More than 100 UC San Diego professors and research scientists elected to join the Center for Microbiome Innovation at its launch. These researchers lead teams working at the leading edge of many interrelated areas, including microbiology, cell and molecular biology, computer science, physical sciences, biomedical engineering, electrical engineering, pharmacology, clinical care, ecology, oceanography, anthropology and more.
Faculty Director, Center for Microbiome Innovation
Pediatrics, Computer Science and Engineering
Advanced computational tools and methods for reading out microbial communities. Investigation of links between microbes and a variety of health conditions (e.g. obesity, autism etc.) Understanding the role microorganisms play in life at all scales, from specific regions of the human body to remote ecosystems.
Executive Director, Center for Microbiome Innovation
Miller-Montgomery is the executive director of the Center for Microbiome Innovation. She leads a team focused on expanding industry and academic collaborations in the field of microbiome research. She comes directly from industry and has worked in large biotech and multinational companies as well as start-ups. Most recently, she was leading MO BIO Labs, a biotech focused on nucleic acid purification.
Physics, Molecular Biology
The Hwa lab employs novel theoretical and experimental methods to develop quantitative, mechanistic models describing the growth and interaction dynamics of gut microbiota.
Skaggs School of Pharmacy & Pediatrics
Microbial metabolite characterization via mass spectrometry technologies for drug discovery, rapid personalized care, forensics, environmental science e.g. reef preservation.
Computer Science and Engineering
Genomic assembly techniques for microbiome research. Drug discovery and identification of useful compounds already in nature.
Modeling communities of bacteria; reading out transcriptomes and translatomes; collecting live microbial cells from the environment to develop building blocks for synthetic microbial communities. Developing tools to predict and shape the functions of synthetic microbial communities.
Metabolic network modeling, systems biology, and development of analysis procedures for genome-scale models. The experimental verification of these models in an effort to gain a systems-level understanding of microbial and host communities for agriculture, drug discovery and beyond.
Pediatrics, Pharmaceutical Sciences
Microbial pathogenesis and innate immunity. Novel approaches to infectious disease therapy based on the host-pathogen interaction and designed to preserve the healthy microbiome.
Calit2, Computer Science and Engineering
Computational infrastructure for collaborative, data-intensive research on microbiome-associated disease, and health, from the individual scale to entire populations.
Associate Professor, Bioengineering
Dr. Coleman is an expert in quantitative and applied probability analysis of biomedical data as well as bio-instrumentation. He has interests in how the microbiome of the skin, gut, and dietary intake intersects with the electrophysiology of the GI system, to develop a deeper description of GI function and its abnormalities in disease.
Microbial community manipulation and design. Development of in vitro systems to dissect the principles and mechanisms of community formation. Advanced approaches for the study of fermented foods.
Medicine, Family Medicine and Public Health
I am interested in studying relationships between the gut microbiome and human behaviors and cardiometabolic disease and cancer risk. To address this, we have recently initiated studies integrating multi-level, molecular “omics” , clinical traits, behavior (e.g., timing and type of diet, physical activity), built environment exposure, and gut microbiome diversity data using systems biomedicine.
Rommie E. Amaro
Chemistry and Biochemistry
State of the art computational methods and applications for multi-scale dynamics from molecules to cells, drug discovery and identification of new druggable sites on flexible targets.
Systems biology analysis of microorganisms with a specific focus on yeasts. Combining single-cell imaging and microfludics technologies to investigate the dynamic behaviors of microorganisms and the host pathogen interactions.
Medicine, Infectious Diseases
I am broadly interested in general infectious diseases, and specifically in tropical infectious diseases. Our research sites in the Peruvian Amazon facilitate answering broad questions about microbial diversity and infectious diseases, particularly how the intestinal microbiome affects tropical diseases such as malaria, leptospirosis and tuberculosis.
In our laboratory we study host factors that mediate chronic liver diseases. In addition, we focus on microbial factors that change in response to liver injury and chronic liver disease and the consequences of intestinal dysbiosis on host biology. We specifically are interested in the enteric microbiome, metagenome and transcriptome associated with liver disease.
We use in vitro and in vivo technologies to study various aspects of chronic liver disease. We specifically use animal models mimicking fatty liver disease, alcoholic and non-alcoholic steatohepatitis, toxic and cholestatic models of liver disease.
