More than 130 UC San Diego professors and research scientists have elected to join the Center for Microbiome Innovation since its launch in 2016. 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.


Click here to learn more about becoming a faculty member or affiliate




Andrew Bartko

Executive Director, Center for Microbiome Innovation


Dr. Bartko’s goal is to inspire, nurture, and sustain vibrant collaborations between UC San Diego’s microbiome experts and industry partners in the life science, nutrition, energy, information technology, clinical and healthcare industries. Specifically, his aim is to focus on creating and commercializing innovative technologies to accelerate microbiome discoveries and healthcare breakthroughs across academic and industry collaborations.

Andrew Bartko

Rob Knight

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.

Knight Lab

Watch Rob's 2018 presentation in Tokyo (LINK-J symposium) on YouTube


Pieter Dorrestein

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.

The Dorrestein Lab

Pieter Dorrestein

Rachel Dutton

Biological Sciences

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.

The Dutton Lab

Jack Gilbert


Pediatrics, Scripps Institution of Oceanography

Ecology, evolution, and metabolic dynamics of microbial ecosystems from environments including built environments, oceans, rivers, soils, air, plants, animals, and humans.

Gilbert Lab

Jeff Hasty

Biological Sciences and Bioengineering

Synthetic biology and biosensor design. Engineering microbes to serve as biosensors; understanding microbial community dynamics.

UCSD Biodynamics Lab


Terry Hwa


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.

Laboratory for Quantitative Microbiology

Paul Jensen

Scripps Institution of Oceanography

Comparative genomics and microbial chemical ecology for discovery of natural products from marine microbes.

Jensen Website

Victor Nizet

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.

Nizet Lab

Bernhard Palsson


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.

Systems Biology Research Group

Pavel Pevzner

Computer Science and Engineering

Genomic assembly techniques for microbiome research. Drug discovery and identification of useful compounds already in nature.

Center for Computational Mass Spectrometry

Manuela Raffatellu



Professor Raffatellu has experise in immunology, microbiology and infectious diseases. Her team is investigating microbial pathogenesis and mucosal immunity using gnotobiotic mice.

Raffatellu Lab

Julie Ryu

Clinical Director Pediatric Respiratory Medicine, Physician Informaticist Rady Children's Hospital


Clinical research in pediatric patients, clinical informatics.

Julie Ryu

Bill Sandborn, MD


Clinical trials for inflammatory bowel disease. Fecal microbiota transplant (FMT) procedures.

Inflammatory Bowel Disease Center

Larry Smarr

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.

Larry Smarr Website

Karsten Zengler

Bioengineering, Pediatrics

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.

Zengler Website

Faculty Members

Eric Allen

Associate Professor

Marine Biology, Molecular Biology

Bioinformatic analysis of metagenomes; bacterial genetics; microbial lipid biosynthesis.

Allen lab

Ilkay Altintas

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.

Workflows for Data Science Center of Excellence

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.

The Amaro Lab

Rommie E. Amaro

Cheryl Anderson

Associate Professor, Co-Director 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.

Anderson Lab

Vineet Bafna

Computer Science and Engineering

Advanced genomic and proteomic research for deeper understanding of microbiome function.

Vineet Bafna Website

Nuno Bandeira

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.

Center for Computational Mass Spectrometry

Kim Barrett

Distinguished Professor


General interest in the role of the microbiome in digestive diseases; publications on probiotics as well as gut-brain-microbiome axis; infectious diarrhea; gut transport and barrier function.

Kim Barrett Profile

Douglas Bartlett


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.

Doug Bartlett

Ethan Bier


Cell and Developmental Biology

We are beginning to look at the role of bacterial toxins in altering the microbiome.

Bier Lab

Cinnamon Bloss

Assistant Professor

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.

The Bloss Lab

Lars Bode

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.

Bode Lab

Brigid Boland

Assistant Professor


I primarily have translational, clinical, and basic research expertise in inflammatory bowel disease. I am collaborating with the Knight and Dorrestein labs on multiple microbiome in IBD projects.

