs is an Assistant Professor-in-Residence in the Division of Digestive Diseases within the UCLA Department of Medicine. His research background is in immunology and the intestinal microbiome. He originally trained under Diane Mathis and Christophe Benoist at Harvard, where he published three first author papers on the immunopathological mechanisms of arthritis in an autoantibody-mediated model. He later joined Jonathan Braun’s lab at UCLA to investigate the interactions of the mucosal immune system and the intestinal microbiome in inflammatory bowel disease (IBD). He utilized human cohorts and transgenic mice to demonstrate that the IBD-associated genes RORC and TL1A, both involved in mucosal immunity, garden the intestinal microbiome. This raises the possibility that genetic risk factors promote IBD through their effects on the microbiome. An ongoing human cohort study with Dr. Braun aims to define the microbial and metabolomics features of IBD in the colonic mucosa and to characterize their relationship to IBD-associated genetic polymorphisms. In a separate translational study, he found that healthy relatives of pediatric IBD patients could be classified by their intestinal microbial and metabolomics profiles into “enterotypes” and “metabotypes” that may predict their future risk for IBD. He has authored a review article, a commentary, and two textbook chapters on intestinal host-microbiome interactions. His current research employs in vivo models and multi’omics analysis of IBD cohorts to define the role of IBD-associated genes in shaping the intestinal microbiome and to identify microbial products that promote IBD.

Relevant Recent Publications

  1. Jacobs JP, Lin L, Goudarzi M, Ruegger P, McGovern DPB, Fornace AJ, Borneman J, Xia L, Braun J. Microbial, metabolomic, and immunologic dynamics in a relapsing genetic mouse model of colitis induced by T-synthase deficiency. Gut Microbes. 2017 Jan; 8(1):1-16.
  2. Jacobs JP, Goudarzi M, Singh N, Tong M, McHardy IH, Ruegger P, Asadourian M, Moon B, Ayson A, Borneman J, McGovern DPB, Fornace AJ, Braun J, Dubinsky M. A Disease-associated Enterotype and Metabotype in Healthy Relatives of Pediatric Inflammatory Bowel Disease Patients. Cellular and Molecular Gastroenterology and Hepatology. 2016 Nov; 2(6):750-66.
  3. Jacobs JP, Braun J. Immune and genetic gardening of the intestinal microbiome. FEBS Letters. 2014 Nov; 588(22):4102-11.

Complete Publications List



Photo of Hon Wai Koon, PhD
Hon Wai Koon, PhD
Assistant Professor, Division of Digestive Diseases, David Geffen School of Medicine at UCLA

Dr. Koon’s research is focused on the synthetic mechanism and roles of the antimicrobial peptide Cathelicidin in inflammatory bowel disease, intestinal infections, colorectal cancer, obesity, and diabetes. Cathelicidin is a natural endogenous anti-microbial peptide that is protective to its host as a part of innate immune system. Our laboratory was the first to show that endogenous cathelicidin ameliorates dextran sulfate (DSS) colitis via bone marrow-derived immune cells. We also found increased expression of cathelicidin in monocytes/macrophages in the colonic mucosa of ulcerative colitis patients. Cathelicidin-deficient mice develop more severe bacterial penetration into intestinal mucosa and associated intestinal inflammation than wild-type mice. Therefore, we understand that endogenous cathelicidin may be a protective response to intestinal infection and inflammation. Moreover, intracolonic administration of the cathelicidin peptide ameliorates C. difficile-mediated colitis in mice. We are now studying the role of cathelicidin in the change of intestinal microflora in the development of obesity and diabetes. Dr. Koon is now investigating the role of a non-peptide cathelicidin-mimic, Ceragenin CSA13, in the protection against intestinal inflammation, C. difficile infection, obesity, and diabetes. This protection may be related to change of intestinal microflora. CSA13 is more chemically stable than natural cathelicidin and may be suitable for clinical use. Our research establishes a new direction of research in digestive diseases using microflora study, clinically relevant human primary cells, fresh intestinal biopsies, biologically induced colitis animal models, and system biology approaches.

Recent Relevant Publications

  1. Koon HW, Shih DQ, Chen J, Bakirtzi K, Hing TC, Law I, Ho S, Ichikawa R, Zhao D, Xu H, Gallo R, Dempsey P, Cheng G, Targan SR, Pothoulakis C. Cathelicidin signaling via the Toll-like receptor protects against colitis in mice. Gastroenterology. 2011 Nov;141(5):1852-63.e1-3. PubMed PMID: 21762664; PubMed Central PMCID: PMC3199285.
  2. Hing TC, Ho S, Shih DQ, Ichikawa R, Cheng M, Chen J, Chen X, Law I, Najarian R, Kelly CP, Gallo RL, Targan SR, Pothoulakis C, Koon HW. The antimicrobial peptide cathelicidin modulates Clostridium difficile-associated colitis and toxin A-mediated enteritis in mice. Gut. 2013 Sep;62(9):1295-305. PubMed PMID: 22760006; PubMed Central PMCID: PMC3737259.

