Statistical modeling, inference and methodology in microbial metagenomics data analysis and computational molecular evolution

Recent research has shown the enormous influence of the microbiome on our lives. Microbial communities play crucial roles in human health, agriculture and the environment.

Despite their undisputed importance, we know very little about how the microbes interact with each other and function together in the microbial community. The main aim of my research program is to develop statistical methods and models to understand the compositions and functions of the microbial communities and their interaction with host genome and/or environment. Microbiome data present new statistical challenges, thus new statistical methods will be needed. These statistical methods will also advance the field of statistics, leading to further potential applications outside of microbiome research. The direct results of the proposed research will provide tools for analyzing the microbiome data. This will have benefits in multiple areas.

On the human health front, knowledge about how the microbiome changes are related to different disease status will have the immediate clinical benefit on diagnostics and choices of treatment regime. For example, understanding the causes of IBD and the response of the microbiome to various treatments could lead to improved treatments in future, including new microbial treatments. There have already been successful applications of microbial treatments for some conditions, such as faecal transplants for treating C. Difficile and L. Plantarum probiotic treatments for preventing neonatal sepsis. Further research will improve these treatments and lead to new treatments.

IBD is an emerging health problem associated with high morbidity and health care costs. IBD affects about 1 in 150 Canadians (among the highest rates in the world) with the estimated economic burden to Canadians as $2.8 billion per year.

Another major health-related area of interest is obesity. Research has indicated a link between the gut microbiome and obesity, but little is known about the connection. The methods in my proposed research will help to shed light on the processes linking obesity and the microbiome, leading to preventative measures and treatment for obesity-related health conditions.

On the environmental side, my collaboration with world renowned scientist, Julie Laroche, allows me to work on ocean microbiome data. The microbiome plays a critical role in the ocean ecosystem, and changes to the microbiome can have repercussions on the higher trophic levels. The effects of pollution and climate change on the ocean microbiome are therefore of great concern. I expect many of the conclusions and methods from this research project will also apply to other environmental microbiome samples.