Our laboratory focuses on the role that microbial communities play in human homeostasis, health and disease. We firmly believe that the various microbial components of human ecosystems including bacteria, viruses, archaea, and fungi are important factors that help determine the natural history of their hosts. Furthermore, their interactions with humans or their interactions with other microbial constituents in these communities likely have consequences for human health.
Our primary focus is on the role of human viral communities, particularly in the oral cavity. We have demonstrated that there are robust communities of viruses present in the human oral cavity, most of which are viruses of bacteria. These viruses likely play a unique role in pathogenesis within the community, as a large proportion of these viruses are involved in lysogeny and bring new gene function into the community that may be utilized by their bacterial hosts. We are actively pursuing the role that RNA and DNA viruses play in these communities in terms of contributing pathogenic potential, as well as their effect on their host bacterial communities. Because of our interest in infectious diseases in humans, we study these communities almost exclusively in humans in health and disease.
A secondary focus of the laboratory is to explore the interactions between viruses and their bacterial hosts through examination of bacterial adaptive immune systems called CRISPRs. We provided the first metagenomic analysis of CRISPRs in human ecosystems, and have demonstrated that Streptococcal species in the human oral cavity are actively adapting immunity to viruses they encounter on a daily basis. We are continuing to pursue characteristics of CRISPRs in human ecosystems, using CRISPRs to trace individual human subjects in both health and disease, to explore the robustness of the immune responses of bacteria against certain viruses, and to track individual bacteria as they may fluctuate in the community.
Another field of interest in the laboratory is to explore the contribution of microbes to metabolism and pathogenesis in human ecosystems. We are particularly interested in human diseases such as periodontitis, which may have polymicrobial etiology.
Areas of Expertise (6)
Drug and Vaccine Development
New York University: M.D., Medicine 2003
Vanderbilt University: Ph.D., Microbiology and Immunology 2001
Vanderbilt University: B.S., Biology 1996
Magna cum laude
- Board Certified American Board of Medical Microbiology: 2014 to present
- Board Certified Infectious Disease: 2008 to present
- Board Certified Internal Medicine: 2006 to present
Media Appearances (7)
Here’s how San Diego scientists are mounting a counterattack against the coronavirus
San Diego Tribune online
Pride and his colleagues are developing a variety of in-house tests that are meant to identify people who are infected and still shedding the virus. It’s a taxing challenge. They’ve had to keep changing tests due to shortages in key chemicals, known as reagents, that are required to conduct the testing.
Coronavirus: How is San Francisco testing at nearly double the rate of LA?
The Mercury News online
To the south, San Diego officials and medical professionals worked to ramp up testing ahead of an expected surge of COVID-19 patients, said UC San Diego infectious disease specialist David Pride. “We’ve got a large amount of testing capacity, but demand is not nearly what we thought it was going to be,” Pride said of the San Diego area.
New COVID-19 Testing Device Gives Results In Minutes
NBC San Diego online
“I can say definitively it does work quite well because we finished our evaluation yesterday and we’re training people so we make certain that they know how to run it,” said Dr. David Pride, Infectious Disease Specialist at UC San Diego Medical Center.
Coronavirus Testing Has Improved In San Diego But Still Not Where Officials Want It To Be
“This is something that most laboratories, including ours, wouldn’t do in normal times,” Pride said. “But we’ve got such large patient demand for testing that we felt like if we diversified early then we would be able to manage to obtain the materials that we needed to meet our patients demand.”
COVID-19 testing in San Diego County expected to ramp up
ABC 10 News San Diego online
"Right now we’re testing around 300, on the upper end about 400 people a day," said Dr. David Pride, the associate director for the Clinical Microbiological Laboratory at UC San Diego Health. "We have been slowly increasing our testing over the course of the past several weeks."
GenMark Receives FDA Emergency Use Authorization for its ePlex® SARS-CoV-2 Test
Yahoo Finance online
“GenMark reached out to us several weeks ago to ask for our help to run the first patient samples on their RUO ePlex SARS-CoV-2 Test,” said David T. Pride, MD, PhD, director of the Clinical Molecular Microbiology Laboratory and associate director of the Microbiology Laboratory at UC San Diego Health. “We completed the validation and were the first lab in the U.S. to go live with the ePlex test.”
UC has a solution to the national shortage of coronavirus testing — do it in house
Los Angeles Times online
“We are taking multiple strategies to substantially increase this capacity in the next few weeks,” Steven Gonias, chief of pathology for UC San Diego Health, and David Pride, associate director for diagnostic microbiology in the UCSD Center for Advanced Laboratory Medicine, said in a statement.
Research Focus (2)
Developing synergistic antibiotic and phage cocktails to target bacterial pathogens
2020 - 2022 Co-Principal Investigator
Model systems to assess the role of viruses in the microbiome
2018 - 2020 Principal Investigator
Fecal Viral Community Responses to High-Fat Diet in MiceAmerican Society for Microbiology
2020 Alterations in diet can have significant impact on the host, with high-fat diet (HFD) leading to obesity, diabetes, and inflammation of the gut. Although membership and abundances in gut bacterial communities are strongly influenced by diet, substantially less is known about how viral communities respond to dietary changes.
Aseptic Barriers Allow a Clean Contact for Contaminated Stethoscope DiaphragmsMayo Clin Proc Innov Qual Outcomes
2020 To determine whether a single-use stethoscope diaphragm barrier surface remains aseptic when placed on pathogen-contaminated stethoscopes. Methods: From May 31 to August 5, 2019, we tested 2 separate barriers using 3 different strains of 7 human pathogens, including extended-spectrum β-lactamase-producing Escherichia coli, methicillin-resistant Staphylococcus aureus, and vancomycin resistant Enterococcus faecium.
Benchmarking urine storage and collection conditions for evaluating the female urinary microbiomeScientific Reports
2019 Standardized conditions for collection, preservation and storage of urine for microbiome research have not been established. We aimed to identify the effects of the use of preservative AssayAssure® (AA), and the effects of storage time and temperatures on reproducibility of urine microbiome results.
Shared and Distinct Features of Human Milk and Infant Stool ViromesFrontiers in Microbiology
2018 Infants acquire many of their microbes from their mothers during the birth process. The acquisition of these microbes is believed to be critical in the development of the infant immune system. Bacteria also are transmitted to the infant through breastfeeding, and help to form the microbiome of the infant gastrointestinal (GI) tract; it is unknown whether viruses in human milk serve to establish an infant GI virome.
Draft Genome Sequence of an Enterococcus faecalis ATCC 19433 Siphovirus Isolated from Raw Domestic SewageAmerican Society of Microbiology
2017 We previously isolated and characterized an Enterococcus faecalis ATCC 19433 siphovirus 15 from raw domestic sewage as a viral indicator of human fecal pollution. Here, we report 16 the draft genome sequence of this bacteriophage.