Active Funding in Microbiome-Related Research

Funding Agency/Grant Number:NIH 1R03DK103964-01A1
Title:“Role of cathelicidin in obesity and diabetes”


Photo of Jennifer Labus, PhD
Jennifer Labus, PhD
Director, Neuroimaging and Biostatistics Core, Oppenheimer Center for Neurobiology of Stress; Associate Professor, Division of Digestive Diseases, David Geffen School of Medicine at UCLA

Dr. Jennifer S. Labus is an Associate Professor in the David GeffenSchool of Medicine at University of California, Los Angeles. She is an investigator and Director for the Neuroimaging and Bioinformatics Core in the Oppenheimer Family Center for Neurobiology of Stress at UCLA. Her research is focused on the interface of stress, pain and emotions and its influence on the role of dysregulation in the pathophysiology of common chronic pain disorders. She has unique expertise in applying advanced statistical and computational technologies to analyze multimodal brain imaging data. She has made seminal contributions to mapping neural networks underlying visceral pain. Dr. Labus’ current research focus lies in applying a biological system based approach using bioinformatics, network analyses, supervised and unsupervised machine learning tools to integrate multimodal brain imaging data with other large scale biological data sets including genetics and metabolomics. This research provides the means to integrate and decipher large amounts of multivariate neuroimaging data to subgroup patients based on objective biological markers, and characterize central nervous system alterations for further pathophysiological investigations targeting treatment of chronic pain and obesity. She has been the recipient of a K08 Career Development award, Effective connectivity of central response in irritable bowel disorder, from the National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK) as well as a RO3 award examining the role of altered attention and emotional arousal networks in IBS. Recently, acting as lead Co-Primary investigator she was awarded R01 funding by the National Institute of Childhood Health and Human Development (NICHD) to use brain imaging data, along with genetic, physiological and biological data, to extensively phenotype women with vulvodynia. Dr. Labus is a co-investigator on several NIH funded grants, international research collaborations, and is actively involved in mentoring graduate students and postdoctoral fellows. As a result of her work she was awarded the Master’s Award in Gastroenterology in 2010 for her outstanding achievements in Basic and Clinical Digestive Sciences. Dr. Labus was also the recipient of the American College of Neuropsychopharmacolgy Travel Award in 2013.

Relevant Recent Publications


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”
Photo of James Liao, PhD
James Liao, PhD
Chancellor’s Professor; Professor, Chemical and Biomolecular Engineering, Chemistry and Biochemistry

Microbial consortia for degradation of lignocellulosic biomass. We are interested in developing microbial systems for fast and cost-effective deconstruction of lignocellulosic biomass in relatively small scale. The end product could be organic acids, methane, or hydrogen.

Photo of Jake Lusis, PhD
Jake Lusis, PhD
Professor, Departments of Medicine, Cardiology, Human Genetics, Microbiology, Immunology & Molecular Genetics, UCLA

My PhD is in biophysics but somehow I ended up doing mouse genetics for my postdoc. I’m still doing mouse genetics, now with a focus on complex genetic traits, particularly those related to cardiovascular and metabolic disorders. With the development of high throughput technologies, such as expression arrays and sequencing, we have found it useful to marry such data with genetic analysis (‘systems genetics’). I also enjoy teaching.

Relevant Recent Publications

  1. Wang Z, Klipfell E, Bennett BJ, Koeth R, Levison BS, Dugar B, Feldstein AE, Britt EB, Fu X, Chung YM, Wu Y, Schauer P, Smith JD, Allayee H, Tang WH, DiDonato JA, Lusis AJ, Hazen SL. (2011) Gut flora metabolism of phosphatidylcholine promotes cardiovascular disease. Nature. 472:57-63. PMCID:PMC3086762
  2. Bennett BJ, Vallim TQ, Wang Z, Shih DM, Meng Y, Gregory J, Allayee H, Lee R, Graham M, Crooke R, Edwards PA, Hazen S, Lusis AJ. (2013) Trimethylamine-N-oxide, a metabolite associated with atherosclerosis, exhibits complex genetic and dietary regulation. Cell Metab. 17:49-60. PMCID:PMC3771112
  3. Elin Org, Brian W. Parks, Jong Wha J Joo, Benjamin Emert, William Schwartzman, Eun Yong Kang, Margarete Mehrabian, Calvin Pan, Rob Knight, Robert Gunsalus, Thomas A. Drake, Eleazar Eskin, and Aldons J. Lusis. (2015) Genetic and environmental control of host-gut microbiota interactions. Genome Res., in press.

Active Funding in Microbiome-Related Research

Funding Agency/Grant Number:NIH PO1 HL28481
Title:“Molecular genetic approaches in atherosclerosis research.”
Goals:This program project is concerned with the identification and characterization of genetic factors contributing to energy homeostasis and metabolic disease. The emphasis is on combined human-mouse approaches.


Photo of Shaily Mahendra, PhD
Shaily Mahendra, PhD
Associate Professor, Department of Civil and Environmental Engineering, UCLA

Dr. Shaily Mahendra is an Associate Professor in the UCLA Department of Civil and Environmental Engineering. She received Ph.D. from University of California, Berkeley, and post-doctoral fellowship from Rice University. Her research interests lie in the area of microbial interactions with chemical contaminants and nanoparticles for applications ranging from ecotoxicology to biodegradation to disinfection. Bacteria and fungi serve as useful indicators of potential toxicity to higher organisms and ecosystem health, but they can also detoxify a variety of environmental pollutants. Conversely, antimicrobial materials can be used for disinfection applications. Her laboratory pursues research projects employing microbiological, molecular biological, and isotopic tools to (a) characterize microbial communities in engineered and natural environments, (b) optimize biological processes to improve the performance of wastewater treatment or bioremediation systems, (c) explore production of biofuels from industrial wastewater, and (d) investigate mechanisms of transformation, toxicity, and trophic transfer of nanoparticles. Thus, a comprehensive study of the implications and applications of the biotechnology and nanotechnology revolutions will enable us to use their benefits without environmental and public health liabilities.

