Microbiology and Parasitology
Andreas J. Baumler
SOM: Medical Microbiology and Immunology (see also: Immunology/Infectious Disease, 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).
STAR students can expect to work on projects related to control of microbiota composition and function by the intestinal epithelium. Students will also receive exposure to mouse handling, infection, sample collection and analysis (e.g., microbiota composition, epithelial metabolism, microbial metabolites).
Please visit Dr. Baumler's website for more information.
Pouya Dini, DVM, PhD, PhD, Dipl. ECAR, Dipl. ACT
Assistant Professor in Equine Reproduction
Department of Population Health and Reproduction (PHR)
(see also: Reproductive Biology, Translational Research)
Research Interests: My research topics include parental gene expression in the placenta and the reciprocal paternal and maternal gene interaction in the equine's placental development and its pathologies, effects of assisted reproductive techniques on the epigenetic of the equine placenta, and host-pathogen interaction during equine placentitis. We use high-throughput sequencing along with classical molecular and cellular biology techniques to explore these topics.
Possible learning outcomes:
1- Culture cells and organoid from reproductive tract (mainly equine)
2- Extract nucleotides and PCR
3- Get familiar with next-generation Sequencing methods
4- Get familiar with in vitro embryo production in equine and bovine
Dr. Dini can be reached via email at pdini@ucdavis.edu.
Angie Gelli, Ph.D.
Dept. of Pharmacology, SOM
(See also: Molecular and Cellular Biology)
My lab studies human fungal pathogenesis of the CNS with a facus on the blood-brain barrier. Trainees in my lab will master molecular and cellular techniques, a 3D BBB spheroid model, and mice models of cryptococcal infection.
If interested, please contact Dr. Angie Gelli: acgelli@ucdavis.edu
Please visit our website for more information.
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
Krista A. Keller, DVM, Dipl ACZM
VM: Medicine & Epidemiology
(see also: Wildlife and Exotic Animal Medicine)
I am a board-certified specialist in zoological medicine and my research, focused on of mycotic infections of reptiles, allows me (and my mentees) to ask clinically relevant questions to drive hypothesis-based research. I am interested in understanding all aspects of the host-microbe-environmental triad as it relates to infectious disease development to drive meaningful recommendations on the diagnosis and treatment of reptiles infected with mycotic agents.
My mentoring philosophy involves handing students a spark (an idea), then allowing them to light the fire (research and develop a research question) and helping them to appreciate all components of research from ideation, hypothesis creation, methodological planning, material list development, data collection and analysis, through dissemination on the local and national level.
STAR students will study elucidating factors surrounding mycotic infections in reptiles. Students will also be exposed to both project planning and design as well as laboratory based microbiological techniques (culture, pipette, dilutions).
I can be reached at kakell@ucdavis.edu.
Tessa LeCuyer, DVM, PhD
Assistant Agronomist, Pathology, Microbiology & Immunology
(See also:Immunology/Infectious Disease, Dermal Biology/Dermatology)
Dr. LeCuyer is a veterinary clinical microbiologist who assists with laboratory diagnosis of infectious diseases in the VMTH. Her research interests include antimicrobial stewardship, detection of antimicrobial resistance and impacts on clinical outcomes, chronic bacterial infections, and improving diagnostic testing.
Potential STAR research projects include: 1) Evaluation of novel therapies for canine otitis, 2) Determination of factors that impact antimicrobial drug selection and treatment outcomes for patients with infectious diseases, 3) Characterization of bacteria that cause recurrent infections (especially urinary tract infections in dogs). Skills to be developed include laboratory techniques, such as bacterial cultivation, PCR, antimicrobial susceptibility testing, and biofilm detection assays, as well as non-laboratory skills such as medical record review, antimicrobial selection skills, bioinformatics, and retrospective data analysis techniques.
Both laboratory based and non-lab based projects are possible.
For more information on projects, email tlecuyer@ucdavis.edu.