Brigid Boland Profile

Jeff Bowman

Assistant Professor

Scripps Institution of Oceanography

My lab is focused on several different aspects of microbial ecology, with a focus on marine microbial ecology in coastal and polar environments. We use a variety of sequence-based approaches (amplicon, metagenomics, genomics, and metatranscriptomics) in combination with ecophysiology data and models to answer questions on microbial ecosystem function.

Bowman Lab

Sheldon Brown

Professor, Director

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.

Arthur C. Clarke Center for Human Imagination

Sara Browne

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.

Sara Browne Profile

Linda Brubaker

MD, Professor

Obstetrics, Gynecology and Reproductive Sciences

Urobiome (the human urinary microbiota/microbiome and related topics).

Linda Brubaker Profile

Jane Burns


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.

UCSD Kawasaki Disease Research Center

John Chang

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.

Chang Lab

Hiu Chu

Assistant Professor


The Chu lab is interested in the complex interactions between the trillions of diverse microbes and the host in the mammalian gastrointestinal tract. We are focused on the fundamental role of commensal microbiota in the education, induction, and maintenance of the host immune system during health and disease.

Chu Lab

Douglas Conrad

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.

Doug Conrad Profile

Matt Daugherty

Assistant Professor

Molecular Biology

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 how the host immune system has evolved to defend against pathogens and how pathogens counter-evolve to defeat host immunity.

Daugherty Lab

Adam DeConde

Assistant Professor


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.

Adam DeConde Profile

Donald Durden

MD, PhD, Professor


Molecular biology of macrophage host parasite interaction including macrophage-microbiota interaction in innate and adaptive immune responses in pediatric disease.

Donald Durden Profile

Peter Ernst

Professor, Director, Center for Veterinary Sciences and Comparative Medicine

Pathology, Medicine

My expertise is in mucosal immunology and examining the effect of gastrointestinal infection and the local microbiome on host responses.

Ernst Lab

William Fenical

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.

Fenical Lab

Gary Firestein

Distinguished Professor, Dean and Associate Vice Chancellor of Translational Medicine, Director of CTRI

Medicine, CTRI

CTRI biorepository assists with collection of microbiome samples for multiple investigators.

Firestein Lab

Stephanie Fraley

Assistant Professor


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.

Fraley Lab

Wenxian Fu

Assistant Professor


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.

Pediatric Diabetes Research Center (PDRC)

Richard Gallo

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.

Gallo Lab

Olivier George

Associate Professor


Dr. George has multiple lines of research on the interaction of the microbiome with alcohol and drugs of abuse. Specific studies investigates the effect of alcohol drinking and oxycodone self-administration on the microbiome and the effect of microbiome manipulations with antibiotics on addiction-like behaviors

George Lab

Lena Gerwick

Research Scientist

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.

Gerwick laboratory

Partho Ghosh

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.

Partho Ghosh Lab

Susan Golden

Distinguished Professor

Molecular Biology

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.

Susan Golden

David Gonzalez

Assistant Professor

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.

The Laboratory of David J. Gonzalez

Gabriel Haddad

Professor and Chair


Cardiovascular health and disease and hypoxia-relation to the microbiome.

Haddad Lab

Nan Hao

Assistant Professor

Molecular Biology

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.

The Hao lab

Robert Heaton

Distinguished Professor of Psychiatry


I am a neuropsychologist with extensive experience in the study of neuroAIDS.

HIV Neurobehavioral Research Center

Suzi Hong

Associate Professor

Psychiatry, Family Medicine and Public Health

Immune responses to microbial stimulation and their implications in mood, emotion, cognition, and behavior.

Hong PNI Lab

Alisa Huffaker

Assistant Professor

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.

Huffaker Lab

Trey Ideker


Medicine, Bioengineering, Computer Science

Our goal is to develop a new type of medicine based on knowledge of the complete physical and functional wiring of the cell, and systems biology. ​We are developing new ways of mapping these wiring diagrams directly from genome-scale and microbiome measurements (genomic, proteomic, and metabolomic) and for using these maps to translate the increasingly complex data gathered from patients to predict disease outcomes and develop better treatments.