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Emeran Mayer, MD, PhD
Director, Oppenheimer Center for Neurobiology of Stress; Division of Digestive Diseases, David Geffen School of Medicine at UCLA

Dr. Emeran Mayer is a Professor in the Departments of Medicine, Physiology and Psychiatry at the David Geffen School of Medicine at UCLA, Executive Director of the Oppenheimer Center for Neurobiology of Stress, and Co-director of the CURE: Digestive Diseases Research Center at UCLA. He is a world renowned gastroenterologist and neuroscientist with 30 years of experience in the study of clinical and neurobiological aspects of how the digestive system and the nervous system interact in health and disease, and his work has been continuously supported by the National Institutes of Health (NIH). He is currently principal investigator on 4 NIH grants including a center grant from ORWH/NIDDK on sex differences in brain gut interactions, a consortium grant by NIDDK on pelvic pain syndromes, a RO1 grant on the effects of cognitive behavioral therapy on brain signatures in IBS and a ROI grant on brain gut microbiome interactions in inflammatory and functional GI disorders (both from NIDDK). He has published over 320 peer-reviewed articles (average H index 90), including 100 chapters and reviews, co-edited four books, and organized several interdisciplinary symposia in the area of visceral pain and mind body interactions. His current research focus is on the role of the gut microbiota in modulating brain gut interactions, and their role in emotion regulation, chronic visceral pain and obesity.

Relevant Recent Publications

  1. Labus JS, Naliboff B, Kilpatrick L, Liu C, Ashe-McNalley C, dos Santos IR, Alaverdyan M, Woodworth D, Gupta A, Ellingson BM, Tillisch K, Mayer EA. Pain and Interoception Imaging Network (PAIN): A multimodal, multisite, brain-imaging repository for chronic somatic and visceral pain disorders. Neuroimage, 2015 Apr 19. pii: S1053-8119(15)00308-0. doi10.1016/j.neuroimage.2015.04.018. [Epub ahead of print] PMID: 25902408
  2. Mayer EA, Knight R, Mazmanian SK, Cryan JF, Tillisch K. Gut Microbes and the Brain: Paradigm Shift in Neuroscience. J Neurosci Nov 12;34(46):15490-6, 2014. PMCID: PMC4228144
  3. Mayer EA, Labus JS, Tillisch K, Cole DE, Baldi P. Towards a Systems View of Irritable Bowel Syndrome, Nat Rev Gastroenterol Hepatol. 2015, in press
Photo of Andrey Mazarati, MD, PhD
Andrey Mazarati, MD, PhD
Professor, Department of Pediatrics, Neurology Division, UCLA

Andrey Mazarati obtained his MD degree from Odessa Medical University in Ukraine, and PhD from the Russian Academy of Medical Sciences. His postdoctoral training was at the Department of Neurology, University of California, Los Angeles (UCLA), under the mentorship of Dr. Claude Wasterlain. Since 1997, Dr. Mazarati has been holding academic positions at UCLA, beginning from Junior Faculty, and presently he is Professor at the Department of Pediatrics.
Early scientific interests included the role of bioactive peptides in epilepsy and epileptogenesis; pharmacoresistance and treatment of refractory status epilepticus.
For the past 12 years, main research interest is mechanisms of neurobehavioral comorbidities of epilepsy, with the emphasis on depression, ADHD, anxiety and autism. Dr. Mazarati has been exploring how epilepsy-triggered brain inflammation affects monoaminergic transmission and dependent comorbidities; and how inherent vulnerabilities in monoaminergic circuits translate in neurobehavioral disorders associated with epilepsy.
Most recent studies include the role of gut microbiome in epilepsy- how inherent variabilities in the gut microbiome composition affect predisposition to epilepsy; changes to microbiome composition and function occurring with the development of epilepsy; and how these changes affect the course of epilepsy.

Relevant Recent Publications

  1. Kumar U, Medel-Matus JS, Redwine HM, Shin D, Hensler JG, Sankar R, Mazarati A (2016) Effects of serotonin and norepinephrine reuptake inhibitors on depressive- and impulsive-like behaviors and on monoamine transmission in experimental temporal lobe epilepsy. Epilepsia, 57:506-515
  2. Medel-Matus J-S, Shin D, Sankar R, Mazarati A. (2017) Inherent vulnerabilities in monoaminergic pathways predict the emergence of depressive impairments in an animal model of chronic epilepsy. Epilepsia, 58: e116-e121
  3. Medel-Matus J-S, Shin D, Dorfman E, Sankar R, Mazarati A. (2018). Facilitation of kindling epileptogenesis by chronic stress may be mediated by intestinal microbiome. Epilepsia Open, 3:290-294
Photo of Jeff F. Miller, PhD
Jeff F. Miller, PhD
Director, California NanoSystems Institute, Fred Kavli Chair in NanoSystems Sciences, Professor, Microbiology, Immunology & Molecular Genetics, Microbiology, Immunology & Molecular Genetics, UCLA

Dr. Miller’s laboratory studies molecular mechanisms of bacterial pathogenesis and the evolution of functional diversity in bacteria and bacteriophage. Multidisciplinary approaches are applied to a variety of interests including: i) biochemical and genetic studies of signal transduction networks that regulate the infectious cycles of Bordetella pertussis, which causes whooping cough, and Burkholderia pseudomallei, which causes life threatening systemic diseases, ii) alterations in host cell signaling pathways by Bordetella and Burkholderia, iv) biofilm formation and the hyper-colonization phenotype of Staphylococcus epidermiditis, and v) microevolutionary adaptation by diversity-generating retroelements, which function to introduce vast amounts of diversity in bacterial target proteins. Our research group includes graduate students, postdoctoral fellows and physician-scientists with expertise in computational biology and modeling, bacterial genomics, bacterial physiology, cell biology, neonatology, and infectious diseases. Numerous former trainees hold tenured or tenure-track academic positions at research universities. Since joining UCLA in 1990, we have received continuous funding from the NIH, as well as support from the American Cancer Society, the US Department of Agriculture, the Pew Foundation, and the Defense Threat Reduction Agency of the Department of Defense.

