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Microbiome Analysis

Methods and Protocols

  • Book
  • © 2018

Overview

Editors:
  1. Robert G. Beiko

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

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    You can also search for this editor in PubMed   Google Scholar

  2. Will Hsiao

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

    View editor publications

    You can also search for this editor in PubMed   Google Scholar

  3. John Parkinson

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

    View editor publications

    You can also search for this editor in PubMed   Google Scholar

  • Includes cutting-edge methods and protocols
  • Provides step-by-step detail essential for reproducible results
  • Contains key notes and implementation advice from the experts

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

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Table of contents (19 protocols)

  1. Front Matter

    Pages i-xi
    Download chapter PDF

  2. Characterizing the Deep Terrestrial Subsurface Microbiome

    • Rebecca A. Daly, Kelly C. Wrighton, Michael J. Wilkins
    Pages 1-15

  3. Freshwater Viromes: From Sampling to Evaluation

    • Catherine Putonti, Zoë Diener, Siobhan C. Watkins
    Pages 17-27

  4. Characterization of Eukaryotic Microbiome Using 18S Amplicon Sequencing

    • Ana Popovic, John Parkinson
    Pages 29-48

  5. Culture and Molecular Profiling of the Respiratory Tract Microbiota

    • Fiona J. Whelan, Laura Rossi, Jennifer C. Stearns, Michael G. Surette
    Pages 49-61

  6. Methods and Strategies to Examine the Human Breastmilk Microbiome

    • Lauren LeMay-Nedjelski, Julia Copeland, Pauline W. Wang, James Butcher, Sharon Unger, Alain Stintzi et al.
    Pages 63-86

  7. Quantification of Vitamin B12-Related Proteins in Marine Microbial Systems Using Selected Reaction Monitoring Mass Spectrometry

    • Erin M. Bertrand
    Pages 87-98

  8. Single-Cell Genomics of Microbial Dark Matter

    • Christian Rinke
    Pages 99-111

  9. 16S rRNA Gene Analysis with QIIME2

    • Michael Hall, Robert G. Beiko
    Pages 113-129

  10. Processing a 16S rRNA Sequencing Dataset with the Microbiome Helper Workflow

    • Gavin M. Douglas, André M. Comeau, Morgan G. I. Langille
    Pages 131-141

  11. Normalization of Microbiome Profiling Data

    • Paul J. McMurdie
    Pages 143-168

  12. Predicting the Functional Potential of the Microbiome from Marker Genes Using PICRUSt

    • Gavin M. Douglas, Robert G. Beiko, Morgan G. I. Langille
    Pages 169-177

  13. Metagenome Assembly and Contig Assignment

    • Qingpeng Zhang
    Pages 179-192

  14. From RNA-seq to Biological Inference: Using Compositional Data Analysis in Meta-Transcriptomics

    • Jean M. Macklaim, Gregory B. Gloor
    Pages 193-213

  15. Subsampled Assemblies and Hybrid Nucleotide Composition/Differential Coverage Binning for Genome-Resolved Metagenomics

    • Laura A. Hug
    Pages 215-225

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

    • Richard R. Rodrigues, Natalia Shulzhenko, Andrey Morgun
    Pages 227-242

  17. Constructing and Analyzing Microbiome Networks in R

    • Mehdi Layeghifard, David M. Hwang, David S. Guttman
    Pages 243-266

  18. Bayesian Inference of Microbial Community Structure from Metagenomic Data Using BioMiCo

    • Katherine A. Dunn, Katelyn Andrews, Rana O. Bashwih, Joseph P. Bielawski
    Pages 267-289

  19. Analyzing Metabolic Pathways in Microbiomes

    • Mobolaji Adeolu, John Parkinson, Xuejian Xiong
    Pages 291-307

  20. Sparse Treatment-Effect Model for Taxon Identification with High-Dimensional Metagenomic Data

    • Zhenqiu Liu, Shili Lin
    Pages 309-318
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Keywords

About this book

This volume aims to capture the entire microbiome analysis pipeline, sample collection, quality assurance, and computational analysis of the resulting data. Chapters detail several example applications of microbiome research, and the protocols described in this book are complemented with short perspectives about the history, current state, and future directions of protocols in microbiomics. Written in the highly successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and tips on troubleshooting and avoiding known pitfalls.

Authoritative and cutting-edge, Microbiome Analysis: Methods and Protocols aims to ensure successful results in the further study of this vital field.

Editors and Affiliations

  • Faculty of Computer Science, Dalhousie University, Halifax, Canada

    Robert G. Beiko

  • Department of Pathology & Laboratory Medicine, University of British Columbia, Vancouver, Canada

    Will Hsiao

  • Program in Molecular Medicine, The Hospital for Sick Children, Toronto, Canada

    John Parkinson

Bibliographic Information

  • Book Title: Microbiome Analysis

  • Book Subtitle: Methods and Protocols

  • Editors: Robert G. Beiko, Will Hsiao, John Parkinson

  • Series Title: Methods in Molecular Biology

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

  • Publisher: Humana New York, NY

  • eBook Packages: Springer Protocols

  • Copyright Information: Springer Science+Business Media, LLC, part of Springer Nature 2018

  • Hardcover ISBN: 978-1-4939-8726-9Published: 09 October 2018

  • Softcover ISBN: 978-1-4939-9376-5Published: 10 December 2019

  • eBook ISBN: 978-1-4939-8728-3Published: 08 October 2018

  • Series ISSN: 1064-3745

  • Series E-ISSN: 1940-6029

  • Edition Number: 1

  • Number of Pages: XI, 324

  • Number of Illustrations: 4 b/w illustrations, 78 illustrations in colour

  • Topics: Genetics and Genomics

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