Ideker Lab

Jules Jaffe

Research Oceanographer

Marine Physical Lab

Oceanic collection methodologies for micro-biome exploration and research.

Jaffe Lab for Underwater Imaging

Mohit Jain

Assistant Professor

Medicine, Pharmacology

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.

Jain Laboratory

Dilip Jeste

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

Psychiatry, Neurosciences

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.

UC San Diego Center for Healthy Aging

Deborah Kado



As the San Diego site principal investigator for the Osteoporotic Fractures in Men (MrOS) Study, we have followed 5,994 men >65 years of age from six sites across the United States since 2000-02. In 2015-16, my colleagues and I have collected 980 stool samples from these men that are available for analyses to examine novel associations between the gut microbiome and a variety of health outcomes.

Exercise Physical Activity Resource Center

Michael Karin

Distinguished Professor


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.

Lab of Gene Regulation and Signal Transuction

Ken Kreutz-Delgado

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.

Calit2/Qualcomm Institute Pattern Recognition Laboratory

Sergey Kryazhimskiy

Assistant Professor

Ecology, Behavior and Evolution

Microbial experimental evolution, population genetics, systems biology, genomics.


Vipin Kumar



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.

Laboratory of Immune Regulation

Michael Kurisu

D.O., Director - Center for Integrative Medicine, Clinical Director - Osteopathic Center San Diego, President - Precision Healthcare Ecosystem, Director and Founder - Project Apollo

Family Medicine and Public Health

We are creating an N=1 self care precision integrative program using micro biome analysis as one data set to track longitudinally care for health.

Project Apollo

Carolyn Kurle

Assistant Professor

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.

Kurle Lab

Louise Laurent

Associate Professor

Reproductive Medicine

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.

Laurent Lab

Scott Lippman

Director, Senior Associate Dean,Associate Vice Chancellor for Cancer Research and Care

Moores Cancer Center, Medicine

Cancer prevention, biology of pre-malignancies.

Scott Lippman

Rohit Loomba

Professor of Medicine, Director, NAFLD Research Center


Clinical phenotyping in nonalcoholic fatty liver disease, twin studies and familial cirrhosis studies.

Loomba Laboratory and NAFLD Research Center

Li-Fan Lu

Assistant Professor

Molecular Biology

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.

Lu Lab

Cressida Madigan

Assistant Professor

Biological Sciences

We're interested in understanding how infectious microbes regulate functions of the nervous system. Often, the immune system is a key mediator of these interactions. To observe and genetically manipulate host-pathogen interactions in an intact animal, we use a unique model: the transparent larvae of zebrafish.

Madigan Lab

Robert Mak

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.

Robert Mak Profile

Prashant Mali

Assistant Professor


Mining, characterization and engineering of microbial CRISPR-Cas systems.

Mali Lab

Michael Matthias

Assistant Professor


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.

Michael Matthias

Stephen Mayfield

Professor and Director of California Center for Algae Biotechnology

Molecular Biology

I work on orally available proteins and their impact on gut and overall health in both animals and humans.

California Center For Algae Biotechnology

James McKerrow

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.

Institute for Engineering in Medicine

Christian Metallo

Assistant Professor


Metabolic flux analysis, metabolomics.

Metabolic Systems Biology

Justin Meyer

Assistant Professor

Ecology, Behavior, and Evolution

Coevolution of hosts with their microbiomes. Microbiome manipulation using synthetic bacteriophage.

Meyer Lab

Siavash Mirarab

Assistant Professor

Electrical and Computer Engineering

Computational methods for taxon identification and for taxonomic profiling of metagenomic samples. Phylogenetics, multiple sequence alignment, and phylogenomics.

Mirarab Lab

Bradley Moore


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.

Moore Laboratory for Marine Microbial Biosynthesis

Hayat Mousa

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.

Neurogastroenterology and Motility Lab

Anna Di Nardo



Skin commensal analysis and interaction with keratinocytes, fibroblasts and mast cells; skin commensals and tolerance; skin commensals and mast cell maturation.

