Microbiology and Parasitology

Amir Ardeshir DVM, MPVM, PhD

(See also: Gastroenterology/Gut Microbiome, Immunology, Systems Biology, Wildlife/Exotic Animal 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 aardeshir@ucdavis.edu for more information.

Andreas J. Baumler

SOM: Medical Microbiology and Immunology (see also: immunology, GI Physiology/Gastroenterology)

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.

Lark L. Coffey, Ph.D.

Davis Arbovirus Research and Training
Center for Vectorborne Diseases
Assistant Professor
Department of Pathology, Microbiology and Immunology

(See also: Pathology/Virology, Vector-Borne Disease Research)

Dr. Coffey  studies the ecology, evolution, and transmission dynamics of mosquito-borne viruses including chikungunya, Zika, West Nile, and St. Louis encephalitis that are significant causes of human disease with no licensed human vaccines or treatments beyond supportive care. The goal of her research is to understand patterns of viral molecular evolution and the viral genetic factors that promote arbovirus emergence and severe disease. Her work focuses on how intrahost viral genetic diversity generated by error-prone viral replication influences infectivity and transmissibility between mosquitoes and people or animals. She and her team also developing cheap and convenient improvements to surveillance in mosquitoes by detecting viral RNA in saliva expectorated by sugar-feeding West Nile virus vectors in California. They are also developing approaches to increase safety of candidate live-attenuated chikungunya virus vaccines by restricting their potential to develop revertant mutations that cause illness in vaccinees. Together with the California National Primate Research Center, the team is developing a non-human primate model of human Zika virus in pregnancy that is being used to define the roles of Zika virus mutations in fetal disease and for pre-clinical testing of therapies and vaccines. 

Please see http://coffeylab.ucdavis.edu for more information.

Barbara Byrne, DVM

Clinical bacteriology


The Byrne laboratory focuses primarily on microbiological questions as they apply to clinical veterinary microbiology. Some research areas include:

  1. Evaluation of the marine health by detection of pathogens in marine mammals, their food sources, and the marine environment and appraisal of their connection with terrestrial sources.
  2. Environmental contamination by zoonotic fecal pathogens.
  3. Genotyping of clinical isolates to determine their relatedness
  4. Use of mass spectrometry for isolate and strain identification

Some possible project areas:

1)     Evaluation of marine mammal isolates for virulence factors
2)     Comparison of clinical isolates for genetic relatedness by pulsed-field gel electrophoresis
3)     Use of mass spectroscopy (MALDI-TOF) to identify and classify bacterial and/or fungal strains

Please visit Dr. Byrne's website at: http://faculty.vetmed.ucdavis.edu/faculty/bbyrne/

Patricia A. Conrad DVM, PhD

VM: Pathology, Microbiology & Immunology (see also: global health/projects)

Dr. Conrad is the Associate Dean for Global Programs, focused on promoting and facilitating international student experience in research and veterinary medicine. She is happy to meet and discuss with students their interest in developing a STAR project outside of the United States and advise on how to connect with researchers/mentors both overseas and at UC Davis. Please contact Dr. Paulina Zielinska pmzielinska@ucdavis.edu, Director for the Global Programs office to arrange an appointment with Dr. Conrad.  Information about the Office and the International Student Externship Program is at http://www.vetmed.ucdavis.edu/global-programs/.

SVM students can apply for funding for global research from both the STAR and Externship Program.


Dr. Conrad is also a veterinary research parasitologist whose research focuses on single-celled protozoal parasites of animals (domestic and free-ranging wildlife) and humans, primarily those that infect the blood and/or neurologic tissues. She and her research collaborators have a major focus on protozoal parasites (Toxoplasma and Sarcocystis neurona) that infect marine mammals including sea otters and these parasites, as well as Giardia and Cryptosporium parasites that are shed in the feces of terrestrial animals, both wild and domestic. These links will help to illustrate Dr. Conrad's research emphases:

Please visit Dr. Conrad's website at: http://faculty.vetmed.ucdavis.edu/faculty/paconrad/

Jonathan Dear, DVM, MAS, DACVIM (SAIM)

VM: Medicine & Epidemiology

(see also: Immunology/infectious disease, vector borne disease)

Dr. Jonathan Dear is a board-certified small animal internal medicine specialist at the University of California, Davis. A graduate of the University of Georgia College of Veterinary Medicine, Dr. Dear completed his residency at UC Davis. Dr. Dear also completed a master's degree in clinical research at the UC Davis School of Medicine. Dr. Dear's clinical interests include urinary and respiratory medicine, while his research interests also include small animal infectious diseases. Dr. Dear is the current president of the International Society for Companion Animal Infectious Disease.

