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.
1. Characterizing the Deep Terrestrial Subsurface Microbiome
Rebecca A. Daly, Kelly C. Wrighton, and Michael J. Wilkins
2. Freshwater Viromes: From Sampling to Evaluation
Catherine Putonti, Zoë Diener, and Siobhan C. Watkins
3. Characterization of Eukaryotic Microbiome using 18S Amplicon Sequencing
Ana Popovic and John Parkinson
4. Culture and Molecular Profiling of the Respiratory Tract Microbiota
Fiona J. Whelan, Laura Rossi, Jennifer C. Stearns, and Michael G. Surette
5. Methods and Strategies to Examine the Human Breastmilk Microbiome
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
Erin M. Bertrand
7. Single-cell Genomics of Microbial Dark Matter
Christian Rinke
8. 16S rRNA Gene Analysis with QIIME2
Michael Hall and Robert Beiko
9. Processing a 16S rRNA Sequencing Dataset with the Microbiome Helper Workflow
Gavin M. Douglas, André M. Comeau, and Morgan G. I. Langille
10. Normalization of Microbiome
Profiling Data
11. Predicting the Functional Potential of the Microbiome from Marker Genes using PICRUSt
Gavin M. Douglas, Robert G. Beiko, and Morgan G. I. Langille
12. Metagenome Assembly and Contig Assignment
Qingpeng Zhang
13. From RNA-seq to Biological Inference: Using Compositional Data Analysis in Meta-transcriptomics
Jean M. Macklaim and Gregory B. Gloor
14. Subsampled Assemblies and Hybrid Nucleotide Composition/Differential Coverage Binning For Genome-resolved Metagenomics
Laura A. Hug
15. Transkingdom Networks: A Systems Biology Approach to Identify Causal Members of Host-Microbiota Interactions
Richard R. Rodrigues, Natalia Shulzhenko, and Andrey Morgun
16. Constructing and Analyzing Microbiome Networks in R
Mehdi Layeghifard, David M. Hwang, and David S. Guttman
17. Bayesian Inference of Microbial Community Structure from Metagenomic data using BioMiCo
Katherine A. Dunn, Katelyn Andrews, Rana O. Bashwih, and Joseph P. Bielawski
18. Analyzing Metabolomic Pathways in Microbiomes
Mobolaji Adeolu, John Parkinson, and Xuejian Xiong
19. Sparse Treatment-E_ect Model for Taxon Identi_cation with High-Dimensional Metagenomic Data
Zhenqiu Liu and Shili Lin
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.
Includes cutting-edge methods and protocols
