Microscopic life forms, or microbes, are the invisible inhabitants of Earth. Despite their small size, these organisms can have significant impacts on their environment, which includes animal and human hosts. Modern analysis of complex populations of diverse microorganisms (the microbiome) associated with a particular environment relies on DNA extracted from samples. Analysis of such DNA can be highly complex, requiring advanced statistical techniques (bioinformatics) to unravel the structures and properties of microbiomes. This fellowship will allow the PI to work with experts at the University of California at San Diego, a leader in application of bioinformatics to ecological research. The PI will develop his own expertise in the rapidly developing field of bioinformatics, acquiring skills that he will then be able to apply to a variety of applications at his home institution (Boise State University). This research project will study the microbiomes of the digestive systems of animals that eat sagebrush, a toxic plant. By comparing the microbiomes of digestive systems following consumption of toxic and non-toxic food, the PI and his collaborators will discover how the microbes deal with these plant-derived chemicals, which may lead to new ways to chemically synthesize plant molecules, discover new antimicrobial drugs, or combat animals that eat commercially and ecologically important plants.
Microbial DNA sequence data are accumulating rapidly, but approaches that uncover the specific functions of microbes are lagging behind. This project will conduct experiments aimed at uncovering the microbial functions that facilitate the ability of animals to eat toxic sagebrush. The PI and collaborators will collect and sequence DNA from the microbiomes of digestive tracts of these animals, and do so over time and between plants with different chemical toxins. This time-series and comparative metagenomics approach will uncover specific microbes and specific genes that enable rapid seasonal adaptation to sagebrush by pigmy rabbits, and adaptation to unique sagebrush chemical profiles in Lepidoptera caterpillars. It is hypothesized that many of the solutions employed by the microbiomes inhabiting these specific organisms will be found in other organisms around the world. In addition, the PI and collaborators will search for non-coding RNA regulatory elements that have evolved in these contexts and enable the microbes to detect and act on chemical signals. This research will advance understanding of sagebrush herbivores and herbivore specialization to toxic plants around the world. Herbivore-plant interactions such as this drive the bio-diversification of the planet, and have numerous ecological and economic consequences for people.