Possible 10-week research projects:

Investigation of tick vectors in areas where Babesia conradae is endemic

-this project will focus on the epidemiology of B. conradae, a protozoal parasite of domestic and wild canids. Tick vectors have been identified most of the Babesia species affecting humans and small animals, however, a competent tick vector for B. conradae has not been identified. The aim of this project would be to trap and identify both soft and hard ticks in areas of California where B. conradae has been diagnosed. Additionally, the project will aim to identify tick species found on trapped coyotes and work to determine whether they harbor known pathogens of domestic dogs.

Validation of a point-of-care assay for disseminated, invasive aspergillosis

-Aspergillosis can be an invasive fungal disease of dogs and is generally associated with a grave prognosis. At present, diagnosis can be made by either identification of the organism via cytology or histopathology (which requires expertise and/or invasive techniques) or urine or serum tests which must be sent out for interpretation. In this project, a student would work to validate a point-of-care Aspergillus antigen test kit, comparing results to the current gold standard. 

Contact information: Jonathan Dear, jddear@ucdavis.edu, 530-752-7133

Angie Gelli, Ph.D.

Microbiology, molecular biology, host-pathogen interactions, blood-brain barrier, fungal pathogens

Dept. of Pharmacology, SOM

Over the past few years our research has focused on understanding how some pathogens are inherently capable of entering the brain, always with the underlying notion that these mechanismsmight be exploited for the development of drug-delivery systems across the blood-brain barrier for the treatment of brain disorders. My research has focused on the human fungal pathogen Cryptococcus neoformans - the leading cause of a life-threatening fungal meningoencephalitis. Approximately 625,000 people die from this infection each year around the globe mostly due to the difficulties associated with destroying the pathogen once it gets into the brain. Most patients succumb to the infection because of increased intracranial pressure and lack of adequate fungicidal drug regime. Not only does this organism represent a medically relevant pathogen with fascinating mechanisms of pathogenesis but also it serves as an excellent model system for studying other fungal pathogens with central nervous system involvement. We use a multidisciplinary approach that includes proteomics and RNA-sequencing to examine the physical and molecular changes in the brain endothelium and to identify gene products in C. neoformans that elicit these changes during attachment to- and migration across the blood-brain barrier.

If interested, please contact Dr. Angie Gelli: acgelli@ucdavis.edu

Visit our websites: http://acgelli.faculty.ucdavis.edu/ and http://pharmacology.ucdavis.edu

Matthias Hess, PhD

Department of Animal Science  (See also: Biochemistry/Cell Biology)

I am a microbiologist with a strong background in biotechnology. My research centers on the multi-scale (from molecule to cell to population to ecosystem) understanding of microbial systems through cultivation-independent as well as cultivation-based techniques. One of the ecosystems my group has been focusing on over the last years is the gut microbiome of ruminants and we have established an artificial rumen system in the laboratory to address questions related to gut and animal health and performance. More recently we have been expanding our work into other animal systems such as fish, pigs and poultry.  

For more information visit Dr. Hess’ website at www.HessLab.com

Smita Iyer, PhD

Department of Pathology, Microbiology, and Immunology

(See also: Infectious Disease/Immunology, Pathology/Virology)

Our lab’s primary research interests center around delineating immunological and molecular mechanisms of CD4 T cell help. Our ultimate goal is to use this information to design an effective HIV vaccine and in parallel understand mechanisms of HIV susceptibility and pathogenesis.

Well-defined projects in the lab in the area of HIV immunology provide motivated students opportunities to contribute to publications while training in biomedical research. Research projects provide opportunities to learn, implement, and analyze data using powerful tools such as flow cytometry in combination with RNA sequencing analysis.

Contact information:

Email: smiyer@ucdavis.edu

Phone: (530) 752-5716 Office
           (530) 754-2688 Lab

Maria Marco, Ph.D.

Microbiota, obesity, IBD, prebiotics, probiotics

Department of Food Science & Technology

My research focuses on the roles of dietary and intestinal microorganisms in obesity and inflammatory bowel diseases. We are employing pre- and probiotic components to study the interactions between bacteria and the host that influence immune and metabolic function. The overarching goal of the research is to define the ecological basis and molecular mechanisms by which beneficial microorganisms contribute to maintaining good health. Examples of research projects include: application of pre-clinical models to evaluate the benefits of pre/probiotics to prevent pre-diabetic states or IBDs,  the molecular analysis of host responses to probiotic bacteria and prebiotic fermentable dietary fiber; application of genetic analysis to investigate the function of specific probiotic Lactobacillus secreted factors in maintaining intestinal homeostasis; intestinal microbiome assessments using high-throughput DNA sequencing methods.