In addition, a very important part of our laboratory is a translational aspect to identify targets for therapy and to generate interventions that are able to prevent or treat liver disease in patients.
Electrical and Computer Engineering
Computational methods for taxon identification and for taxonomic profiling of metagenomic samples. Phylogenetics, multiple sequence alignment, and phylogenomics.
We perform basic and translational research in the intersection of circadian biology, gut physiology, and the gut microbiome and how the three interact to cause obesity, diabetes, steatohepatitis, dyslipidemia, and other associated metabolic disorders. Specifically, we study the reciprocal interaction between the luminal environment (both the gut microbiome and the content) and intestinal cells.
Microbiota introduce small molecule mediators into human circulation which in turn modulate human health and disease. Our laboratory at UC San Diego utilizes mass spectrometry based metabolomics in conjunction with population scale human biosamples and large-scale data integration to map the environmental landscape of human disease, including the role of the microbiome.
Chief Data Science Officer
San Diego Supercomputer Center
Next generation workflows and analytical tools for optimized reproducible processing of biomedical big data on heterogeneous computational and data infrastructure.
I have studied and am interested in how the human microbiome is associated with HIV disease pathogenesis and immune function, including end organ damage.
Professor, Division Chief Endocrinology and Metabolism
Medicine - Endocrinology
The Webster lab is interested in the dysregulation of glucose and lipid metabolism and the origin of insulin resistance in obesity, fatty liver disease and steatohepatitis. We are also interested in the role of dendritic cells in innate immunity and insulin resistance.
Studying the relationship between gut, skin, and mouth microbiome and mood or anxiety disorders in individuals with acute psychiatric symptoms.
Associate Adjunct Professor
I am investigating the relationship between environmental factors (e.g. acute stress, diet, sleep, smoking, space travel) with the genome in the development of age related disorders. I have a sample bank of longitudinal and twin cohorts for omics and the microbiome studies. I am currently conducting a pilot study of the gut microbiome on monozygotic twins from the Vietnam Era Twin Study of Aging.
SIO/Marine BIology Research Division
Culture-dependent and independent analyses of environmental (mostly marine) microbial communities. The former includes techniques for aerobe/anaerobe, chemoheterotroph/chemoautotroph, batch and flow through cultivation, mesophiles, thermophiles, psychrophiles, and piezophiles. Molecular analyses include Illumina tag analyses, genomics, single-cell genomics, and metagenomics.
Dr. Laurent is a Maternal Fetal Medicine subspecialist with an interest in understanding the genetic, developmental and environmental factors leading to pregnancy complications, such as preterm birth and preeclampsia. She is a co-founder of the UCSD Perinatal Biorepository, which longitudinally collects a variety of biospecimens and clinical data from healthy and complicated pregnancies.
Associate Professor of Pediatrics, Director of the UCSD Mother Milk Infant Center of Research Excellence (MoMI CoRE), President of the International Society for Research in Human Milk and Lactation (ISRHML)
The Bode lab is dedicated to research on human milk oligosaccharides (HMO), a group of complex carbohydrates that are highly abundant in human milk, but not in infant formula. HMO contribute to shaping the infant gut microbiome with short-and long-term impact on infant health and disease. We aim to identify maternal factors that drive HMO composition and discover how HMO benefit infant health.
Dean, Skaggs School of Pharmacy & Pharmaceutical Sciences; Associate Vice Chancellor for Health Sciences
Diversity of intestinal microbiome and its response to infection by intestinal parasites. For example, interaction of E. histolytica and intestinal microbiome as a determinate of the pathogenesis of amebiasis.
Ecology, Behavior, and Evolution Section
Our research focuses on reconstructing foraging ecology and movement patterns for wild vertebrates and we use those data to understand community ecology and how best to achieve species conservation. We work on multiple species and deciphering the microbiomes of wild animals could inform differential survivorship and population trajectories among individuals or across sub-populations.
Helicobacter pylori infection and innate immunity. Examination of the complex interactions between the host, H. pylori, and the gastric microbiota in determining disease outcome. Our goal is to characterize the gastric microbiota, which could be used as a biomarker to identify H. pylori-infected individuals at high risk of developing serious disease.