Photo of Anna-Barbara Moscicki, MD
Anna-Barbara Moscicki, MD
Chief, Adolescent Medicine; Professor of Pediatrics, David Geffen School of Medicine at UCLA

Dr. Moscicki is Professor of Pediatrics at UCLA, Division Chief of Adolescent Medicine, Dr. Moscicki’s career has focused on adolescent gynecology and STI research with a specific focus in Human Papillomavirus, HIV infection and mucosal immunology. She trained in STI epidemiology and mucosal immunology. Dr. Moscicki has been the PI of a natural history study of HPV in adolescents and young women since 1990, one of the longest running HPV cohorts of which she was awarded an NIH MERIT. She has over 200,000 stored specimens from this cohort including cervical lavages, cervical biopsies, anal swabs, oral gargles, serum and blood clots. She serves on numerous national and international committees, including the W.H.O., N.I.H., American Society for Colposcopy and Cervical Pathology, and the American Cancer Society. Her work was influential in forming the new cervical cancer screening guidelines and triage of abnormal cytology in young women. She is also involved in health outcomes in perinatally HIV infected children including sexual risk behaviors, substance use, oral health, microbiomes, and HPV.

She has been involved in HIV research for over 20 years including member of the Adolescent Medicine HIV/AIDS Research Network, Adolescent Therapeutic Network , IMPAACT and PHACS. In PHACS, she is a member of the scientific Leadership Group, and co-chair of the Adolescent Working Group and co-PI of the Oral Health study in PHACS which focuses on the role of the microbiome in oral health.

Relevant Recent Publications

  1. Daud, II, Scott ME, Ma Y, Shiboski S, Farhat S, Moscicki AB. Association between toll-like receptors expression and human papillomavirus type 16 persistence. Int J Cancer 2011;128(4):879-86.
  2. Hwang LY, Scott M, Ma Y, Moscicki AB. Higher levels of cervicovaginal inflammatory and regulatory cytokines and chemokines in healthy young women with immature cervical epithelium. Journal of Reproductive Immunology 2011; 88:66-71.
  3. Moscicki AB, Kaul R, Ma Y, Scott ME, Daud, II, Bukusi EA, Shiboski S, Rebbapragada A, Huibner S, Cohen CR. Measurement of mucosal biomarkers in a phase 1 trial of intravaginal 3% StarPharma LTD 7013 gel (VivaGel) to assess expanded safety. J Acquir Immune Defic Syndr 2012;59(2):134-140.
  4. Weinberg A, Song LY, Saah A, Brown M, Moscicki AB, Meyer III WA, Bryan J, Levin MJ for the IMPAACT/PACTG P1047 team. Humoral, mucosal and cell-mediated immunity against vaccine and non-vaccine genotypes after administration of quadrivalent human papillomavirus vaccine to HIV-infected children. Journal of Infectious Diseases. 2012; 206(8):1309-1318.
  5. Scott ME, Shvetsov YB, Thompson PJ, Hernandez BY, Zhu X, Wilkens LR, Killeen J, Vo D, Moscicki AB, Goodman MT. Cervical Cytokines and Clearance of Incident Human Papillomavirus Infection: Hawaii HPV Cohort Study. International Journal of Cancer. 2013; 133(5):1187-96.
  6. Moscicki AB, Ma Y, Farhat S, Jay J, Hanson E, Benningfield S, Jonte J, Godwin-Medina C, Wilson R, Shiboski S. Natural history of anal human papillomavirus infection in heterosexual women and risks associated with persistence. Clin Infect Dis 2014;58(6):804-11
  7. Scott ME, Ma Y, Farhat S, Moscicki AB. Expression of nucleic acid-sensing Toll-like receptors predicts HPV16 clearance associated with an E6-directed cell-mediated response. Int J Cancer. Oct 23 2014. [e-pub ahead of print]

Active Funding in Microbiome-Related Research

Funding Agency/Grant Number:NIH NCI R37CA051323-26
Title:“Natural history of HPV”
Funding Agency/Grant Number:NIH NICHD U01 HD052102
Title:“Oral Health in Perinatally HIV infected adolescents”


Photo of Mohamad Navab, PhD
Mohamad Navab, PhD
Adjunct Professor of Medicine, Department of Cardiology, David Geffen School of Medicine at UCLA

Dr. Mohamad Navab is a Professor in the Departments of Medicine, Cardiology at the David Geffen School of Medicine at UCLA, with 32 years of research experience in the study of atherosclerosis, lipids and artery wall metabolism. His work has been continuously supported by the National Institutes of Health (NIH). He is CoProject Leader on an NIH PPG/grant that is going into its 31st year. He has published 195 peer-reviewed articles (average H index 90), including 100 chapters and reviews, co-edited two books, and organized three interdisciplinary symposia in the area of lipids and artery wall metabolism. His current research focus is on the role of the role of small intestine, systemic inflammation and cardiovascular function. He has been involved in studies of gut microbiota in dyslipidemia and the effect of HDL mimetic peptides on it.

Relevant Recent Publications

Source and role of intestinally derived lysophosphatidic acid in dyslipidemia and atherosclerosis. Navab M et al. J Lipid Res. 2015;56:871-87

Transgenic 6F tomatoes act on the small intestine to prevent systemic inflammation and dyslipidemia caused by Western diet and intestinally derived lysophosphatidic acid. Navab M, et al. J Lipid Res. 2013;54:3403-18

Intestine may be a major site of action for the ApoA-I mimetic peptide 4F whether administered subcutaneously or orally. Navab M, et al. J Lipid Res. 2011; 52:1200-10.