Di Nardo Lab

Tanya Nguyen

Assistant Professor


Our research is focused on the gut microbiome in aging and serious mental illnesses, such as schizophrenia, and its role in the physiological, clinical, and cognitive presentation of these populations. We study the relationships between the microbiome, aging biomarkers (e.g., inflammation), and cognition that will further advance understanding of the gut-brain axis.

Sam and Rose Stein Institute for Research on Aging

Sanjay Nigam

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.

Sanjay Nigam Profile

Anthony O'Donoghue

Assistant Professor

Pharmaceutical Chemistry

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.

O'Donoghue Lab

Marygorret Obonyo

Assistant Professor


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.

Marygorret Obonyo Profile

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.

Olefsky Laboratory

Brian Palenik

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.

Palenik Lab

Abraham Palmer

Professor and Vice Chair for Basic Research


We are examining microbiome in a cohort of more than 5,000 genetically diverse rats that have been deeply phenotyped for behavioral and physiological traits. We are performing genome wide association analysis (GWAS) for OTUs and are also testing for correlations between OTUs and behavioral and physiological traits.

Palmer Lab

Kevin Patrick


School of Medicine/Calit2

Kevin Patrick, MD, MS is Professor of Family and Preventive Medicine at the University of California, San Diego, Editor-in-Chief of the American Journal of Preventive Medicine and Director of the Center for Wireless and Population Health Systems at the Qualcomm Institute at UCSD. His research explores how to use mobile and social technologies to measure and improve environmental exposures and health-related behaviors for individuals and across populations.

Kevin Patrick Profile

Martin Paulus

Adjunct Professor


Studying the relationship between gut, skin, and mouth microbiome and mood or anxiety disorders in individuals with acute psychiatric symptoms.

Laureate Institute for Brain Research

Kit Pogliano

Biological Sciences

Application of multiple omics techniques to understand how to reshape microbial communities. Synthetic biology at the whole-microbiome level.

Pogliano Lab

Kimberly Prather

Distinguished Chair in Atmospheric Chemistry, Director, Center for Aerosol Impacts on Chemistry of 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.

Prather group

David Pride

Assistant 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.

Pride Laboratory

Lawrence (Lance) Prince

Associate Professor


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.

Prince Lab

Brinda Rana

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.

Rana Lab

Aspen Reese

Assistant Professor

Biological Sciences

Ecology of host-microbe interactions. Contributions of microbial plasticity to host evolution with a focus on domestication and industrialization. Wild mouse models for gut microbiome studies.

The Reese Lab

Diana Rennison

Assistant Professor

Biological Sciences

I am interested in the evolutionary ecology of host-microbiome interactions. My lab studies the evolutionary processes that shape gut microbial diversity among vertebrate hosts occupying divergent niches.

Rennison Lab

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.

Center for Healthy Eating and Activity Research

Jesus Rivera-Nieves

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.

Rivera Lab

David Rosenberg

Visiting Professor


My focus is using sophisticated imaging-genetic studies in childhood onset neuropsychiatric disorders such as OCD, and examining the neural correlates of the microbiome as it may relate to/predict course of illness.

Brain Research of Neuropsychiatric Disorders Lab

Tajana Rosing


Computer Science

I have worked with Rob Knight for the last few years on accelerating microbiome related data analysis and would like to contribute in this way to the research at CMI.


Oliver Ryder

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.

Conservation Genetics at SD Zoo

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.

Gordon Saxe, MD, PhD

Eric Schmelz


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.

The Schmelz Lab

Bernd Schnabl

Associate Professor

Medicine, Gastroenterology

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.

Schnabl lab

Dorothy Sears

Associate Professor

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.

Dorothy Sears Lab

Jonathan Shurin


Ecology, Behavior and Evolution

I am an aquatic ecologist studying how climate affects the interactions between micro-organisms and other members of their food webs, and their roles in chemical cycles and ecosystem processes.

Shurin lab

Davey Smith



I have studied and am interested in how the human microbiome is associated with HIV disease pathogenesis and immune function, including end organ damage.

Center for AIDS Research

Shankar Subramaniam


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.