Center for Marine Biotechnology and Biomedicine
The laboratory expertise involve the evolution and functional aspects of cyanobacterial genomes and heterotrophic bacterial interaction, transcriptional regulation, biosynthesis of secondary metabolite pathways as well as development of techniques to further be able to enhance the discovery of secondary metabolite pathways by selective amplification of these followed by heterologous expression.
Assitant Professor, Director of Molecular Microbiology
My laboratory focuses on identifying viral members of the human microbiome and in identifying their contributions to human health and disease. We are working on understanding the ecology of viruses and their consequences for our close contacts, characterizing their contributions to community antibiotic resistance, and developing model systems to understand how they respond to perturbations.
Role of microbiome in virus associated CNS impairment, neuronal autoimmunity, aging and neurodegenerative diseases
Director, Professor of Medicine
As Director of the Center for Renal Translational Medicine and the Institute of Metabolomic Medicine (IMM), our expertise is relevant to the Center for Microbiome Innovation. With P. Dorrestein (Co-Director, IMM) and the JCVI, we have identified a key role for mitochondria and the microbiome for diabetic complications. Expertise: targeted metabolomics, mass spec imaging, biostats, bioinformatics.
MD, AGAF, Clinical Director Pediatric Gastroenterology, Director Neurogastroenterology and Motility Center,
Dr. Mousa is leading a national initiative in evaluating the interaction between gut flora and the enteric nervous system (ENS). She has an open biorepository project banking and analyzing the ENS (tissue samples) and the microbiome in patients with motility disorders.
Dr. Mousa is also collaborating with Dr. Knight on evaluating the development of gut flora and enetric system in neonates.
The Thackray lab is interested in understanding the role of the microbiome in Women's Health and reproductive disorders. We recently demonstrated that metabolism and the gut microbiome is altered in a mouse model of polycystic ovary syndrome (PCOS) using 16S rRNA gene sequencing and metabolic profiling. We are currently investigating whether the gut microbiome plays a causal role in PCOS and the mechanisms involved. We are also interested in using an endocrinology perspective to understand sex-dependent effects on microbiome/host interactions.
The S. Golden lab focuses on the mechanism and physiological consequences of prokaryotic circadian clocks and on cyanobacterium-eukaryote interspecies interactions. Expertise spans microbial genetics, biophysical measurements of protein interactions, real-time monitoring of gene expression, and metabolomics.
We apply culture-independent molecular, and 16S rDNA and shotgun metagenome sequencing approaches to study the relationships among Leptospira ecology and evolution, and spatial patterns of human disease. This, within the context of prospective cohort studies in at-risk populations in the Peruvian Amazon region of Iquitos.
Professor and Director of California Center for Algae Biotechnology
I work on orally available proteins and their impact on gut and overall health in both animals and humans.
MD PhD, Professor of Pediatrics, Chief, Division of Pediatric Nephrology
Pediatrics, Pediatric Nephrology
Chronic kidney disease(CKD) is associated with ‘leaky gut’, and bacterial DNA translocation; resulting in systemic inflammation. Stool operational taxonomic units (OUTs) from Brachybacterium, Catenibacterium, Enterobacteriaceae, among others, are markedly increased in CKD. We are currently studying the role of the NLRPs inflammasome on intestinal microbial flora and cachexia in CKD mice.
Professor of Marine Biology,SIO Department Chair
Genomics of unicellular phototrophs especially cyanobacteria and small eukaryotes. Understanding how these organisms interact in mixed communities such as found in microbiomes.
Professor of Medicine, Director, NAFLD Research Center
Clinical phenotyping in nonalcoholic fatty liver disease, twin studies and familial cirrhosis studies.
My lab was the first to show the role of intestinal barrier disruption in the pathogenesis of colorectal cancer. We have also uncovered tumorsuppressive mechanisms related to immune system-gut microbiota interactions.
Dr. Fraley is pioneering the development of microbial detection technologies that can can discover, identify, and quantify organisms at the single cell level within complex populations of microbes. She is also interested in human-bacterial interactions mediated by small RNAs.
