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Characterization of Eukaryotic Microbiome Using 18S Amplicon Sequencing

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Microbiome Analysis

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

Abstract

With the advent of low-cost, high-throughput sequencing, taxonomic profiling of complex microbial communities through 16S rRNA marker gene surveys has received widespread interest, uncovering a wealth of information concerning the bacterial composition of microbial communities, as well as their association with health and disease. On the other hand, little is known concerning the eukaryotic components of microbiomes. Such components include single-celled parasites and multicellular worms that are known to adversely impact the health of millions of people worldwide. Current molecular methods to detect eukaryotic microbes rely on the use of directed PCR analyses that are limited by their inability to inform beyond the taxon targeted. With increasing interest to develop equivalent marker-based surveys as used for bacteria, this chapter presents a stepwise protocol to characterize the diversity of eukaryotic microbes in a sample, using amplicon sequencing of hypervariable regions in the eukaryotic 18S rRNA gene.

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Author information

Authors and Affiliations

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

    Ana Popovic & John Parkinson

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

    Ana Popovic & John Parkinson

Authors
  1. Ana Popovic
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  2. John Parkinson
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Corresponding author

Correspondence to John Parkinson .

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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Popovic, A., Parkinson, J. (2018). Characterization of Eukaryotic Microbiome Using 18S Amplicon Sequencing. 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_3

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  • DOI: https://doi.org/10.1007/978-1-4939-8728-3_3

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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

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