Where do human-associated bacteria live when not inside a host? How closely related are "environmental" isolates to those within humans? Over the next semester, my group will continue to examine on the phylogenetic history of an opportunistic pathogen, Proteus mirabilis. As background, P. mirabilis is found as a resident of the human (and other animals) guts but can escape the intestines through rapid migration and cause recurring disease in the bladder. The migration requires collective movement and interactions among P. mirabilis cells. Indeed, many bacteria within a community can interact, communicate, and perform collective behaviors, such as self versus non-self recognition and competition. This project's primary objective is to determine how individual populations of Proteus spp. can outcompete and persist in natural environments and hosts. To do so, we will analyze P. mirabilis samples isolated from varied Berkeley-based locations and perform comparative analyses of the genome sequences to identify shared genes and metabolic pathways essential for environmental survival. We will also conduct behavioral assays to characterize these isolates and compare the results to human-associated isolates. We posit that a deep analysis of P. mirabilis genomes would reveal the genetic diversity between environmental and host-associated strains, which, when correlated with the aforementioned behavioral differences, could reveal specific genomic elements for future molecular studies. In the longer term, by using genetics and molecular biology methods, we can elucidate the identified genes' functions in competition and propagation or protection against other living organisms (e.g., antibiotic production).
Visit www.gibbslab.org to learn more about our research.
An undergraduate on this project will learn the lab’s techniques, read the background literature (with guidance from Dr. Gibbs), and participate in group discussions. This student will also aid in collecting environmental samples from proximal Berkeley locations and the isolation of P. mirabilis from these samples. Depending on the student’s progress, the goal is to perform microbial physiology experiments on the isolated bacterial samples, such as growth curves and competition assays. This student will hopefully also isolate genomic DNA for whole-genome sequencing and contribute to the bioinformatics analyses of these results. Dr. Gibbs and this student will minimally meet biweekly to discuss this project.
To be successful, students need to be willing to learn new techniques, some statistical analysis, and be precise in their experimental methods and lab notebook maintenance (once trained). No prior experience in microbiology is necessary. This laboratory is biosafety level 2; students must complete all appropriate training courses before starting research.