Dr. David J. Baumler

Dr. David J. Baumler, Assistant Professor of Molecular Food Safety Microbiology

View David Baumler's profile on LinkedIn




As of 2014, Dr. David J. Baumler is an Assistant Professor of Molecular Food Safety Microbiology in the Department of Food Science and Nutrition, the Biotechnology Institute, and Microbial and Plant Genomic Institute at the University of Minnesota.   His research program is focused on experimental and computational Systems Biology methods to study pathogenic and commensal microorganisms during interactions with hosts and in environments such as foods.  He is also a chili pepper consultant for farmers and the food/beverage industry in the Midwest.   Aside from his research, he is also a family fun musical entertainer named Davey Doodle and looks forward to performing entertaining and educational songs to the Twin Cities community.  Dr. Baumler received a B.S in Biochemistry, a M.S. in Food Microbiology and Safety, and a Ph.D. in Cellular and Molecular Biology from the University of Wisconsin-Madison.  His Post-doctoral research at the Genome Center of Wisconsin focused on Microbial Comparative Genomics, Bioinformatics, Pedagogical Teaching Methods, the Evolution and Cultivation of >100 types of Chili Peppers, and the Systems Biology of Infectious Disease.    He also serves as a reviewer for numerous PLOS, BioMed Central, and ASM journals.

Teaching Philosophy

The focus of my research and teaching is in the area of Food Microbiology and Microbial Systems Biology.  My teaching philosophy is focused on interdisciplinary training, and I plan to bring new tools and approaches of inquiry-based active learning to the classroom to enhance student learning by integrating experimental research with the topics of food microbiology, genomics, bioinformatics, and systems biology.


The central focus of our research is in areas that use genomics, systems biology, food microbiology methods to:

-Study infectious disease of foodborne pathogens and beneficial microbial flora during interactions with hosts through a combination of experimental and computational methods using genome-scale metabolic models.

-Genomics of foodborne pathogens

-Microbiome research throughout the food supply chain from farm to fork

-Characterize flavor profiles, antimicrobial properties, and genomics of >500 varieties of chili (chile) peppers for use in the food industry and to improve human health

-New technologies for non-thermal processing of foods

-Worldwide food safety

Selected Scholarship

Kantar, M.B., Anderson, J.E., Lucht, S.A., Mercer, K., Bernau, V., Case, K.A., Le, N.C., Frederiksen, M.K., DeKeyser, H.C., Wong, Z.Z., Hastings, J.C., Baumler, D.J. 2016. Vitamin Variation in Capsicum Spp. Provides Opportunities to Improve Nutritional Value of Human Diets.PLoS One. Aug 17;11(8):e0161464.

Ding, T., Case, K.A., Omolo, M.A., Reiland, H.A., Metz, Z.P, Diao, X., and D.J. Baumler. 2016. Predicting essential metabolic genome content of niche-specific enterobacterial human pathogens during simulation of host environments. PLOS One. Feb 17;11(2):e0149423.

Reiland, H.A., Omolo, M.A, Johnson, T.J., and D.J. Baumler. 2014. A survey of Escherichia coli O157:H7 virulence factors: The first 25 years and 13 genomes. Advances in Microbiology. 4:7.

Omolo, M.A., Wong, Z-Z., Mergan, A.K., Hastings, J.C., Le, N.C., Reiland, H.A., Case, K.A., and D.J. Baumler. 2014. Antimicrobial properties of chili peppers. J. Infectious Diseases and Therapy. 2:145.

Baumler, D.J., Ma, B. Reed, J.L., and N.T. Perna. 2013. Inferring ancient enterobacterial metabolism using ancestral core metabolic models. “Highly Accessed” June 11; 7:46.

Baumler, D.J., Banta, L.M., Hung, K.F., Schwarz, J.A., Cabot, E.L., Glasner, J.D., and N.T. Perna. 2012. Use of comparative genomics for inquiry-based learning to dissect virulence of Escherichia coli O157:H7 and Yersinia pestis. Cell Biology Education-Life Science Education (CBE-LSE) journal March 1; 11(1):81-93.

Baumler, D.J., Peplinski, R.M., Glasner, J.D., Reed, J.L, and N.T. Perna. 2011. The Evolution of Metabolic Networks of E. coli. BMC Systems Biology journal “Highly Accessed” Nov 1; 5(1):182.

Jeong, K.C, Kang, M.Y, Kang, J., Baumler, D.J., and C.W. Kaspar. 2011. Feeding chitosan microparticles reduces Escherichia coli O157:H7 shedding in cattle. Applied and Environmental Microbiology Apr;77(8):2611-6. Epub 2011 Feb 18.

Baumler, D.J., Hung, K.F., Cabot, E.L., Glasner J.D., Greene J.M., and N.T. Perna. 2008. Annotation of the bacteriophage 933W genome: an in-class interactive web-based exercise. American Society of Microbiology’s Microbelibrary. Curriculum Resources Collection; http://www.microbelibrary.org/

Glasner, J.D., Plunkett III, G., Anderson, B.D., Baumler, D.J., Biehl, B.S., Burland, V., Cabot, E.L., Darling, A.E., Mau, B., Neeno-Eckwall, E.C., Pot, D., Qiu, Y., Rissman, A.I., Worzella, S., Zaremba, S., Fedorko, J., Liss, P., Rusch, M., Shaker, M., Shaull, L., Shetty, P., Whitmore, J., Blattner, F.R., Greene, J.M., and N.T. Perna. 2008. Enteropathogen resource integration center (ERIC) – bioinformatics support for research on biodefense-relevant enterobacteria. Nucleic Acids Research 36:D519-523.

Baumler, D.J., Hung, K.F., Jeong, K.C., and C.W. Kaspar. 2008. Molybdate treatment and sulfate starvation decrease ATP and DNA levels in “Ferroplasma acidarmanus”. Archaea Dec;2(3):205-209.

Jeong, K.C., Hung, K.F., Baumler, D.J., Byrd, J.J., and C.W. Kaspar. 2008. Acid stress damage of DNA is prevented by Dps binding in Escherichia coli O157:H7. BMC Microbiology “Highly accessed” Oct 15;8:181.

Baumler, D.J. and C.W. Kaspar. 2007. Morphology of the acidophilic archaeon “Ferroplasma acidarmanus” strain fer1. Visual Collection; http://www.microbelibrary.org/