HDL and cardiovascular disease: atherogenic and atheroprotective mechanisms. Navab M, Nat Rev Cardiol. 2011;8:222-32

Mechanisms of disease: proatherogenic HDL–an evolving field. Navab M, Nat Clin Pract Endocrinol Metab. 2006 ;2:504-11.


Photo of Aydogan Ozcan, PhD
Aydogan Ozcan, PhD
Professor, Department of Electrical Engineering and Bioengineering, UCLA; Associate Director, California NanoSystems Institute (CNSI)

Dr. Ozcan is the Chancellor’s Professor at UCLA and an HHMI Professor with the Howard Hughes Medical Institute, leading the Bio- and Nano-Photonics Laboratory at UCLA School of Engineering and is also the Associate Director of the California NanoSystems Institute (CNSI). Dr. Ozcan holds 32 issued patents (all of which are licensed) and >20 pending patent applications and is also the author of one book and the co-author of more than 400 peer reviewed research articles in major scientific journals and conferences. Dr. Ozcan is a Fellow of SPIE and OSA, and has received major awards including the Presidential Early Career Award for Scientists and Engineers (PECASE), International Commission for Optics (ICO) Prize, SPIE Biophotonics Technology Innovator Award, SPIE Early Career Achievement Award, ARO Young Investigator Award, NSF CAREER Award, NIH Director’s New Innovator Award, ONR Young Investigator Award, IEEE Photonics Society Young Investigator Award and MIT’s TR35 Award for his seminal contributions to near-field and on-chip imaging, and telemedicine based diagnostics. Dr. Ozcan is also the recipient of the National Geographic Emerging Explorer Award, National Academy of Engineering (NAE) The Grainger Foundation Frontiers of Engineering Award, Popular Science Brilliant 10 Award, Gates Foundation Grand Challenges Award, Popular Mechanics Breakthrough Award, Netexplorateur Award, Microscopy Today Innovation Award, and the Wireless Innovation Award organized by the Vodafone Americas Foundation as well as the Okawa Foundation Award.

A. Greenbaum, Y. Zhang, A. Feizi, P. Chung, W. Luo, S.R. Kandukuri, and A. Ozcan, ”Wide-field Computational Imaging of Pathology Slides using Lensfree On-Chip Microscopy,” Science Translational Medicine (AAAS) (2014)

Q. Wei, W. Luo, S. Chiang, T. Kappel, C. Mejia, D. Tseng, R. Chan, E. Yan, H. Qi, F. Shabbir, H. Ozkan, S. Feng, and A. Ozcan, ”Imaging and Sizing of Single DNA Molecules on a Mobile-Phone,” ACS Nano (2014)

A. Greenbaum, W. Luo, T-W. Su, Z. Göröcs, L. Xue, S.O. Isikman, A.F. Coskun, O. Mudanyali, and A. Ozcan, ”Imaging without lenses: achievements and remaining challenges of wide-field on-chip microscopy,” Nature Methods (2012) DOI:10.1038/nmeth.2114


Photo of Laurent Pilon, PhD
Laurent Pilon, PhD
Professor, Mechanical and Aerospace Engineering, UCLA

Laurent Pilon is Professor in the Mechanical and Aerospace Engineering Department at UCLA. He received his PhD in Mechanical Engineering from Purdue University in 2002. His expertise is at the crossroad between applied optics, transport phenomena, materials, and interface science. Applications focuses on sustainable energy technologies including (i) photobiological production of added-value products, (ii) mesoporous materials for photocatalysis and energy storage applications, (iii) waste heat and mechanical energy harvesting. He is the recipient of the 2005 National Science Foundation CAREER Award, the 2008 Bergles-Rohsenow Young Investigator Award in Heat Transfer from ASME, and the 2009 Young Scientist Award in Radiative Transfer from the Journal of Quantitative Spectroscopy and Radiative Transfer. He was elected Senior Member of SPIE in 2011. He also received the 2005 Northrop Grumman Excellence in Teaching Award from the UCLA School of Engineering and Applied Science and the 2011 Henry and Susan Samueli Teaching Award from the UCLA MAE Department.


Photo of Robert Schiestl, PhD
Robert Schiestl, PhD
Professor, Departments of Pathology and Laboratory Medicine, Environmental Health Sciences, Radiation Oncology, Jonsson Comprehensive Cancer Center, UCLA

Robert H. Schiestl has obtained his PhD from the University of Vienna at the age of 23 years. He was postdoctoral fellow at Edmonton, Alberta, Rochester, NY, and Chapel Hill, NC before being professor at Harvard at the age of 31 where he stayed for 10 years. Since 15 years he is professor at UCLA with 187 publications, 10 patents and 2 startup companies.
Intestinal microbiota plays a role in the nutrient metabolism, modulation of the immune system, arthritis, obesity and intestinal inflammation. In the literature there have been huge differences in the same Atm deficient mice in different labs reported. When our lab moved from Harvard to UCLA we found a similar difference in genetic instability and logevity. When we changed the intestinal microbiota back to conventional microbiota we could reproduce the phenotype at Harvard. We tested Atm deficient mice for genotoxicity, genetic instability, DNA damage, inflammation markers, cancer latency and longevity and high throughput sequencing of the intestinal microbiota. Isogenic mice from different housing facilities showed a four fold difference in life expectancy, a 4.5 fold difference in genetic instability and DNA damage. The onset of lymphomas was significantly 2 fold different. We sequenced the microbiota of both facilities and found Lactobacillus johnsonii 456 as dominant bacterial strain in the health beneficial microbiota. Just this bacterium by itself reduced genotoxicity, reduced inflammation and reduced levels of cytotoxic T cells in the liver and blood. We also found similar differences in Trp53 deficient and even in wildtype mice. The underlying mechanisms is probably due to inflammation promotion or suppression mediated by the intestinal microbiota. The understanding of this effect may lead to a breakthrough in the understanding of the causes of carcinogenesis, which might lead to prevention of AT, a currently incurable progressive disease and possibly other cancer-prone DNA repair deficient diseases or even wildtype mice and people.

