Gastroenterology & GI Physiology

Amir Ardeshir DVM, MPVM, PhD

(See also: Immunology/Infectious Diseases, Microbiology/Parasitology, Wildlife/Exotic Animal Medicine, Non-Human Primate Medicine)

Dr. Amir Ardeshir is an Associate Scientist at the California National Primate Research Center. His research focus is on the establishment of the gut communities (microbiota) in infancy and their role in programming the immune system in non-human primate models. He is interested in the following questions: What underlying mechanisms affect the establishment of the gut microbiota in infancy? And, how does the early age microbiota modulate the immune systems development?

Please contact Dr. Ardeshir at for more information.

Andreas J. Baumler, PhD

SOM: Medical Microbiology and Immunology (see also: Immunology, Microbiology)

I am a microbiologist interested in the interaction of enteric pathogens with their hosts. We use mouse models to study Salmonella pathogenesis and host response. The main goals of this work are to interrogate mechanisms that enable typhoidal Salmonella serovars, such as Salmonella typhi, to evade innate immune recognition and mechanisms that enable non-typhoidal Salmonella serovars, such as Salmonella typhimurium, to take advantage of the host inflammatory response to edge out competing gut microbes. Furthermore, we use day-of-hatch chickens to investigate how Salmonella enteritidis colonizes the infant gut. We are also interested in how the gut microbiota confers colonization resistance against Escherichia coli and other commensal Enterobactericeae and in understanding the pathogenesis of colonic crypt hyperplasia caused by Citrobacter rodentium in mice, which is an animal model for infection with enterohaemorrhagic E. coli (EHEC).

Please visit Dr. Baumler's website for more information.

Sheila E. Crowe, M.D.*

Affiliated with UC Veterinary Medical Center – San Diego

Dr. Crowe investigates mechanisms of epithelial cell damage in gastrointestinal inflammation to increase our understanding of inflammatory and malignant disorders of the digestive tract. In particular, she studies oxidative damage to epithelial cells by H. pylori, which has been shown to control the transcription of genes that regulate cell growth, repair and programmed death processes. The lab now has a novel mouse model made by the Mouse Biology Program at UC Davis to study DNA damage in the digestive tract and studies are underway to phenotype the mouse and examine how bacteria induce oxidative stress and DNA damage.

Please contact Peter Ernst or Christina Sigurdson first for more information.

Lars Eckmann, M.D.*

Affiliated with UC Veterinary Medical Center – San Diego

Dr. Eckmann investigates the cellular and molecular pathogenesis of infections with enteric pathogens and the mechanisms underlying the regulation of intestinal inflammation. His studies employ animal models of intestinal infection and inflammation and apply molecular, microbiological and histological approaches to elucidate the key genes and cellular and molecular mechanisms that govern intestinal host defenses against enteric pathogens and regulate inflammatory responses in the gastrointestinal tract. Current studies define host defense mechanisms against the protozoan pathogen Giardia and the bacterial pathogens Escherichia coli and Salmonella.

Please contact Peter Ernst or Christina Sigurdson first for more information.

Peter Ernst, D.V.M., Ph.D.

Affiliated with UC Veterinary Medical Center – San Diego

Director of the Center of Veterinary Sciences and Comparative Medicine Director of the Division of Comparative Pathology and Medicine
Co-Director of UCVMC
Professor of Pathology, UC San Diego
Professor of Pathology, Microbiology, and Immunology, UC Davis

Our general research interests are in the area of comparative (human to mouse) mucosal immunology with specific projects in immune-epithelial cell interactions involved in the microbial pathogenesis of acute and chronic diseases of the gastrointestinal tract. Our current emphasis is on the role of adenosine as an anti-inflammatory mediator and how it protects from disruption in the microbiota that trigger disease.

Link to Dr. Ernst’s current publications
Link to Dr. Ernst’s website

Please contact Dr. Ernst for more information:

Melanie Gareau, Ph.D.

