Submitted by Karine Gibbs on
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 the phylogenetic history of an opportunistic pathogen, Proteus mirabilis. As background, P. mirabilis is a resident of the human (and other animal) guts but can escape the intestines through rapid migration and cause recurring disease in the bladder. Reports show environmental isolation of Proteus spp., suggesting that these bacteria live freely outside a host. This project's primary objective is to determine how Proteus spp. persists in natural environments and hosts. To do so, we will analyze samples isolated from Berkeley-based locations for bacterial composition, prepare genomic DNA from the microbial communities for sequencing, and analyze the sequence data, starting with amplicon sequencing. If the sequencing data shows the presence of Proteus spp., we will isolate individual strains using standard microbiological assays. We will then use whole genome sequencing and comparative genomic analyses with the laboratory wild-type strain to identify genes and metabolic pathways necessary for environmental survival. The student will also conduct behavioral assays to characterize these isolates and compare the results to those of human-associated isolates. An analysis of Proteus spp. genomes will reveal the genetic diversity between environmental and host-associated strains. These data could also uncover specific genomic elements for future molecular studies when correlated with the aforementioned behavioral differences. If no Proteus spp. is identified in the sequencing data, the student will work with lab members to further characterize the soil samples, starting with a metagenomics analysis. In the longer term, by using genetics and molecular biology methods, we aim to elucidate the genes that function in competition, propagation, or protection against other living organisms, such as antibiotic production.
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 aid in collecting environmental samples from proximal Berkeley locations. Depending on the student’s progress, their goals will be to isolate genomic DNA from microbial communities for DNA sequencing and contribute to the bioinformatics analyses, starting with amplicon sequencing. This student will hopefully also perform microbial physiology experiments on isolated bacterial samples, such as isolation, growth curves, and competition assays. Dr. Gibbs and this student will meet biweekly to discuss this project; a member of the Gibbs Lab will provide direct experimental support.
Students should be willing to learn new techniques and some statistical analysis. They must also be precise in their experimental methods and lab notebook maintenance (once trained). Prior experience in microbiology is not required. The Gibbs laboratory is biosafety level 2; students must complete all appropriate training courses before starting research. This project is well-suited for students interested in community interactions, computational analysis, or environmental microbiology.