Building Strength in Omics

Supporting multiple University of Calgary Research Strategies and the Faculty of Science Grand Challenge “Understanding Earth’s Evolving Systems”, and Alberta Research and Innovation Framework (ARIF) aims “Economic Diversification and Job Creation” and “Healthy Alberta”.

Collaborations with Department of Bioscience: Ian Lewis. Cumming School of Medicine: Paul Gordon. Veterinary Medicine: Derek McKay. North Carolina State University Manuel Kleiner. Delft University of Technology: Martin Pabst.

The research from the Group addresses complex microbial communities, referred as “microbiomes”. Such communities can for example be human microbiomes, groundwater microbiomes, microplastic microbiomes, or the microbiomes of an oil sands tailings pond. Microbiomes perform key processes in all these ecosystems. Well-tuned microbiomes are key to desired outcomes such as successful bioremediation or improved human and animal health. Microbiomes consist of hundreds to thousands of different microbial species, which interact in unknown ways. This leads to a vast amount of complexity and a need for big data approaches to realize successful outcomes.

We aim to advance the fields of both metagenomics and metaproteomics by providing training, better tools, and new approaches. For example, our team organized and ran no-profit international workshops providing hands-on training to fifty participants from various countries. We also developed software, databases, and web-platform enabling entry-level researchers and students to better and more effectively analyze their metagenomics data.

Proteomics could be a powerful complement to metagenomics, especially because these are experimentally independent approaches, with each compensating for the bias of the other. Crucially, proteomics depends on mass spectrometry, so it can be combined with isotopic approaches, bridging the gap between molecular biology and geoscience. Proteomics is relatively under-used in microbial ecology today. Our team is publishing a series of studies to highlight the potential of proteomics to microbial ecologists. These papers also provide detailed protocols for proteomics facilities, generally operating in a medical context, empowering them to use better workflows to handle samples of microbial communities. We also developed a new proteomics approach to determine the natural isotopic fingerprint of individual species within complex microbial communities. Our current research is extending this approach to realize step changes in the precision and sensitivity for stable isotope probing/proteomics applications.