Professor of Intelligent Systems, Statistical Signal Processing and Robotics; Director Calit2/Qualcomm Institute Pattern Recognition Laboratory
Electrical and Computer Engineering
Pattern Recognition and Machine Learning for analysis of the Microbiome and detection/prediction of Microbiome-related indicators of health and illness. Development of high-throughput low-power. VLSI chips supporting real-time Pattern Recognition in wearable/embeddable sensors.
Bioengineering, Computer Science & Engineering, Cellular & Molecular Medicine
In the past I have worked on bioinformatics related with the microbiome. My current research interests are in systems biology and systems medicine.
Degradomics; Proteomics; Biofluid assay development; Development of anti-parasitic and anti-fungal agents; Characterization and chemical inhibition of proteases at host-pathogen interface; Microbial Biofilms, Neutrophil Proteases.
Pharmaceutical Sciences, Marine Biotechnology and Biomedicine
The Moore research laboratory focuses on the discovery, characterization, and application of marine bacterial metabolites in human health. We employ a multi-disciplinary genomics-guided discovery approach that has resulted in the development of new genome mining methods and the rational discovery of new chemical entities and enzyme biocatalysts from marine microbial/host systems.
Associate Professor, Director of Step Family Cardiac Wellness and Rehabilitation Center
I am collaborating with Dr. Rob Knight on examining how the microbiome impacts treatments and outcomes in patients with cardiovascular disease. Assessing changes in the microbiome in patients with congestive heart failure and how the microbiome may predict readmission for heart failure. Examining how dietary changes impact the microbiome in patients after myocardial infarction.
Kyung (Kay) Rhee
Associate Professor, Medical Director Medical Behavioral Unit Rady Children's Hospital, Research Director Hospital Medicine
We are examining the change in pediatric microbiomes associated with weight loss, changes in diet, and the use of probiotics. We are also interested in the development of the microbiome in early childhood and how different diets and environments affect this. Finally we are examining how differences in microbiome composition may affect other disease states such as anorexia and anxiety.
Associate Professor, CoDirector Center for Health Promotion and Health Equity
Family Medicine and Public Health
Main areas of expertise are nutrition, epidemiology, clinical trials, and health behavior change. Dr. Anderson is the co-Director of the Center for Community Health Promotion and Health Equity and conducts research relevant to under-served populations.
Professor and Chairman
Discovery and analysis of the mechanism(s) of action by which bacteria resident on the skin surface influence epithelial and immune cell functions. Understanding mechanisms by which the host innate immune system regulates the composition of the microbiome.
Professor of Medicine
The inflammatory bowel diseases (IBD) are triggered by an overactive immune response to the intestinal microflora. We aim to understand whether the exacerbated inflammation observed in integrin beta7 mice deficient mice and on a subset of patients IBD receiving integrin-blocking antibodies is triggered by an imbalance of the intestinal microflora.
Distinguished Professor of Oceanography and Pharmaceutical Science
Center for Marine Biotechnology and Biomedicine
The Fenical lab has more than 25 years experience in the cultivation of bacteria and fungi in small and large scale. Included was a study to evaluate the antibiotic produced by Staphylococcus epidermitis.
Professor and Chair
Chemistry & Biochemistry
Infectious diseases caused by microbial pathogens exert a huge toll on human welfare. To find ways to intervene, we are studying how proteins produced by microbial pathogens interact with human proteins, and how these interactions lead to infectious disease. To attack this problem, we use a combination of structural biology, biochemistry, and reverse genetics.
Associate Professor, CCMS Executive Director
Construction, crowdsourced annotation and curation of metabolomics and proteomics mass spectrometry datasets and knowledge bases supporting microbiome research. Algorithms and computational infrastructure to analyze and correlate microbiome data from millions of private and public LCMS runs in hundreds of datasets in our GNPS resource at http://gnps.ucsd.edu.
Distinguished Professor, Dean and Associate Vice Chancellor of Translational Medicine, Director of CTRI
CTRI biorepository assists with collection of microbiome samples for multiple investigators.
Kumar laboratory has been interested in the identification and characterization of novel cellular and molecular mechanisms in immune regulation mediated by innate-like NK T cell subsets as well as regulatory CD4 and CD8 T cell subsets in inflammatory and autoimmune diseases. We have been exploring how gut microbiome influences these immune regulatory mechanisms to control inflammation.