Bioinformatics and Systems Biology

Gurol Suel


Molecular Biology

Uncovered coordination of metabolic states among distant bacteria within biofilm communities. Discovered electrical cell-to-cell signaling in microbial biofilm communities.

Suel Lab

Pam Taub

Associate Professor, Director of Step Family Cardiac Wellness and Rehabilitation Center

Cardiovascular Medicine

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.

Taub Cardiovascular Research Lab

Varykina Thackray

Associate Professor

Reproductive Medicine

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.

Thackray Lab

Emily Troemel



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.

Troemel Lab

Ming Tsuang

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.

Center for Behavioral Genomics, Department of Psychiatry, University of California, San Diego

Ajit Varki

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.

Varki Lab

Joseph Wang

Distinguished Professor


Developing engineering tools (biosensors and nanomachines) for advancing microbiome RD.

Nanobioelectronics Laboratory

Nick Webster

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.

Webster Lab

Nadir Weibel

Research Assistant Professor

Computer Science and Engineering

Interactive visualization and analysis of network-based interactions.

Human-Centered and Ubiquitous Computing Lab

Amir Zarrinpar

Assistant Professor

Internal Medicine

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.

Kun Zhang

Associate Professor


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.

Laboratory of Integrative Genomics

Sheng Zhong



Microbiomes in liquid biopsy including serum and saliva.

Zhong Lab

Faculty Affiliates

Laura Crotty Alexander

Assistant Professor


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.

Laura Crotty Alexander Profile

Lihini Aluwihare


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.

Aluwihare Lab

Maria Rosario (Happy) Araneta

Professor of Epidemiology

Family Medicine & Public Health

Diabetes, weight phenotype, preterm birth, HIV/AIDS, fetal origins of disease.

Division of Epidemiology

Scott Baden



High performance computation.

Scientific Computation/Computer Languages and Systems Software

John Bradley

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.

John Bradley

Lakshmi Chilukuri

Associate Teaching Professor

Molecular Biology

Introducing undergraduate students to the concept of microbiomes, their complexity, importance, and to methods of study

Lakshmi Chilukuri Profile

Shane Crotty

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.

Shane Crotty

Sheila Crowe

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.

Sheila Crowe Profile

Lisa Eyler

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.

Biopsychological Research on Aging Inflammation and Neuropsychiatry (BRAIN) Lab

Pascal Gagneux



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.

Gagneux Lab

Chris Glass



Influence of antibiotic treatment on severity of viral infection.

Glass Laboratory

James Golden


Molecular Biology

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.

J. Golden lab

Shelley Lawrence

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.

Nizet Lab

Emily Lukacz

Professor of Clinical Reproductive Medicine, Division Director, Fellowship Program Director

Reproductive Medicine

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.

Emily Lukacz

Michael McCarthy

Assistant Professor


Biological basis of psychiatric disorders, biological predictors of treatment outcomes in psychiatric disorder

Clinical Chronobiology

Jill Mesirov

Professor, Associate Vice Chancellor Health Sciences Computing

Genetics, Computer Science and Engineering

Bioinformatics, Computational Biology.

Mesirov Lab

Jim Moore

Associate Professor Emeritus


I have broad familiarity with nonhuman primate behavioral ecology and natural history, potentially useful for interpretation of microbiome adaptations.

Ugalla Primate Project

Sandip Patel

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.

Sandip Patel

Wayne Pfeiffer

Distinguished Scientist

San Diego Supercomputer Center

Genomic analysis, including variant calling, de novo assembly, and phylogenetics, high-performance computing.

San Diego Supercomputer Center

Sheila Podell

Bioinformatics Programmer

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.

Sheila Podell Profile

Lada Rasochova

Executive Director

California Institute for Innovation and Development

Technology commercialization with emphasis on translation of early stage technologies from the laboratory to the market.


Jennifer Smith

Associate Professor

Marine Biology

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.

Smith Lab

Glenn Tesler


Mathematics, Computer Science and Engineering, Bioinformatics

Helped develop the algorithms for the single-cell assembler SPAdes, the assembly quality evaluation tool QUAST, and related software.

Glenn Tesler Profile

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