Analyzing Genetic Variability and Diversity of Microbial Communities in Geothermal Hot Springs using Metagenomic Read Recruitment
By: Juan Carlos Gomez
Department: Microbiology
Faculty Advisor: Dr. José R. de la Torre
Metagenomics has enabled the limitation of studying uncultured microorganisms by allowing direct extraction and sequencing of entire genomes from microbial communities present in the environment. My research focuses on metagenomes that were collected and sequenced from a single terrestrial geothermal system known as the Great Boiling Spring (GBS) located in northern Nevada. This geothermal system harbors microbial communities growing over a temperature gradient of (60℃, 70℃, & 85℃). Analyzing this metagenomic data can help us understand the genetic diversity, ecological roles, and adaptation of microorganisms present in the environment. One commonly used approach to study this data is metagenomic read recruitment, by matching individual short sequences from the metagenome, known as reads, to the genomes of key reference organisms. The reads can then be plotted onto a graph based on the match's location and the percent identity to the reference genome, giving information on regions of genetic variability known as genomic islands within the natural population. My goal is to create three types of graphs: (1) a scatter plot of matching reads based on match position and percent identity, (2) a plot of the number of matching reads (coverage) at different positions along the reference genome, and (3) a histogram of the matching reads based on the percent identity of the matches. For these analyses, I used BLASTN to search for matches of metagenomic reads to genomes of known species from the GBS microbial community. I have used these results to identify genomic regions that vary between the reference organisms and the population present in the spring. These flexible genomic regions are indicative of genetic adaptation to the local physical environment, as well as a response to viral predation within the hot spring.