Microbiome Analysis: Methods and Protocols

ISBN-13: 9781493987269 / Angielski / Twarda / 2018 / 324 str.

Robert Beiko; John Parkinson; Will Hsiao

Spis treści

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

Blurb

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.