Our Mission

The Weimer MicroLab focuses on systems biology of bacterial pathogens and host/microbe interactions. We do this by integrating multiple “-omics” technologies in various biological systems ranging from the environment to stem cells to food. Our group is focused on the survival of pathogens in the environment and host and defining how bacteria persist, associate, and alter their environment, especially during nutrient starvation and non-culturability that leads to novel metabolic and host association conditions. The lab is focused on the initial steps of host association and the genomic requirements that impact chronic conditions, particularly chronic inflammation due to organisms transmitted in the food supply that establish long-term associations in the microbiome. These programs are fueled by large-scale whole-genome sequencing in Genomes4Health

To support these efforts our group has an active program of rapid molecular detection systems for bacteria and their products from food and the environment that includes capture/concentration strategies as well as metaRNAseq approaches that are coupled to metabolomics to define metabolic changes. This program leverages genomic information to determine robust biomarkers and traits that can be diagnostic for microbes.


Areas of Active Research:

  • Molecular ecology, physiology, and genome diversity of pathogens and probiotics – Salmonella, Campylobacter, Listeria, Lactic Acid Bacteria 

  • Molecular diagnostics development using population genomics

  • Metagenomics of the microbiome of humans, animals, and the environment

  • Epigenetics of bacteria during infection and survival

  • Host and bacterial metabolism during infection and commensalism

  • Natural antibacterial compound discovery

  • Bioinformatics of regulatory networks for metabolic control analysis using flux, gene expression, and metabolomics

  • Integration of multi-omics data sets for discovery of molecular and metabolic regulation of bacterial associations in growth, persistence, and non-culturability