Cell and Developmental Biology
The Huffaker lab examines the role of endogenous plant innate immune signaling pathways in mediating interactions with pathogenic and endophytic microbes. Our research examines the questions of how plants recognize other organisms, how plant immune programs are regulated and how these events affect individual and community interactions.
Family Medicine & Public Health
My expertise is in assessing the built environment. We are currently starting to collect gut microbiome data in one of our studies. We hope to relate outdoor time to health of the gut.
Professor, Director, Center for Veterinary Sciences and Comparative Medicine
My expertise is in mucosal immunology and examining the effect of gastrointestinal infection and the local microbiome on host responses.
Cell and Developmental Biology
Regulation, biosynthesis and metabolomics of microbial elicited plant defenses as an untapped resource for diverse antimicrobial natural products. Use of crop plants as relevant models to understand the role of host biochemical responses in mediating predominant and agriculturally relevant microbiome-rhizosphere interactions.
Adjunct Professor, Director of Genetics/Kleberg Chair at SD Zoo ICR
Evolution, Behavior, and Ecology
Evaluation of convergence in composition of microbiome communities across species, especially as related to disease and reproduction.
Professor, Endowed Chair Translational Research
Collecting initial urine samples from patients with recurrent urinary tract infections and being treated with antibiotics plus hyperbaric oxygen. Wish to determine effect hyperbaric oxygen therapy has on urinary microbiome in this selected patient population.
MD, PhD, Professor
Molecular biology of macrophage host parasite interaction including macrophage-microbiota interaction in innate and adaptive immune responses in pediatric disease.
Associate Professor of Medicine
Our lab is focused on mechanisms underlying T lymphocyte fate specification and function in the context of microbial infections and inflammatory bowel disease. We are interested in exploring the interactions between the mucosal immune system and the microbiome.
Gordon Saxe, MD, PhD
Director of Integrative Nutrition, Chair, Krupp Endowed Fund
Family Medicine and Public Health
Preventive Medicine, Nutritional Epidemiology, dietary intervention clinical trials, medicinal foods, and natural products.
Visual Arts, Arthur C. Clarke Center for Human Imagination
I create interactive visualizations of large scale, evolutionary, symbiotic, phenomena. This work can provide a computational model to aid understanding of how microbiome ecosystems can change over time.
Our research focuses on single-cell genomics, including method development and applications. We were funded by the NIH Human Microbiome Project in 2009 for method development related to single-cell genome sequencing. We also have been developing efficient and unbiased method for metagenomics sequencing of environmental microbial samples with very limited materials.
Distinguished Chair in Atmospheric Chemistry, Director, Center for Aerosol Impacts on Climate and the Environment
Chemistry and Biochemistry and Scripps
Studies of microbes in the ocean and the mechanisms by which they become transferred to the atmosphere. Field investigation into how microbes impact clouds and precipitation processes.
Pharmacology and Pharmacy
A critical next step in understanding the impact of the microbiome on health is the characterization of microbial biochemistry. This will allow for a better understanding of the meta-proteome consisting of the human host, the microbiota, and alterations of homeostasis by invading pathogens. In combination with microbiology techniques, we employ quantitative multiplexed proteomics to this end.
Jerrold Olefsky, MD
Associate Dean for Scientific Affairs, Professor of Medicine
Endocrinology and Metabolism
We have performed microbiome sequencing in lean and obese mice with and without a variety genetic manipulations. We find that our KO mice display a marked change in microbiome composition. In addition, we have identified a peptide product of the bacteria overrepresented in the obese microbiome that leaks into the bloodstream, directly causes a hyperglycemic insulinopenic phenotype.
Psychiatry, Family Medicine and Public Health
My expertise is in the design and execution of empirical studies to inform ethical issues raised by new biomedical technologies. I leverage methods from clinical trial design and the social sciences. Major projects have included studies on topics such as direct-to-consumer genomics, clinical/personal genome sequencing, wearable biosensors, and personal health big data.
Our lab is investigating intestinal infections in the nematode C. elegans, which has intestinal cells that share structural similarities with human cells. In particular we study a natural pathogen of C. elegans named Nematocida parisii, which is an intracellular fungal-related pathogen that belongs to the Microsporidia phylum. We also study surveillance immunity against bacterial pathogens.
