My research focuses on understanding microbial physiology and metabolic processes in predominantly anaerobic environments. This research relies on a diversity of techniques to elucidate microbe-microbe and microbe-host interactions, including 16S rRNA based community analysis, genomics, metagenomics, transcriptiomics, metatranscriptiomics, and proteomics, coupled with more traditional microbiology techniques such as enzymology and culture-bases experiments. We work in many different systems including humans, 13 lined ground squirrels and wastewater treatment.
I am investigating the interactions between methanogenic Archaea, the gut microbiome and the humans they inhabit. These Archaea can influence host health by removing harmful compounds, like trimethylamines. Trimethylamines are produced by bacteria during the break down of carnitine and phosphatidylcholine and can cause atherosclerosis if they reach the liver. We are working to identify the bacteria that produce trimethylamines and elucidate their interactions with these methanogens.
I am also applying what I have learned about host-microbe interactions and microbial physiology to the microbiota of hibernating mammals. The gut microbiome of hibernating mammals contains many uncultured microorganisms. Using metagenomics and metabolomics analyses, we have gained insight into both the potential functions of the microbiome as well as snapshots of microbial activity. These predictive tools and glimpses into what the microbiome is doing during hibernation. By studying individual microorganisms from the hibernating ground squirrel cecum, we can begin to understand how a microbiome survives and thrives in the environment of the intestine during the drastic changes that occur during hibernation. These microbes may play critical roles in fat metabolism and vitamin production to benefit the host.