Microbiome Analysis: Methods and Protocols

✍ Scribed by Robert G. Beiko, Will Hsiao, John Parkinson

• Publisher: Springer New York;Humana Press
• Year: 2018
• Tongue: English
• Leaves: 324
• Series: Methods in Molecular Biology 1849
• Edition: 1st ed.
• Category: Library

✦ Synopsis

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.

✦ Table of Contents

Front Matter ....Pages i-xi
Characterizing the Deep Terrestrial Subsurface Microbiome (Rebecca A. Daly, Kelly C. Wrighton, Michael J. Wilkins)....Pages 1-15
Freshwater Viromes: From Sampling to Evaluation (Catherine Putonti, Zoë Diener, Siobhan C. Watkins)....Pages 17-27
Characterization of Eukaryotic Microbiome Using 18S Amplicon Sequencing (Ana Popovic, John Parkinson)....Pages 29-48
Culture and Molecular Profiling of the Respiratory Tract Microbiota (Fiona J. Whelan, Laura Rossi, Jennifer C. Stearns, Michael G. Surette)....Pages 49-61
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
Quantification of Vitamin B12-Related Proteins in Marine Microbial Systems Using Selected Reaction Monitoring Mass Spectrometry (Erin M. Bertrand)....Pages 87-98
Single-Cell Genomics of Microbial Dark Matter (Christian Rinke)....Pages 99-111
16S rRNA Gene Analysis with QIIME2 (Michael Hall, Robert G. Beiko)....Pages 113-129
Processing a 16S rRNA Sequencing Dataset with the Microbiome Helper Workflow (Gavin M. Douglas, André M. Comeau, Morgan G. I. Langille)....Pages 131-141
Normalization of Microbiome Profiling Data (Paul J. McMurdie)....Pages 143-168
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
Metagenome Assembly and Contig Assignment (Qingpeng Zhang)....Pages 179-192
From RNA-seq to Biological Inference: Using Compositional Data Analysis in Meta-Transcriptomics (Jean M. Macklaim, Gregory B. Gloor)....Pages 193-213
Subsampled Assemblies and Hybrid Nucleotide Composition/Differential Coverage Binning for Genome-Resolved Metagenomics (Laura A. Hug)....Pages 215-225
Transkingdom Networks: A Systems Biology Approach to Identify Causal Members of Host–Microbiota Interactions (Richard R. Rodrigues, Natalia Shulzhenko, Andrey Morgun)....Pages 227-242
Constructing and Analyzing Microbiome Networks in R (Mehdi Layeghifard, David M. Hwang, David S. Guttman)....Pages 243-266
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
Analyzing Metabolic Pathways in Microbiomes (Mobolaji Adeolu, John Parkinson, Xuejian Xiong)....Pages 291-307
Sparse Treatment-Effect Model for Taxon Identification with High-Dimensional Metagenomic Data (Zhenqiu Liu, Shili Lin)....Pages 309-318
Back Matter ....Pages 319-324

✦ Subjects

Life Sciences; Genetics and Genomics