James Ryan is enrolled in his second year at the University of Ottawa’s M.Sc. Program in Biochemistry (spec. Bioinformatics) under the supervision of Dr. Daniel Figeys and Dr. Mathieu Lavallée-Adam. He obtained a B.Sc. Combined Honours in Biochemistry & Molecular Biology and Computer Science from Dalhousie University in 2016.
Research Interests
The human gut microbiome exists as a community of microorganisms in symbiosis with its host. Prebiotics are functional compounds that modulate this microbial community, promoting growth and activity of bacteria beneficial to human health. Identifying and quantifying prebiotics’ effects on microbiomes is crucial to understanding their roles in shaping gut flora composition and function; however, these effects are clouded by the complex interactions between the microbiome’s trillions of microorganisms, which include roughly 1000 bacterial species. Comprehensively characterizing bacterial species-specific and microbiome-systemic shifts resulting from prebiotics is an important bioanalytical problem. To this end, I assess microbiome responses to resistant starches (RS), a group of prebiotics, through a combined metaproteomics and bioinformatics approach. Ex vivo gut microbiome samples exposed to different RS treatments are assessed for changes in bacterial protein/biochemical pathway expression and taxonomic composition. A bioanalytical assay generating label-free quantitative mass spectrometry metaproteomics data tests for these effects experimentally. Further, a bioinformatics pipeline is being designed and implemented to parsimoniously assign peptide quantification measurements amongst homologous proteins to bacterial species using linear programming, producing protein and bacterial abundance data that elucidates prebiotic-modulated biochemical pathways and microbiome species abundances. This pipeline will enable rapid determination of prebiotic-mediated microbiome responses and elucidate possible targets for host-beneficial microbiome modulation.
Program Goals
- Gain knowledge of analytical methods for microbiome and biochemistry research
- Improve programming and software development techniques surrounding bioinformatics
- Complete a research project focusing on the microbiome in a multidisciplinary context