Xunde Li, PhD
Microbiology and Food Safety
Dr. Li is a researcher (research microbiologist) at the Department of PHR. His research interests are in the areas of microbiological food safety related to antimicrobial resistance. Potential research topics include prevalence of foodborne pathogens and antimicrobial resistance in retail food using conventional bacteriological methods and novel sequencing approaches.
Please contact Dr. Li via email at xdli@ucdavis.edu
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
VMTRC
(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 students:
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
Hannah Savage, DVM, PhD, DACVM
Assistant Professor of Microbiology
Department of Pathology, Microbiology, and Immunology
(see also: Immunology/Infectious Disease)
The Savage lab studies interactions between pathogens, the microbiota, and host. In particular, I currently focus on how the microbiota promotes a heathy colonocyte immunometabolism and how this interaction is altered during disease, putting the host at risk of infection with pathogens and pathobionts. My overall research goal is to understand the basis behind these host-microbiota interactions during health so that host health can be supported with therapeutics during microbial disruption to prevent a loss of colonization resistance.
Potential STAR student projects: 1) Investigate effects of chemotherapy in a mouse model and potential treatment options to improve outcomes during chemotherapy, focusing on prevention of systemic infections. 2) Investigating how high Candida albicans burden can be protective against other pathogens in a mouse model. 3) Investigating potential management of ileitis/Crohn’s disease in a mouse model. STAR students will learn how to do techniques such as mouse necropsies for intestinal samples, bacterial plating, qPCR, RT-PCR, histopathology, DNA preparation for sequencing, -omics analysis, and/or flow cytometry.
I may also have veterinary species-based projects available (example: analysis of changes in dog microbiota and intestinal environment during chemotherapy treatment) depending on funding.
Please contact Dr. Savage at hpsavage@ucdavis.edu for more information.
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.
Dr. Smith can be reached via email at wasmith@ucdavis.edu.
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/Infectious Disease)
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.
We are using mouse models to study how bacterial pathogens (Salmonella, Brucella, Chlamydia) interact with the immune system to cause infection. STAR students can learn immunology and microbiology skills as well as molecular biology approaches to study inflammation and host and microbial gene expression.
Please visit Dr. Tsolis' website for more information.
Bart Weimer, PhD
(See also: Genetics/Genomics, Immunology/Infectious Disease, Genetics/Genomics)
Dr. Weimer is a microbiologist that combines genomics to study the intersection between the host and microbiome. This ranges from single organisms that are zoonotic to the complex microbiome communities of various tissues of animals and humans. He leads the 100K Pathogen Genome Project that is focused on population microbial genomics to understand genomic diversity of infectious microbes but also virulence, antimicrobial resistance, zoonotic transmission dynamics, clinical diagnostics, and global traceability. This project also provides a basis for reference genomes for metagenomic studies that integrate metabolism and host association that impact health and disease.
His group studies problems that range from single gene and single organism disease impacts on disease and diagnostics to community interactions that impart host changes via small molecules between the epithelium and distant tissues. His work with bacterial/stem cell interactions is one model for movement of bacteria between different sites in the body. His group ranges from bench experiments to population bioinformatics to metabolomics of microbial systems.
Some focus areas for his lab are: Some focus areas for his lab are: Linking genetic variation to zoonotic organisms - gut and oral applications = genomics and metagenomics.
Dr. Weimer can be reached via email.
Sebastian Winter, MSc, PhD
Department of Internal Medicine, UC Davis Health
(See also: GI Physiology/Gastroenterology, Immunology/Infectious Disease)
Summer research students in the Winter lab will participate in the following:
1. Defining the molecular mechanisms of how the gut microbiota influences mucosal and systemic inflammation.
2. Defining the disease-associated metabolism of enteric pathogens such as Salmonella, Yersinia, and E. coli. Skills: Bacterial genetics, mouse genetics, metabolomics, bacterial culture and growth experiments, quantifying gut inflammation.
Dr. Winter can be reached via email.