Bart C. Weimer, Ph.D. is the Chair and Professor of Microbiology in the Department of Population Health and Reproduction within the School of Veterinary Medicine at the University of California, Davis. His research is focused on the intersection of food, health, and the microbiome using bacterial population genomics. Included in his research direction is the use of systems biology, population genomics, and machine learning to examine the role of bacteria to be bioactive. He leads the 100K Pathogen Genome Sequencing Project, which enables reference genomics for surveillance, population evolution, and metagenomic studies. He is active in various international organizations for microbiology and science including the American Society for Microbiology and the American Association for the Advancement of Science. His lab is fortunate to receive extensive funding from many sources including the US federal government, the food industry, and the analytical genomics industry, that seek to impact the global attention to bacterial spread and persistence. Dr. Weimer has a leadership role in microbial genomics and bacterial physiology that brings about collaborations at the interface of adjacent fields with the aim of bringing new ideas into microbiology so as to leverage new approaches to study critical questions within bacterial growth, evolution, and persistence in humans, animals, plants, and the environment broadly. Dr. Weimer is the founding editor-in-chief for Bacteria, a section editor for Virulence, an editor for Microorganisms, and on the editorial board of four additional scientific journals. He has trained over 45 Ph.D. students, published over 190 peer-reviewed papers that are broadly cited, and has been awarded multiple patents related to bacteria and their ability to change our environment. He has published 6 books, 30 book chapters, and 194 manuscripts.
Graduate Students & Staff
My research focuses on understanding the genetic and metabolic underpinnings of novel forms of biological nitrogen fixation. I aim to promote sustainable agricultural practices by studying unique nitrogen-fixing bacteria associated with mucilage-secreting maize and potentially extending the benefits of symbiotic nitrogen fixation to other crops. Before joining the Weimer Lab, I completed a BS in Biological Sciences with a concentration in microbiology at California State University, Stanislaus. While at CSU Stanislaus, I conducted research on bacteria isolated from compost and studied the temporal differences of their degradative enzyme profiles. As a second-year Microbiology Ph.D. student, I plan on using genomics, metabolomics, and bioinformatics to elucidate uncharacterized mechanisms of nitrogen fixation. In my free time, I enjoy watching sci-fi movies, hanging out with my wife and cats, and playing soccer.
As a microbiology Ph.D. student in the Weimer Lab, I aim to expand my career in infectious disease research by leveraging bioinformatics to engage population-scale complexity. My research interests lie in using population genomics to explore diversity and make sense of differences within microbial populations. My current projects consist of genomic variation in Helicobacter pylori associated with cancer in humans, Corynebacterium pseudotuberculosis genomic diversity and antimicrobial resistance from animals, and diversity with virulence and antimicrobial resistance dynamics in bovine respiratory Pasteurellaceae pathogen populations. I additionally contribute to Weimer group collaborations, consisting of wide-ranging projects from viruses to microbiomes, working with groups across Davis and around the world. Prior to joining the Weimer Lab, I worked at multiple institutions in infectious disease research: as a research assistant at Harvard University, I assayed genetic diversity in malaria populations in relation to disease control; as a post-bacc. research scholar at the University of Rochester, I investigated atypical molecular pathogenesis of Vibrio cholerae; as an undergraduate at the University of Texas at Austin, I performed disease ecology fieldwork for Leishmania in Texas, while I earned B.S. degrees in biochemistry and microbiology. Building on my past research experience and incorporating the techniques and approaches of the Weimer Lab, I work to provide comprehension to emerging challenges in infectious diseases and public health interests in my current work and future career.
I joined Weimer Lab in 2013 with experiences in biotech, molecular, biochemical, and analytical fields. Prior to joining Weimer Lab, I worked for a biotech company, studying crop trait improvements through gene transformation. That experience covered molecular vectors generation, transgenic efficacy test, chemical analysis on end products as well as toxicity study for regulatory purposes. My main role in this lab is whole genome sequencing and metagenome sample handling that is included in the 100K Pathogen Genome Project. This has led to standardization of large-scale whole genome sequencing library construction, develop and optimize protocols for metaRNA seq sample preparation from many difficult sample types. Sequencing using Illumina platform is the primary effort but I have adapted Nanopore ultra-long reads sequencing as well. Additionally, I oversee daily laboratory activities.
Narine Arabyan, Ph.D., Microbiology
Poyin Chen, Ph.D., Microbiology
Ning Chin, M.S., Forensic Sciences
Ashleigh Flores, M.S.
Shawn Higdon, Ph.D., Plant Sciences
Allison Weis, Ph.D., Microbiology
DJ Darwin Bandoy, DVM, Ph.D., Microbiology