Relevant Recent Publications

  1. Yamamoto, L. I. Maier , A. T. Dang , D. Berry , J. Liu, P. M. Ruegger , J. Yang, P. A. Soto, L. L. Presley, R. Reliene , A. M. Westbrook , B. Wei , A. Loy , C.r Chang , J. Braun , J. Borneman, R. H. Schiestl (2013) Intestinal bacteria modify lymphoma penetrance in genetically susceptible mice via inflammation-mediated systemic host oxidative stress and leucocyte genotoxicity- Cancer Research 73(14):4222-4232 July 15, 2013 PMCID: PMC3718495
  2. Westbrook, A. and R.H. Schiestl (2010) Atm deficient mice exhibit increased sensitivity to dextran sulfate sodium-induced colitis characterized by elevated DNA damage and persistent immune activation. Cancer Research 70, 1875, March 1, 2010. PMCID: PMC2831166
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Adam Stieg, PhD
Associate Director, California NanoSystems Institute; Research Scientist, California NanoSystems Institute, UCLA

Dr. Adam Z. Stieg currently serves as the Associate Director of Shared Resources, Scientific Director of the Nano and Pico Characterization Core Facility and Interim Technical Director of the Integrated Systems Nanofabrication Cleanroom at the California NanoSystems Institute (CNSI). He also serves as the Director of the Sci|Art NanoLab. Dr. Stieg earned his B.S. with honors in Chemistry from Drew University and both his M.S. and Ph.D. in Inorganic and Physical Chemistry from UCLA. He is a member of the CNSI Executive and Education Committees. As a scientist and educator, Dr. Stieg continues to focus on the development of integrated approaches to study material systems at the interface of traditional boundaries. Through the implementation of original experimental techniques, with a specialized focus in multi-environment, high-performance scanning probe microscopes, his research seeks to bridge the gap between our current understanding of nanomaterials and their fundamental properties with how these systems tend toward complexity at increased scales of space and time. Numerous ongoing, collaborative efforts involve the study of molecular machines, nanoparticles for targeted drug delivery, inorganic carbon-based materials, directed stem cell differentiation and the pursuit of physically intelligent systems through neuromorphic computation. His research activities are augmented by active collaboration with artists and designers on various projects, installations, and public exhibitions that directly inform the scientific process and provide motivation to develop new educational content that conveys the need for creativity in innovation.


Photo of Kirsten Tillisch, MD
Kirsten Tillisch, MD
Director, Mind Body Research Program, Oppenheimer Center for Neurobiology of Stress; Associate Professor, Department of Medicine, David Geffen School of Medicine at UCLA

Dr. Kirsten Tillisch completed her undergraduate work at the Otis Institute of Parsons School of Design, earning a Bachelor of Fine Arts with Honors. She obtained her medical degree from the David Geffen School of Medicine at UCLA and was elected to the medical honor society Alpha Omega Alpha. She continued on at UCLA to complete her training in internal medicine and gastroenterology, graduating in 2003. Her clinical interests are functional bowel disorders such as irritable bowel syndrome, functional dyspepsia, and cyclic vomiting syndrome. Her research interests include brain-gut interactions , the effects of nonpharmacological therapies on functional gastrointestinal disorders, and pharmacological treatment of irritable bowel syndrome. Her recent research projects include defining resting state brain dysfunction in irritable bowel syndrome patients, evaluating the role of gut microbiota modulation on emotional processing in the brain, and assessment of neurokinin-1 receptor antagonists effects on the gut and brain in irritable bowel syndrome. She is a member of the Neuroimaging Program of the Gail and Gerald Oppenheimer Family Center for Neurobiology of Stress.

Relevant Recent Publications

  1. Mayer EA, Tillisch K, Gupta A. Gut/brain axis and the microbiota. J Clin Invest. 2015 Mar 2;125(3):926-38. doi: 10.1172/JCI76304. Epub 2015 Feb 17. Review. PubMed PMID: 25689247; PubMed Central PMCID: PMC4362231.
  2. Mayer EA, Knight R, Mazmanian SK, Cryan JF, Tillisch K. Gut microbes and the brain: paradigm shift in neuroscience. J Neurosci. 2014 Nov 12;34(46):15490-6. doi: 10.1523/JNEUROSCI.3299-14.2014. Review. PubMed PMID: 25392516; PubMed Central PMCID: PMC4228144.
  3. Mayer EA, Padua D, Tillisch K. Altered brain-gut axis in autism: comorbidity or causative mechanisms? Bioessays. 2014 Oct;36(10):933-9. doi: 10.1002/bies.201400075. Epub 2014 Aug 22. Review. PubMed PMID: 25145752.
  4. Tillisch K, Labus JS. Neuroimaging the microbiome-gut-brain axis. Adv Exp Med Biol. 2014;817:405-16. doi: 10.1007/978-1-4939-0897-4_18. Review. PubMed PMID: 24997044.
  5. Tillisch K. The effects of gut microbiota on CNS function in humans. Gut Microbes. 2014 May-Jun;5(3):404-10. doi: 10.4161/gmic.29232. Epub 2014 May 16. Review. PubMed PMID: 24838095; PubMed Central PMCID: PMC4153780.
  6. Tillisch K, Labus J, Kilpatrick L, Jiang Z, Stains J, Ebrat B, Guyonnet D, Legrain-Raspaud S, Trotin B, Naliboff B, Mayer EA. Consumption of fermented milk product with probiotic modulates brain activity. Gastroenterology. 2013 Jun;144(7):1394-401, 1401.e1-4. doi: 10.1053/j.gastro.2013.02.043. Epub 2013 Mar 6. PubMed PMID: 23474283; PubMed Central PMCID: PMC3839572.