Please visit Dr. Marco’s website: http://www.marcolab.net

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

VM: Medicine and Epidemiology

(see also: GI Physiology/Gastroenterology, Genetics and Genomics)

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: smarsilio@ucdavis.edu

Victor Nizet, M.D.*

Affiliated with UC Veterinary Medical Center – San Diego

(See also: Immunology/Infectious Disease)

Dr. Nizet is a Pediatric Physician-Scientist, Infectious Diseases Specialist and Chief of the Division of Pediatric Pharmacology & Drug Discovery at UCSD School of Medicine and Skaggs School of Pharmacy & Pharmaceutical Sciences. Dr. Nizet leads a large and productive basic and translational research program focused upon the innate immune system, bacterial pathogenesis and the development of new immune-based infectious disease treatment strategies including novel antibiotics, targeted neutralization of bacterial virulence phenotypes, and pharmacologic augmentation of host phagocyte function.

Please contact Peter Ernst pernst@ucsd.edu or Christina Sigurdson csigurdson@ucsd.edu first for more information

Emmanuel Okello, BVM, MSc, PhD


(see also: Epidemiology, Genetics and Genomics)

Dr. Emmanuel Okello is an Assistant CE Specialist in Antimicrobial Stewardship at UC Davis, School of Veterinary Medicine. The goal of his research and extension program is to develop antimicrobial stewardship guidelines and best management practices that reduce antimicrobial resistance while maintaining the health and welfare of the herds and flocks. Okello’s specific areas of interest include the use of alternatives to antibiotics to control infectious diseases in livestock, development and evaluation of vaccines and rapid diagnostics tests, and improved management practices for disease prevention.

Please contact Dr. Okello for prospective STAR projects (eokello@ucdavis.edu). Website: https://www.vetmed.ucdavis.edu/faculty/emmanuel-okello

Richard Pereira, DVM, PhD

SVM: Population Health and Reproduction

(See also: Epidemiology, Food Animal Medicine/Food Safety, Genetics/Genomics)

Dr. Pereira research focuses on evidence based medicine on antimicrobial resistance in livestock and judicious use of antimicrobials through interventions that promote livestock health and well-being. Maintaining the effectiveness of antimicrobial drugs to treat infections is of relevance to the health of both animal and human populations. Recent project investigated enteric microbiota of calves using metagenomic sequencing approaches, and herd management impacts on prevalence of resistant enteric bacteria, including evaluation of drug use, feeding practices, and housing management of dairy calves and heifers.

Epidemiology is the foundation of his research which also employs statistics, microbiology, and molecular and genomic approaches. Using these tools, some current research projects include investigating and identifying risk factors for selection and spread of antimicrobial resistance in Salmonella from livestock, and investigating impacts on drug resistance and animal health from feeding pre-weaned calves waste milk (milk containing drug residues) with the aim of identifying interventions to reduce unwanted impacts from this practice.

Previous projects accomplished include:
Spatial-temporal trends in antimicrobial resistant Salmonella isolates recovered from Northern California dairy cattle at a veterinary microbiology laboratory between 2002 and 2017.

Potential 10 week projects for Summer 2018:
Antimicrobial resistance in bacteria causing metritis in dairy cows.

Evaluation of on-farm factors affecting antimicrobial drug on the dairy farms.

Contact information: rvpereira@ucdavis.edu

Please visit Dr. Pereira's website at: www.vetmed.ucdavis.edu/faculty/results.cfm?fid=22811

Karen Shapiro, DVM, MPVM, PhD

VM: Pathology, Microbiology & Immunology (See also: Epidemiology, Wildlife/Zoonoses)

Dr. Shapiro is an infectious disease researcher focusing on transmission of zoonotic pathogens that pose a health risk to wildlife populations and people through water or food. Her research program targets the transport and fate of zoonotic pathogens in watersheds and coastal ecosystems; effects of landscape change and climate variability on disease transmission; impacts of water scarcity and impaired quality on human and animal population health, and food safety. Specific projects where STAR students could become involved with include development and validation of molecular methods for detection of zoonotic protozoan parasites in food and water.

CONTACT:  kshapiro@ucdavis.edu

Woutrina Smith, DVM, Ph.D.

Infectious disease epidemiology (see also: epidemiology, global health)

VM: Medicine & Epidemiology

Dr. Smith is an infectious disease epidemiologist with a special interest in One Health and the molecular epidemiology of zoonotic diseases. She works at local and global study sites where interactions among humans, animals and their environments lead to research questions that can be addressed using laboratory and fieldwork approaches to characterize and manage health at an inidividual, population, and ecosystem level. Her research involves zoonotic protozoa such as Cryptosporidium, Giardia, and Toxoplasma, as well as bacteria that include Mycobacterium, Salmonella, and Campylobacter.

