Lab Members

Principle Investigator

Dr. Thomas Sharpton  
We aim to develop testable hypotheses about how humans and their microbiome interact, and strive to understand the evolutionary and ecological processes that influence community assembly, maintenance, and function within a host. Ultimately, this knowledge will be used to discover disease mechanisms, identify predicative and diagnostic biomarkers of disease, and develop tools to treat disease through manipulation of the microbiome.


Dr. Christopher Gaulke  
Broadly, I am interested in developing high throughput molecular and computational tools for the interrogation of host-microbe interactions. I am particularly interested in using the zebrafish model to examine the impact of environmental contaminants on microbial community structure and function.
Dr. Keaton Stagaman  
The gut microbiome is a complex and dynamic community with an incredible metabolic potential. The makeup of the microbiome (i.e., its constituent species and their genes) is influenced by multiple processes including selection by the host, interactions between the microbes, and (my focus) exposure to environmental compounds such as toxins and drugs. The metabolic capabilities of the microbiome influence how such environmental compounds are processed within the host: potentially mitigating or exacerbating toxic effects. My goal, using observational studies in humans and experiments in model organisms, is to ascertain how the environment influences the metabolic potential of the microbiome, and in turn, how the microbiome alters the effects of environmental compounds on the development and health of the host.

Graduate Students

Courtney Armour  
The goal of my research is to understand how the complex community of microorganisms that inhabit the intestines, known as the gut microbiome, influence vertebrate health and evolution. The primary aims of my research are: to determine (1) which microbiome functions consistently stratify healthy and diseased humans, (2) which microbiome functions are conserved across mammals, and (3) whether evolutionarily conserved microbiome functions are critical to health. Overall, this research will provide insight into the importance of specific microbiome functions to maintaining host health and will highlight their potential contribution to the evolutionary fitness of vertebrates.
Holly Arnold  
Holly is a DVM / PhD student at the Carlson College of Veterinary Medicine and Sharpton lab. Broadly, she is interested in developing bioinformatic analyses of the microbiome as a diagnostic test in companion animals or to improve productivity of food animals. Her current research project is to integrate both microbial phylogenetic information with microbial community data to improve disease detection in companion animals. An ongoing goal of the work is to understand if there are particular clades of microorganisms which are preferentially recruited to the mammalian gut, and clarify physiological functions these clades of microbes provide to the host.
Ian Humphreys  
Culturable bacteria represent a small fraction of the total microbial diversity found in nature. As a result, I'm interested in leveraging computational techniques to glean insight into microbial systems. While high-throughput sequencing technology drives this field, the impact of using these short sequences is poorly understood. My current research focuses on how sampling techniques influence phylogeny and thus our interpretation of evolutionary history and diversity in microbiomes.
Nicole Kirchoff  
My research interests surround the ecology and interactions of microorganisms in varying ecosystems. Currently, I'm considering research questions regarding the role of microbes in shaping psychological phenotypes. My main project is investigating the link between gut microbial composition and aggression in dogs.
Quinn Washburn  
The goal of my research is to develop the next generation of high throughput cultivation methods for understanding microbial communities. I am focusing on methods for quantifying enrichment culture composition in a high throughput format that can be automated and applied to low cell density cultures. I am employing this method to study the zebrafish gut microbiome and dark ocean bacterioplankton.


Alexandria Wilson  
I combine culture based and computational techniques to understand the microbial diversity of the zebrafish (Danio rerio) gut microbiome.

Former Lab Members

Dr. Yanfen Cheng Dr. Melissa Conley Kyle Duyck
Lexi Gauthier Holman Jue Sean McNall