Photo of Elizabeth Volkmann, MD, MS
Elizabeth Volkmann, MD, MS
Clinical Instructor, Division of Rheumatology, Department of Medicine, David Geffen School of Medicine at UCLA

Dr. Elizabeth Volkmann is a Clinical instructor in the Department of Medicine, Division of Rheumatology at UCLA. She is the Founder and Director of the Connective Tissue Disease-Interstitial Lung Disease (CTD-ILD) Integrative Clinic Program at UCLA. She received her medical degree from UCLA David Geffen School of Medicine, and subsequently completed her residency in Internal Medicine and fellowships in Rheumatology and Medical Education at UCLA. During her fellowship, she participated in the Specialty Training and Advanced Research (STAR) Program and earned her Master of Science degree in Clinical Research.

Her clinical and research expertise is in systemic sclerosis (scleroderma), a rare and disabling autoimmune disease that affects gastrointestinal function in the majority of patients. She is currently the principal investigator of an innovative study to characterize the gastrointestinal tract microbiome in patients with systemic sclerosis. This study aims to investigate the hypothesis that the systemic sclerosis disease state is associated with altered colonic microbial composition at the human mucosal-luminal interface, and to determine whether certain microbial genera contribute to symptoms of gastrointestinal tract dysfunction in patients with systemic sclerosis. If affirmed, such genera could provide specific targets for intervention to avert or treat this important clinical dimension of systemic sclerosis.

Recent Relevant Publications/Presentations:

  1. Volkmann ER, Chang, Y-L, Barroso N, et al. Systemic sclerosis is associated with a unique colonic microbial consortium. Annals Rheumatic Diseases 2015;74:151.
  2. Volkmann ER. Systemic sclerosis is associated with a unique colonic microbial consortium. Oral Presentation at the European League Against Rheumatism Annual Congress, 2015. Rome, Italy.


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David Walker, PhD
Professor, Department of Integrative Biology and Physiology, UCLA

Dr. Walker is a Professor in the department of Integrative Biology and Physiology at the University of California, Los Angeles (UCLA). He is also a faculty member of the Molecular Biology Institute at UCLA. Dr. Walker completed his Ph.D. degree at the University of Manchester, UK. He then went on to carry out postdoctoral work with Seymour Benzer at the California Institute of Technology. He joined the faculty at UCLA as an Assistant Professor in 2007 and was promoted to Associate Professor in 2012 and full Professor in 2015. Dr. Walker has a long-standing interest in the biological mechanisms of aging. In recent years, his research group has made important insights into the relationship between intestinal aging and organismal aging. In this work, Dr. Walker is exploring the relationships between age-related changes in microbiota composition, intestinal physiology and the health and viability of the aging host organism.

Dr. Walker is the recipient of several awards, including an Ellison Medical Foundation New Scholar in Aging award as well as a Career Development Award from the UCLA Older Americans Independence Center. Most recently, Dr. Walker is the recipient of a Julie Martin Mid-Career Award in Aging Research from the American Federation for Aging Research (AFAR).

Relevant Recent Publications:

  1. Clark, R.I., Salazar, A, Yamada, R, Fitz-Gibbon, S, Morselli, M, Alcaraz, J, Rana, A, Rera, M, Pelligrini, M, Ja, WW, Walker. D.W. (2015) Distinct shifts in microbiota composition during Drosophila aging impair intestinal function and drive mortality. Cell Reports (in press)
  2. Ulgerhait, M, Rana, A, Rera, M, Graniel, J, Walker D.W. (2014) AMPK modulates tissue and organismal aging in a non-cell-autonomous manner. Cell Reports 8: (6), p1767–1780.
  3. Rera, M, Clark, R.I., Walker D.W. (2012) Intestinal barrier dysfunction links metabolic and inflammatory markers of aging to death in Drosophila. Proc Natl Acad Sci USA 109(52): 21528-33.
  4. Rera, M, Bahadorani S, Cho J, Koehler, C, Hur, JH, Ulgerhait, M, Jones, DL, Walker DW. (2011). Modulation of longevity and tissue homeostasis by the Drosophila homolog of PGC-1. Cell Metabolism 14(5):623-34

Active Funding in Microbiome-Related Research

Funding Agency/Grant Number:NIH 1R01AG049157
Title:“Role of Intestinal Homeostasis in Organismal Aging”
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Paul Weiss, PhD
UC Presidential Chair; Distinguished Professor of Chemistry & Biochemistry and of Materials Science & Engineering; ACS Nano Editor-in-Chief