Please visit Dr. Smith at: http://www.vetmed.ucdavis.edu/faculty/results.cfm?fid=18101

Jay Solnick, MD, Ph.D.

MED: Infectious Diseases (see also: immunology)
Center for Comparative Medicine

Dr. Solnick is a microbiologist and infectious disease physician whose research seeks to understand the pathogenesis of Helicobacter pylori, a bacterium that causes peptic ulcers and gastric cancer. There are two major lines of investigation in his laboratory. First, how does the bacterium modify outer membrane proteins and other surface structures to avoid host immunity and persistently colonize the gastric epithelium? Second, what is the role of defensins and other innate immune effectors in the chronic colonization by H. pylori? These and related questions are addressed using a wide range of molecular and biochemical methods, as well as primate and murine animal models.

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

Esteban Soto-Martinez, MSc, DVM, PhD, Dipl. ACVM

VM: Medicine and Epidemiology (See also: Immunology, Pathology, WIldlife/Zoonoses)

Dr. Esteban Soto is a board certified veterinary microbiologist who has an interest in aquatic animal health. Our laboratory main research interests are to understand the pathogenesis of important infectious diseases of wild and aquatic animals, and to develop strategies to protect animals from these diseases. Members in our laboratory study One Health, Aquatic Animal Disease, and Fish Disease through a combination of microbiological, molecular, and epidemiological methods. Current projects involve studying the ecology, diversity and host-pathogen interaction of Francisella noatunensis, Piscirickettsia salmonis, Veronaea botryosa, Erysipelothrix rhusiopathiae, Flavobacterium spp., Saprolegnia ferax, Koi herpes virus and other fish pathogens; and studying the ecology, diversity and host-pathogen interaction of hypermucoid Klebsiella pneumoniae in marine mammals.

Please email Dr. Soto-Martinez for more information - sotomartinez@ucdavis.edu

Nam K. Tran, PhD, MS, FACB

SOM: Department of Pathology and Laboratory Medicine

(See also: Pathology/Virology)

My expertise is in clinical chemistry and point-of-care testing for critical care and emergency settings. This includes the development and implementation of innovative biomedical devices and technologies for improving the quality of patient care. These technologies include molecular pathogen detection methods for early detection of sepsis, novel biomarkers of organ dysfunction (e.g., acute kidney injury, myocardial infarction, etc), and point-of-care devices (i.e., medical testing at or near the site of patient care) for testing in emergency medicine and critically ill populations. Our team works closely with Biomedical Engineering, as well as the Divisions of Burn Surgery, and Trauma/Emergency Surgery from the School of Medicine. We are also heavily involved with clinical trials including a large multicenter randomized controlled study evaluating the impact of quantitative, PCR-based detection of Staphylococcus aureus in burn sepsis patients. Translational studies with the veterinary medicine involve the use of anti-fibrinolytic therapy in severe hemorrhage models (e.g., swine and sheep), and pharmacokinetic/pharmacodynamic (PK/PD) modeling of drugs in both animal and human models of injury.

Contact: nktran@ucdavis.edu

Please visit Dr. Tran's website at: https://www.ucdmc.ucdavis.edu/pathology/our_team/faculty/tranN.html

Renée Tsolis

Department of Medical Microbiology and Immunology, School of Medicine

(see also: immunology, wildlife/exotics)

Dr. Tsolis is a microbiologist studying host-pathogen interactions leading to disease during infection. Her laboratory uses a variety of animal models to study how two groups of zoonotic pathogens, non-typhoidal Salmonella and zoonotic Brucella species, interact with the immune system to cause disease. For non-typhoidal Salmonella species, Dr. Tsolis' group is interested in learning why underlying co-morbidities such as malaria and malnutrition increase the incidence of death from systemic infection in the developing world, and her laboratory has developed mouse models to gain insight into immunomodulatory effects of Vitamin A deficiency and malaria. For Brucella, the laboratory has developed models to understand both chronic infection that this group of organisms causes within the mononuclear phagocyte system and to interrogate placental infections in pregnant animals that lead to abortion in domestic animals. Collaborations with UCD research Dr. Luckhart in the Medical Microbiology department, Dr. McSorley in the Center for Comparative Medicine and Dr. Stephensen in the USDA Western Human Nutrition Research Center have been instrumental in establishing this interdisciplinary research program. The long-term goal of Dr. Tsolis' work is to uncover basic principles of how bacterial pathogens manipulate the immune response to cause disease and ensure their transmission to the next host.

Dr. Tsolis' research is described here: https://www.ucdmc.ucdavis.edu/medmicro/Faculty_MR/Tsolis/tsolis_index_mr.html