By Ray Chen, SDSC Research Experience for High School (REHS)
West Hub affiliates at Boise State University leverage the power of high performance computing to assist in the processing of microbiome pipelines as part of the school’s Genomes Underlying Toxin Tolerance (GUTT) program, a National Science Foundation EPSCoR RII Track-2 aimed at conducting research and educational projects across the states of Idaho, Nevada and Wyoming. A recent, successful GUTT activity has been the establishment of the Microbiome Hub, led by Boise State University’s Postdoctoral Research Scientist Stephanie Galla and Professor Jennifer Forbey.
“There are many pipelines to choose from when it comes to sequencing analysis,” said Galla. “On top of that, it can be tricky for incoming researchers to navigate these choices while learning the Linux command line for the first time.”
Across ecological communities, an evolutionary arms race occurs between plants and the herbivore species that rely on them for food. As plants evolve to synthesize different toxic chemicals to prevent them from being consumed, plant-eaters and the microbial bacteria they host evolve resistance to these toxins to be able to process and consume them. Furthering scientific understanding of this phenomenon has critical applications in multiple fields, including conservation biology and the agricultural industry.
Through the Microbiome Hub, GUTT researchers learn more about microbial communities—not only in their hosts’ digestive systems—but in the phenotypes expressed by vertebrate herbivores. For example, bacteria in the guts of animals can help with digestion, but have also been tied to different behavioral and demographic trends. GUTT researchers utilize sets of bioinformatic tools known as “microbial pipelines” to analyze genetic data using supercomputers and find the function of microorganisms. Having readily available pipelines can improve researchers’ ability to make these discoveries in an efficient way. Streamlining this analysis process is a key goal of Galla’s GUTT Microbiome Hub project.
“Data from this project are FAIR and the methods Dr. Galla is developing for data stewardship at the edge are translational,” said Elizabeth Leake, Director of Research Computing at Boise State. “By sharing with the West Big Data Hub, her work enables others to accelerate the process of discovery in a range of research applications with similar challenges,” she added.