Integrating and modeling host-microbiome interactions

“Microbiome” is a relatively new term to describe the entire set of microbes and their functions within a particular environment. Researchers are sampling various microbiomes including the ocean, soil, and host-associated (e.g. plant, animal and human). The host-associated microbiomes are crucial components of their hosts contributing metabolic capabilities, defence against unwanted pathogens, and training of the host immune system. These microbiomes are complex communities consisting of thousands of species and millions of genes that interact, not only amongst themselves, but also with their environment. To understand these interactions requires computational methods that help process large datasets and identify biologically relevant patterns. This research program pursues several new computational strategies for understanding the mechanisms within these microbial communities and how they interact with their hosts. In particular, it attempts to build methods that can predict when closely related microbes have different functional capabilities, improve host sample classification, and integrate information arising from diverse independent microbiome studies. This research program is crucial for leveraging the most knowledge from on-going microbiome research around the world and will provide the foundations for translating this knowledge into real world applications. These include more efficient and cost effective methods for profiling microbiomes, the ability to use the microbiome to improve diagnosis or treatment of various human diseases, and to identify novel microbes and microbial functions that are key determinants in host-microbial interactions.