Microbiota-gut-brain axis

VM: Anatomy, Physiology and Cell Biology

Dr. Gareau is a physiologist primarily interested in studying the microbiota-gut-brain axis. It is increasingly being recognized that the microbes that live the gastrointestinal tract, collectively referred to as the intestinal microbiota, can contribute to modulating cognition and mood. The research focus of her laboratory is in determining how manipulating the microbiota within the gut, using models of infection with bacterial pathogens or administration of beneficial probiotic bacteria, can change cognitive function, anxiety, and depression-like behaviors in mouse models of disease. Dr. Gareau has a particular interest in how the microbiota-gut-brain axis responds to stimulation with psychological stressors and under conditions of intestinal inflammation, such as in models of inflammatory bowel disease (IBD). Ongoing projects in the laboratory include studying behavior in mouse models of IBD and following pathogenic E. coli infection.

If interested, please contact Dr. Gareau:

Peter J. Havel, DVM, PhD

Department of Molecular Biosciences
School of Veterinary Medicine and Department of Nutrition
Director, Endocrinology and Metabolism Core
Mouse Metabolic Phenotyping Center

(See also: Biochemistry, Endocrinology/Metabolism, Pharmacology, Translational Medicine)

Our highly translational research program is actively investigating the regulation of energy homeostasis and carbohydrate/lipid metabolism, and involvement of endocrine systems in the pathophysiology of obesity, diabetes, and cardiovascular disease. My laboratory is studying the mechanisms regulating the secretion of pancreatic and gastrointestinal, and adipocyte hormones. The role of endocrine, metabolic, and dietary factors in regulating energy balance, insulin action, and lipid/carbohydrate metabolism is studied in animal models (rodents and nonhuman primates) and humans. We are conducting studies on the prevention and treatment of diabetes in a rat model of type 2 diabetes developed in our laboratory (UCD-T2DM Rat) that is more similar in pathophysiology to type 2 diabetes in humans than other available models (Am. J. Physiol., 2008). We have used the UCD-T2DM model for 15 additional published studies on the pathophysiology of T2DM and for investigating pharmacological and surgical approaches for the treatment and prevention of T2DM. We have been involved in clinical studies and experiments in animal models investigating the effects of bariatric surgery procedures on how these endocrine changes are involved in improvements of carbohydrate and lipid metabolism and the resolution of type 2 diabetes observed after surgery. Another major focus of the research is the role of diet composition (such as dietary fat and fructose) in the development and progression of obesity, diabetes, and dyslipidemia including studies in animal models and clinical studies in humans. In addition, our laboratory has been conducting translational studies funded by the NIH, ADA, and pharmaceutical/ biotechnology industry sources at the California National Primate Research Center in a diet-induced rhesus monkey model of metabolic syndrome with insulin resistance and dyslipidemia (Clinical. Trans. Sci., 2011, ILAR Journal, 2017) as extensions of our studies in rodent models and as preclinical investigations that generate data and hypotheses that are then tested in clinical studies in humans. We have demonstrated that consumption of fructose, but not glucose-sweetened beverages for 10 weeks increases visceral adiposity and lipids and decreases insulin sensitivity in humans (J. Clin. Invest., 2009). We also recently completed a comprehensive NIH-funded dose-response study of the metabolic effects of sugar- sweetened beverages (Am. J. Clin. Nutr., 2015) and are currently studying the metabolic effects of dietary sugars under ad libitum versus energy-balanced conditions.

Stanley Marks , BVSc, PhD, Dip. ACVIM (Internal Medicine, Oncology), Dip. ACVN

VM: Medicine & Epidemiology

Dr. Marks is a veterinary gastroenterologist and nutritionist who runs the Companion Animal Gastrointestinal Laboratory. His research group have been characterizing enteric bacteria (Clostridial species, Campylobacter jejuni, Salmonella spp.) and protozoa (Giardia, Cryptosporidium, Tritrichomonas foetus) associated with diarrhea in dogs and cats, and evaluating diagnostic tests and therapeutic strategies to eradicate the organisms. Dr. Marks is also actively involved in research involving esophageal motility disorders and gastroesophageal reflux (GER), using high-resolution manometry (HRM), esophageal pH/impedance, videofluoroscopy swallow assessment, and esophagoscopy. His laboratory has multiple ongoing studies evaluating the effects of motility modifiers, acid suppressants, and anti-inflammatories on esophageal motility and GER.

