Microbiome Analysis

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 ...

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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.

Robert G. Beiko

Faculty of Computer Science

Dalhousie University

Halifax, NS, Canada

Will Hsiao

Department of Pathology & Laboratory Medicine

University of British Columbia

Vancouver, BC, Canada

John Parkinson

Program in Molecular Medicine The Hospital for Sick Children

Toronto, ON, Canada

Department of Biochemistry and Department of Molecular Genetics

University of Toronto

Tor...

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Robert G. Beiko

Faculty of Computer Science

Dalhousie University

Halifax, NS, Canada

Will Hsiao

Department of Pathology & Laboratory Medicine

University of British Columbia

Vancouver, BC, Canada

John Parkinson

Program in Molecular Medicine The Hospital for Sick Children

Toronto, ON, Canada

Department of Biochemistry and Department of Molecular Genetics

University of Toronto

Toronto, ON, Canada

Preface..................................................................... v Contributors................................................................. ix
1 Characterizing the Deep Terrestrial Subsurface Microbiome . . . . . . . . . . . . . . . . . 1
Rebecca A. Daly, Kelly C. Wrighton, and Michael J. Wilkins
2 Freshwater Viromes: From Sampling to Evaluation ......................... 17
Catherine Putonti, Zoe Diener, and Siobhan C. Watkins
3 Characterization of Eukaryotic Microbiome Using 18S Amplicon Sequencing .......... 29
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Preface..................................................................... v Contributors................................................................. ix
1 Characterizing the Deep Terrestrial Subsurface Microbiome . . . . . . . . . . . . . . . . . 1
Rebecca A. Daly, Kelly C. Wrighton, and Michael J. Wilkins
2 Freshwater Viromes: From Sampling to Evaluation ......................... 17
Catherine Putonti, Zoe Diener, and Siobhan C. Watkins
3 Characterization of Eukaryotic Microbiome Using 18S Amplicon Sequencing .......... 29
Ana Popovic and John Parkinson
4 Culture and Molecular Profiling of the Respiratory Tract Microbiota. . . . . . . . . . 49
Fiona J. Whelan, Laura Rossi, Jennifer C. Stearns, and Michael G. Surette
5 Methods and Strategies to Examine the Human Breastmilk Microbiome . . . . . . 63
Lauren LeMay-Nedjelski, Julia Copeland, Pauline W. Wang,
James Butcher, Sharon Unger, Alain Stintzi, and Deborah L. O’Connor
6 Quantification of Vitamin B12-Related Proteins in Marine Microbial Systems Using Selected Reaction Monitoring Mass Spectrometry................................................. 87
Erin M. Bertrand
7 Single-Cell Genomics of Microbial Dark Matter ............................ 99
Christian Rinke
8 16S rRNA Gene Analysis with QIIME2 ................................... 113
Michael Hall and Robert G. Beiko
9 Processing a 16S rRNA Sequencing Dataset with the Microbiome Helper
Workflow .....................................................................................131
Gavin M. Douglas, Andre ́ M. Comeau, and Morgan G. I. Langille
10 Normalization of Microbiome Profiling Data............................... 143
Paul J. McMurdie
11 Predicting the Functional Potential of the Microbiome from Marker Genes Using PICRUSt ....................................................................................... 169
Gavin M. Douglas, Robert G. Beiko, and Morgan G. I. Langille
12 Metagenome Assembly and Contig Assignment ............................ 179
Qingpeng Zhang
13 From RNA-seq to Biological Inference: Using Compositional
Data Analysis in Meta-Transcriptomics .................................... 193
Jean M. Macklaim and Gregory B. Gloor
14 Subsampled Assemblies and Hybrid Nucleotide
Composition/Differential Coverage Binning for Genome-Resolved Metagenomics.... 215
Laura A. Hug
15 Transkingdom Networks: A Systems Biology Approach to Identify
Causal Members of Host–Microbiota Interactions .......................... 227
Richard R. Rodrigues, Natalia Shulzhenko, and Andrey Morgun
16 Constructing and Analyzing Microbiome Networks in R .................... 243
Mehdi Layeghifard, David M. Hwang, and David S. Guttman
17 Bayesian Inference of Microbial Community Structure
from Metagenomic Data Using BioMiCo.................................. 267
Katherine A. Dunn, Katelyn Andrews, Rana O. Bashwih, and Joseph P. Bielawski
18 Analyzing Metabolic Pathways in Microbiomes............................. 291
Mobolaji Adeolu, John Parkinson, and Xuejian Xiong
19 Sparse Treatment-Effect Model for Taxon Identification
with High-Dimensional Metagenomic Data................................ 309
Zhenqiu Liu and Shili Lin
Index...................................................................... 319
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