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Microbiome Analysis pp 227–242Cite as

Transkingdom Networks: A Systems Biology Approach to Identify Causal Members of Host–Microbiota Interactions

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

Abstract

Improvements in sequencing technologies and reduced experimental costs have resulted in a vast number of studies generating high-throughput data. Although the number of methods to analyze these “omics” data has also increased, computational complexity and lack of documentation hinder researchers from analyzing their high-throughput data to its true potential. In this chapter we detail our data-driven, transkingdom network (TransNet) analysis protocol to integrate and interrogate multi-omics data. This systems biology approach has allowed us to successfully identify important causal relationships between different taxonomic kingdoms (e.g., mammals and microbes) using diverse types of data.

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Acknowledgments

The authors thank Karen N. D’Souza, Khiem Lam, and Dr. Xiaoxi Dong for their help in writing the book chapter. This work was supported by the NIH U01 AI109695 (AM) and R01 DK103761 (NS).

Author information

Authors and Affiliations

  1. College of Pharmacy, Oregon State University, Corvallis, OR, USA

    Richard R. Rodrigues & Andrey Morgun

  2. College of Veterinary Medicine, Oregon State University, Corvallis, OR, USA

    Natalia Shulzhenko

Authors
  1. Richard R. Rodrigues
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  2. Natalia Shulzhenko
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  3. Andrey Morgun
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Corresponding authors

Correspondence to Richard R. Rodrigues or Andrey Morgun .

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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Rodrigues, R.R., Shulzhenko, N., Morgun, A. (2018). Transkingdom Networks: A Systems Biology Approach to Identify Causal Members of Host–Microbiota Interactions. 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_15

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  • DOI: https://doi.org/10.1007/978-1-4939-8728-3_15

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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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