Please visit Dr. Marks's website at:

Sina Marsilio, Dr. med. vet., PhD, DACVIM (SAIM), DECVIM-CA

VM: Medicine and Epidemiology

(see also: Genetics and Genomics, Microbiology/Parasitology)

I am a small animal internist with a special clinical and research focus in small animal gastrointestinal diseases. My current research focuses on the intestinal microbiome and its disruption during acute and chronic intestinal diseases. In addition, I am currently launching several projects on the use of fecal microbiota transplantation as a therapeutic tool for intestinal disease. I am also actively involved in translational research using stem cells in animals with gastrointestinal disease. I am looking forward to mentor students with an active interest in small animal gastrointestinal and translational research and who would like to be involved in clinical research projects.

Please email Dr. Marsilio for more information:

Jon Ramsey, Ph.D.

Associate Professor

My research focuses on energy metabolism as it relates to obesity and aging. Calorie restriction, without malnutrition, is the only intervention that has consistently been shown to increase maximum life span in mammalian species. My research is investigating possible mechanisms for the retardation of aging with calorie restriction. In the area of obesity, my research focuses on the role alterations in energy expenditure play in either assisting or opposing weight loss. Also, I am interested in preventing obesity in companion animals by better determining the energy requirements of cats and dogs.

Please visit Dr. Ramsey's website at:

Helen Raybould

VM: Anatomy, Physiology & Cell Biology

My research interest focuses on neurobiology of the gastrointestinal tract. The overall goal of the research is aimed at understanding that mechanism by which neurons that innervate the gut are activated in response to luminal stimuli such as nutrients and how these mechanisms may be altered in disease such as obesity, inflammation and irritable bowel disease. We use a number of different techniques including integrative physiological measurement of GI function, neurotransmitter receptor expression and localization, cell culture and measurement of secretion from endocrine cells, electrophysiological experiments to record nerve activity.

Please visit Dr. Raybould's website at:

Colin Reardon, Ph.D.

Immunology, IBD, T1D (see also: immunology)

VM: Anatomy, Physiology, & Cell Biology

Dr. Reardon is an immunologist specializing in the regulation of immunology. He is particularly interested in the mechanisms of communication between the nervous and immune systems. Although thought of as disparate fields of study, these two systems have co-evolved and are now appreciated to influence each other. Dr. Reardon’s research focuses on the modification of immune outcomes by neurotransmitters, and on the recently discovered production of the neurotransmitter acetylcholine (Ach) by B- and T-cells. Dr. Reardon’s research has previously identified that the commensal microbiota is involved in the regulation of Ach production by these immune cells. . Various projects are currently ongoing in the laboratory that will seek to establish the role of specific neurons in modulating immunopathologies, including inflammatory bowel disease and diabetes. Based on this, testing of small molecule agonists, and neurostimulator devices (in collaboration with biomedical engineers) to modulate immunopathologies will be performed in the laboratory. To accomplish this a variety of complementary techniques will be used including flow cytometry, confocal and intravital microscopy.

If interested, please contact Dr. Reardon

Jesus Rivera-Nieves, M.D.*

Affiliated with UC Veterinary Medical Center – San Diego

Dr. Rivera-Nieves works on the pathogenesis of Crohn’s disease. Leukocytes of the granulocytic, monocytic and lymphocytic lineages are active participants in the chronic inflammatory process. Their recruitment from the circulation is regulated by adhesion molecules and chemokine receptors interacting with their respective ligands expressed or presented by intestinal endothelia cells. These adhesive interactions represent attractive therapeutic targets for the modulation of the destructive chronic inflammatory process. Proof of concept for the viability of this strategy has been provided by the efficacy of natalizumab, which interferes with integrin alpha-4-VCAM-1, MAdCAM-1 interactions. Using novel murine models of Crohn’s-like ileitis, Dr. Rivera-Nieves has continued to explore potential molecules that may be targeted, within the leukocyte recruitment cascade.

Please contact Peter Ernst or Christina Sigurdson first for more information