Behavioral Genomics Endowed Chair and University Professor, University of California and Distinguished Professor of Psychiatry and Director, Center for Behavioral Genomics, Department of Psychiatry, University of California, San Diego
Dr. Tsuang is interested in the connection between the microbiome and neuropsychiatric disorders.
Professor of Medicine
Airway Microbiome research, Airway Metabolomics, Airway Metagenomics, Cystic Fibrosis. Correlation of clinical metrics and phenotypes with airway metagenomic, metabolomic and genomic datasets.
Uncovered coordination of metabolic states among distant bacteria within biofilm communities. Discovered electrical cell-to-cell signaling in microbial biofilm communities.
Senior Associate Dean for Healthy Aging and Senior Care, Estelle and Edgar Levi Chair in Aging, Distinguished Professor of Psychiatry and Neurosciences, Director, Sam and Rose Stein Institute for Research on Aging
Although I am not a microbiome researcher per se, I have strong interest in biomarkers of aging in the general population as well as in people with serious mental illnesses, such as those with schizophrenia as well as those infected with HIV. We have a variety of biomarker data in our research subjects. It will be very helpful to obtain microbiome data in these subjects.
Lawrence (Lance) Prince
The Prince laboratory studies development of the innate immune response. Using both human and mouse models, we investigate macrophage development and function. Relevant to prematurity and preterm birth, our laboratory is examining how early exposures to microbial products affects immune function in fetal and neonatal cellular niches.
Distinguished Professor of Medicine and Cellular & Molecular Medicine, Co-Director, UCSD/Salk Center for Academic Research and Training in Anthropogeny (CARTA), Co-Director, Glycobiology Research and Training Center (GRTC), Adjunct Professor, Salk Instit
Departments of Medicine and Cellular & Molecular Medicine
Current research efforts focus on fundamental studies of cell surface sugars called sialic acids and their roles in biology, evolution, and disease–particularly multiple differences between humans and our closest evolutionary cousins, which are relevant to understanding unique aspects of human biology and disease. Sialic acids are both metabolized and expressed by components of the microbiome.
Dept of Pediatrics
At the Kawasaki Disease Research Center, we are testing hypotheses about the etiology of KD. One initiative is metagenomic sequencing of the throat flora of KD patients and febrile control children. this is being pursued in collaboration with Prof. Michael Levin at Imperial College, London. The second initiative is related to examining the microbiome of tropospheric winds associated with KD.
Associate Professor of Medicine
Global Researchers working with large cohorts of HIV infected patients both adult and pediatric, within the US, Mozambique , South Africa and Mexico. Cohorts include High Risk Pre-Exposure Prophylaxis , newly infected anti-retroviral naive (ARV) and ARV experienced subjects. Extensive lifestyle data obtained by continuous monitoring and metabolic profiles available on most subjects.
Study immune regulation at the mucosal interface. Specifically, our research aims at exploring the dynamic regulation of key cellular and molecular players, regulatory T (Treg) cells and microRNAs (miRNAs), respectively, in maintaining immune homeostasis in the presence or absence of commensal and pathogenic microbes.
Professor of Pediatrics, Medicine, and Cellular and Molecular Medicine
Our laboratory studies the main transporters regulating plasma levels of microbiome-derived small molecules. These transporters (OAT1 and others), whcih we study in vitro and in vivo, mediate movement of small molecules into body tissues and body fluid compartments (e.g., urine, CSF). Some of the transported microbiome-derived molecules act as "uremic toxins" in kidney disease.
Our research focuses on immune regulation of tissue homeostasis. We are interested in understanding how gut microbiome and derived metabolites impact the development of autoimmune diseases. One ongoing collaborative project is to dissect obesity-associated gut microbiota and metabolic pathways in patients with type 1 diabetes.
My clinical expertise lies in the medical and surgical treatment of chronic rhinosinusitis. Chronic rhinosinusitis is an inflammatory disorder in part a function of a dysbiosis of the sinonasal cavity. My research niche is in describing and refining outcomes of interventions for chronic rhinosinusitis.
