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Analyzing Metabolic Pathways in Microbiomes

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Microbiome Analysis

Part of the book series: Methods in Molecular Biology ((MIMB,volume 1849))

Abstract

Understanding the metabolic activity of a microbial community, at both the level of the individual microbe and the whole microbiome, provides fundamental biological, biochemical, and clinical insights into the nature of the microbial community and interactions with their hosts in health and disease. Here, we discuss a method to examine the expression of metabolic pathways in microbial communities using data from metatranscriptomic next-generation sequencing data. The methodology described here encompasses enzyme function annotation, differential enzyme expression and pathway enrichment analyses, and visualization of metabolic networks with differential enzyme expression levels.

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Acknowledgments

This work was supported through funding from the Natural Sciences and Engineering Research Council (RGPIN-2014-06664), and the University of Toronto’s Medicine by Design initiative which receives funding from the Canada First Research Excellence Fund. Computing resources were provided by the SciNet HPC Consortium. SciNet is funded by the Canada Foundation for Innovation under the auspices of Compute Canada, the Government of Ontario, Ontario Research Fund—Research Excellence, and the University of Toronto.

Author information

Authors and Affiliations

  1. Program in Molecular Medicine, The Hospital for Sick Children, Toronto, ON, Canada

    Mobolaji Adeolu, John Parkinson & Xuejian Xiong

  2. Department of Biochemistry and Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada

    John Parkinson

Authors
  1. Mobolaji Adeolu
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  2. John Parkinson
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  3. Xuejian Xiong
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Corresponding author

Correspondence to Xuejian Xiong .

Editor information

Editors and Affiliations

  1. Faculty of Computer Science, Dalhousie University, Halifax, NS, Canada

    Robert G. Beiko

  2. Department of Pathology & Laboratory Medicine, University of British Columbia, Vancouver, BC, Canada

    Will Hsiao

  3. Program in Molecular Medicine, The Hospital for Sick Children, Toronto, ON, Canada

    John Parkinson

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Adeolu, M., Parkinson, J., Xiong, X. (2018). Analyzing Metabolic Pathways in Microbiomes. In: Beiko, R., Hsiao, W., Parkinson, J. (eds) Microbiome Analysis. Methods in Molecular Biology, vol 1849. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-8728-3_18

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  • DOI: https://doi.org/10.1007/978-1-4939-8728-3_18

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  • Publisher Name: Humana Press, New York, NY

  • Print ISBN: 978-1-4939-8726-9

  • Online ISBN: 978-1-4939-8728-3

  • eBook Packages: Springer Protocols

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