My lab studies communities of microbial eukaryotes (protists) with the goal of understanding their diversity and distribution across environments. Eukaryotes, which include the familiar plants, animals, and fungi, are incredibly diverse and consist of many microbial lineages of amoebae, flagellates, ciliates, algae, and parasites. We use high-throughput sequencing to characterize microbial communities. Our analyses use a phylogenetic framework of the eukaryotic tree of life to gain an evolutionary perspective on microbial community diversity. Currently there are three focal areas of research.
1. Eukaryotes in the human microbiome
All animals have evolved in association with a consortium of microbes, and microbes make up huge part of who we are as humans: 90% of the cells in our bodies are microbial. Research in recent years has revealed that these microbes influence aspects of our lives ranging from disease, immune system development, nutrition and even behavior. Western life styles have greatly altered our microbial consortium. These insights come almost exclusively from bacteria, but we have many reasons to suspect that eukaryotic microbes also play an important role at the community level. To begin to elucidate the role of eukaryotes within the microbiome community my lab is collaborating with other researchers to understand the normal human microbiome, so that we can better determine how it is altered during westernization and in disease states. We are also assessing microbial eukaryotic communities in other vertebrate hosts to discover broader ecological and evolutionary patterns.
2. Microbial eukaryotic communities across environmental gradients
Determining how organismal diversity is distributed across environments is one of the fundamental goals of ecology. High throughput sequencing methods enable us to characterize microbial communities at unprecedented levels of detail. My lab will use a combination of environmental surveys and lab experiments to understand some of the major transitions that structured microbial eukaryotic communities. We are setting up field sites in coastal BC to study salinity gradients. We are also interested in better understanding the ecology and evolution of microbial communities that are ubiquitously associated with non-vertebrate animal hosts.
3. Improving infrastructure for eukaryotic community analyses
All of these projects require a curated database so that taxonomic information can be assigned to the environmental sequences. My lab is working in conjunction with the SILVA ribosomal database to improve eukaryotic taxonomy in the database and make this information available to the broader research community. We also work to improve the phylogenetic tree and associated resources that enable phylogenetically informed microbial community analyses.