Pathogens and their hosts are locked in a constant struggle for evolutionary dominance, resulting in escalating molecular ‘arms races’. Our research combines these evolutionary principles with virology and mechanistic biochemistry to discover host the host immune system has evolved to defend against pathogens and how pathogens counter-evolve to defeat host immunity.
Assistant Professor, Cancer Immunotherapy Program, Experimental Therapeutics, Thoracic Oncology
Predictive biomarkers related to cancer immunotherapy, with particular interest in microbiome editing to facilitating response to immune checkpoint blockade.
Chief, Division of Infectious Diseases
Dept of Pediatrics, Division of Infectious Diseases
As a pediatric infectious diseases physician, my role has been to investigate therapy, primarily for bacterial infections. Recognizing limitations of classical microbiology, I am currently collaborating in an investigation of the microbiome/metabolome in children with cystic fibrosis.
Professor of Clinical Reproductive Medicine, Division Director, Fellowship Program Director
I am currently involved in projects aimed at characterizing the urogenital microbiome in women with lower urinary tract symptoms including incontinence and recurrent urinary tract infections.
Associate Professor In Residence
Psychiatry, Stein Institute for Research on Aging
I am particularly interested in the link between brain and behavior and the potential mediating role of inflammation and immune factors and possible interaction with the microbiome.
Carbohydrate antigens and their roles in microbe-host co-evolution. Virus-mucus interactions. Primate innate immune receptors that target self and microbial non-self glycans. Anti-glycan immunity in the male and female reproductive tracts. Comparative primate milk oligosaccharides.
California Institute for Innovation and Development
Technology commercialization with emphasis on translation of early stage technologies from the laboratory to the market.
Assistant Professor of Pediatrics
As a neonatologist, I am interested in establishing collaborations with other scientists to facilitate research into how the microbiome is established and develops in the neonate. Currently, I am working with Dr. Stephanie Fraley to develop nucleic acid sequencing technology with machine learning for the rapid and accurate diagnosis of neonatal sepsis.
Associate Professor Emeritus
I have broad familiarity with nonhuman primate behavioral ecology and natural history, potentially useful for interpretation of microbiome adaptations.
Professor, Director Research, Division of Gastroenterology
I am a clinician-scientist gastroenterologist with longstanding interests in the mucosal-luminal interface of the esophagus, stomach, small and large intestine including interactions of food, microbes and the mucosa with a focus on the epithelium.
San Diego Supercomputer Center
Genomic analysis, including variant calling, de novo assembly, and phylogenetics, high-performance computing.
Associate Teaching Professor
Introducing undergraduate students to the concept of microbiomes, their complexity, importance, and to methods of study
We have expertise in cyanobacterial growth, genetics, gene regulation, synthetic biology, and transcriptomics. We routinely use fluorescent reporter genes to monitor gene expression in individual cells in a population. Some of our recent research is focused on using a random barcode labeled transposon library and deep sequencing to identify cyanobacterial genes related to cyanobacterial grazing.
Scripps Institution of Oceanography
Our research environments include high elevation oligotrophic lakes and marine pelagic environments. Our previous focus has been on functional gene and microbial species composition analyses in the context of chemical gradients and organic compound transformations. More recently we have also been examining metatranscriptomes and metagenomes from both lake and marine environments.
Marine Biology Research Division
Development of computational tools and analytical pipelines for the assembly, phylogenetic binning, functional annotation, and community analysis of microbial genomes and host-associated metagenomes.
Jennifer Smith and her team of students and postdocs are marine community ecologists who focus on how humans impact coastal ecosystems. The Smith lab uses a variety of tools including field and laboratory experiments to determine how different factors influence benthic community structure, organismal ecophysiology, species diversity and microbial ecology from coral reefs around the world.
Laura Crotty Alexander
Host defenses and airway microbial pathogenesis. How inhalation of cigarette smoke and e-cigarette vapor change underlying microbiomes in the host, and the host-pathogen interaction.
Professor, LJI / Adj. Professor UCSD
Vaccine Discovery/ UCSD SOM Medicine
We study recurrent tonsillitis in humans, which is caused by a bacterial infection and may be associated with microbiome changes. We also extensively study human CD4 T cell and B cell biology in the context of infectious diseases and vaccines.