Paul S. Weiss holds a UC Presidential Chair and is a distinguished professor of chemistry & biochemistry and of materials science & engineering at UCLA. He received his S.B. and S.M. degrees in chemistry from MIT in 1980 and his Ph.D. in chemistry from UC Berkeley in 1986. He was a postdoctoral member of technical staff at Bell Laboratories from 1986-88 and a visiting scientist at IBM Almaden Research Center from 1988-89. He served as the director of the California NanoSystems Institute and held the Fred Kavli Chair in NanoSystems Sciences at UCLA from 2009-2014. Before coming to UCLA, he was a distinguished professor of chemistry and physics at Penn State, where he began his academic career in 1989. His interdisciplinary research group includes chemists, physicists, biologists, materials scientists, mathematicians, electrical and mechanical engineers, and computer scientists. Their work focuses on the ultimate limits of miniaturization, exploring the atomic-scale chemical, physical, optical, mechanical, and electronic properties of surfaces and supramolecular assemblies. He and his students have developed new techniques to expand the applicability and chemical specificity of scanning probe microscopies. They have applied these and other tools to the study of catalysis, self- and directed assembly, and molecular and nanoscale devices. They work to advance nanofabrication down to ever smaller scales and greater chemical specificity in order to operate and to test functional molecular assemblies, and to connect these to the biological and chemical worlds. He develops multiplexed biomolecular sensor arrays for biomedical, neuroscience, and microbiome applications. He is developing new tools to measure the ocean microbiome and environment simultaneously.

Weiss has been awarded a NSF Presidential Young Investigator Award, the B. F. Goodrich Collegiate Inventors Award, a Sloan Fellowship, the ACS Nobel Laureate Signature Award for Graduate Education in Chemistry, a Guggenheim Fellowship, a NSF Creativity Award, and the ACS Award in Colloid and Surface Chemistry, among others. He was elected a fellow of: the American Association for the Advancement of Science, the American Physical Society, the American Vacuum Society, the ACS, the American Academy of Arts and Sciences, the American Institute for Medical and Biological Engineering, and an honorary fellow of the Chinese Chemical Society. He was a visiting professor at the University of Washington, Department of Molecular Biotechnology and Kyoto University, Electronic Science and Engineering Department and Venture Business Laboratory, and a distinguished visiting professor at the Kavli Nanoscience Institute and the Joint Center for Artificial Photosynthesis at Caltech. He is a visiting scholar at the Kavli Institute for Bionano Science & Technology and the Wyss Institute for Biologically Inspired Engineering at Harvard University (2015-16). He has been named the Institut National de la Recherche Scientifique (INRS) Chaire d’excellence Jacques¬Beaulieu at the Centre for Energy, Materials and Telecommunications. Weiss is the founding editor-in-chief of ACS Nano (2007-). At ACS Nano, he won the Association of American Publishers, Professional Scholarly Publishing PROSE Award for 2008, Best New Journal in Science, Technology, and Medicine, and ISI’s Rising Star Award a record ten times, and co-wrote the technology roadmap for the microbiome initiative.

Tools for the microbiome: Nano and beyond, J. S. Biteen, P. C. Blainey, M. Chun, G. M. Church, P. C. Dorrestein, S. E. Fraser, J. A. Gilbert, J. K. Jansson, R. Knight, J. F. Miller, A. Ozcan, K. A. Prather, E. G. Ruby, P. A. Silver, S. Taha, G. van den Engh, P. S. Weiss, G. C. L. Wong, A. T. Wright, and T. D. Young, ACS Nano 10, 6 (2016). DOI: 10.1021/acsnano.5b07826 – appears tomorrow

Printable ultrathin metal oxide semiconductor-based conformal biosensors, Y. S. Rim, S.-H. Bae, H. Chen, J. L. Yang, J. Kim, A. M. Andrews, P. S. Weiss, Y. Yang, and H. R. Tseng, ACS Nano 9, 12174 (2015).

Fabrication of high-performance ultrathin In2O3 film field-effect transistors and biosensors using chemical lift off lithography, J. Kim, Y. S. Rim, H. Chen, H. H. Cao, N. Nakatsuka, H. L Hinton, C. Zhao, A. M. Andrews, Y. Yang, and P. S. Weiss, ACS Nano 9, 4572 (2015).


Photo of Xia Yang, PhD
Xia Yang, PhD
Associate Professor, Department of Integrative Biology & Physiology, UCLA

Xia Yang is currently Associate Professor in the Department of Integrative Biology and Physiology and a member of the Institute of Quantitative and Computational Biology at UCLA. Her lab focuses on developing and applying multi-tissue multi-omics systems biology methodologies and approaches to understand the gene networks perturbed by genetic and environmental risks of complex human diseases including cardiometabolic and brain disorders

Relevant Recent Publications

  1. Arneson D, Bhattacharya A, Shu L, Makinen VP, Yang X. Mergeomics: A Web Server for Identifying Pathological Pathways, Networks, and Key Regulators via Multidimensional Data Integration. BMC Genomics 17:722, 2016.
  2. Shu L, Chan KHK, Zhang G, et al. Yang X. Shared Genetic Regulatory Networks for Cardiovascular Disease and Type 2 Diabetes in Multiple Populations of Diverse Ethnicities in the United States. PLOS Genetics 13(9): e1007040, 2017.
  3. Krishnan KC, Kurt Z, Barrere-Cain R, et al., Lusis AJ, Yang X. Integration of Multi-omics Data from Mouse Diversity Panel Highlights Mitochondrial Dysfunction in Non-Alcoholic Fatty Liver Disease. Cell Systems 6:1-13. 2018.
  4. Arneson D, Zhuang Y, Byun HR, et al., Yang X. Single Cell Molecular Alterations Reveal Target Cells and Pathways of Concussive Brain Injury. Nature Communications 9: 3894, 2018.
  5. Shu L, Meng Q, Tsai B, et al., Yang X. Prenatal Bisphenol A Exposure in Mice Induces Multi-tissue Multi-omics Disruptions Linking to Cardiometabolic Disorders. Endocrinology 160: 409-429, 2019. PMC6349005.

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