Host-Microbiome Functional ‘Omics

The International Microbiome Centre (IMC) Functional ‘Omics’ program in partnership with the Calgary Metabolomics Research Facility (CMRF) and Southern Alberta Mass Spectrometry (SAMS) Centre is a centralized facility specializing in metabolomics and proteomics for determining the function of microbiomes within their environment.

Vision

Our vision is to harness the power of microbiome metabolomics and proteomics for better living.

Mission

Our mission is to be leaders in microbiome ‘omics’ research through providing expertise and service. IMC functional ‘omics’ provides state-of-the-art metabolomic and proteomic technologies for advancement of microbiome research to a broad audience of researchers (internal and external), industry and government including animal health, agriculture, energy and the environment. IMC expertise and resources in functional ‘omics’ allows for unravelling of complex host-microbiome dynamics and for the identification of molecular markers underpinning chronic diseases. IMC is facilitating the development of a global network of expertise and service to enable collaborations and partnerships that will promote translation of microbiome research. IMC functional ‘omics’ will provide a basis for access to expertise and information on microbiome metabolomics and proteomics advancements, access and experts.

Metabolomics

The CMRF offers the following standardized services. Custom assays can be developed on a one-on-one basis.


General metabolite profiling

  • Covers over 250 central carbon metabolites
  • <10 minute assay
  • Identifies all common microbial nutrients and waste products
  • Thermo Fisher Scientific Q-Exactive HF coupled to a Vanquish Flex UHPLC

Metabolic flux analysis

  • Measures the activity of intracellular pathways
  • Traces isotopically labeled nutrients through downstream pathways
  • Identifies metabolic pathways that are inhibited/ stimulated in disease states
  • Thermo-Fisher Scientific Q-Exactive high-resolution mass spectrometer coupled to a Thermo-Fisher Vanquish UHPLC separation system (configured for ion-pairing chromatography)

Quantitative analysis

  • Targeted quantification of key biomarkers in biological samples (eg. short chain fatty acids)
  • Quantitative scale-up of novel metabolite discoveries
  • Thermo Fisher Quantum Access Max triple quadrupole mass spectrometer (QqQ) coupled to a Vanquish Flex UHPLC

Microbiome Proteomics

The Southern Alberta Mass Spectrometry (SAMS) center provides rapid, quantitative assessments of microbial proteomes both in the context of the microbiome and infectious disease.


In solution LC-MS/MS sample prep

  • Accurate protein identification
  • SP3-based protein concentration and cleanup
  • Multiplex formatting for bacterial lysis, protein concentration, and sample cleanup

Tandem Mass Tag (TMT) proteomic quantification

  • Precise proteomic quantitation
  • High-throughput, multiplex formats
  • 10x faster overall MS run time for large sample sets

LC-MS/MS protein identification

  • Low throughput protein and proteome characterization
  • Affordable analyses for up to 10 samples/day


Personnel

Dr. Ian Lewis

Ian Lewis, PhD, Director, Metabolomics, Proteomics and Lipidomics, International Microbiome Centre

Dr. Ian Lewis is an assistant professor and Alberta Innovates – Health Solutions Translational Health Chair in Metabolomics in the Department of Biological Sciences at the University of Calgary. Lewis earned a PhD in biochemistry from the University of Wisconsin-Madison and completed his postdoctoral training at Princeton University. He was recruited by UCalgary to launch a research program that harnesses state-of-theart technology to detect and combat infectious diseases. As a part of this program, Lewis built the Calgary Metabolomics Research Facility (CMRF), an analytical lab that specializes in unravelling the complex host-pathogen metabolic interactions that occur during infections. Recently, he partnered with Alberta Public Laboratories (formerly Calgary Laboratory Services [CLS]) to launch a suite of new diagnostic tools and treatment practices that may significantly reduce the number of people who die from infection.

Select Publications

Flannigan K et al. (2018) An intact microbiota is required for the gastrointestinal toxicity of the immunosuppressant mycophenolate mofetil. J. Heart Lung Transplant.37(9): 1047-1059

Motta JP et al. (2018) Iron Sequestration in Microbiota Biofilms as a Novel Strategy for Treating Inflammatory Bowel Disease. Inflamm. Bowel Dis. 24(7): 1493- 1502

Moges R et al. (2018) Anti-Inflammatory Benefits of Antibiotics: Tylvalosin Induces Apoptosis of Porcine Neutrophils and Macrophages, Promotes Efferocytosis, and Inhibits Pro-Inflammatory CXCL-8, IL1, and LTB4 Production, While Inducing the Release of Pro-Resolving Lipoxin A4 and Resolvin D1. Front. Vet. Sci. (5)57

Gauthier PT et al. (2018) Lifelong Exposure to PCBs in the Remote Norwegian Arctic Disrupts the Plasma Stress Metabolome in Arctic Charr. Environ. Sci. Technol. 52(2): 868-876

Schräder CU et al. (2018) Lysine Propionylation To Boost Sequence Coverage and Enable a “Silent SILAC” Strategy for Relative Protein Quantification. Anal. Chem. 90 (15): 9077–9084

Lu W et al. (2017) Metabolite Measurement: Pitfalls to Avoid and Practices to Follow. Annu. Rev. Biochem. 86: 277-304

Bingeman T et al. (2017) Digestomics: an emerging strategy for comprehensive analysis of protein catabolism Curr. Opin. Biotechnol. 43:134-140

Contact

Shaunna Huston, ACCN RN, BSc, PhD Immunology

Director, Programs and Business, International Microbiome Centre

Phone: 403-220-6074
Email: imc@ucalgary.ca