Metagenomics for Microbiology

Metagenomics for Microbiology

1st Edition - November 7, 2014

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  • Editors: Jacques Izard, Maria Rivera
  • Paperback ISBN: 9780124104723
  • eBook ISBN: 9780124105089

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Concisely discussing the application of high throughput analysis to move forward our understanding of microbial principles, Metagenomics for Microbiology provides a solid base for the design and analysis of omics studies for the characterization of microbial consortia. The intended audience includes clinical and environmental microbiologists, molecular biologists, infectious disease experts, statisticians, biostatisticians, and public health scientists. This book focuses on the technological underpinnings of metagenomic approaches and their conceptual and practical applications. With the next-generation genomic sequencing revolution increasingly permitting researchers to decipher the coding information of the microbes living with us, we now have a unique capacity to compare multiple sites within individuals and at higher resolution and greater throughput than hitherto possible. The recent articulation of this paradigm points to unique possibilities for investigation of our dynamic relationship with these cellular communities, and excitingly the probing of their therapeutic potential in disease prevention or treatment of the future.

Key Features

  • Expertly describes the latest metagenomic methodologies and best-practices, from sample collection to data analysis for taxonomic, whole shotgun metagenomic, and metatranscriptomic studies
  • Includes clear-headed pointers and quick starts to direct research efforts and increase study efficacy, eschewing ponderous prose
  • Presented topics include sample collection and preparation, data generation and quality control, third generation sequencing, advances in computational analyses of shotgun metagenomic sequence data, taxonomic profiling of shotgun data, hypothesis testing, and mathematical and computational analysis of longitudinal data and time series. Past-examples and prospects are provided to contextualize the applications.


Current researchers studying the use of metagenomic methods in molecular biology, microbiology, genomic expression, infectious disease, and cancer research

Table of Contents

    • List of Contributors
    • Preface
    • Chapter 1: Steps in Metagenomics: Let’s Avoid Garbage in and Garbage Out
      • Abstract
      • Why metagenomics?
      • It all starts with the study design
      • Have a statistical analysis plan in place before starting
      • Metadata is needed to provide context to the analysis
      • Sampling: the basis of good results
      • Sample storage
      • Sample extraction
      • Choosing the right platform
      • Data storage and data analysis
      • Data and publication
      • Let’s talk about the status quo
      • Acknowledgments
    • Chapter 2: Long-Read, Single Molecule, Real-Time (SMRT) DNA Sequencing for Metagenomic Applications
      • Abstract
      • Full-length 16S rRNA gene sequencing
      • Discussion
    • Chapter 3: Ribosomal RNA Removal Methods for Microbial Transcriptomics
      • Abstract
      • Introduction
      • Size selection by gel electrophoresis
      • Denaturing high-performance liquid chromatography
      • 5′ phosphate-dependent exonuclease digestion
      • RNase H digestion
      • Subtractive hybridization with rRNA-specific probes
      • Biased 3′ polyadenylation against rRNA
      • Selective priming in cDNA synthesis
      • cDNA library normalization
      • Combination of methods
      • Conclusions and perspectives
    • Chapter 4: High-Throughput Sequencing as a Tool for Exploring the Human Microbiome
      • Abstract
      • Introduction
      • Organizing metagenomic reads by mapping onto reference genomes
      • Taxonomic classification/binning
      • Structuring metagenomic short reads into a gene catalog by de novo assembly
      • Clustering metagenomic gene catalogs
      • Advanced metagenomic analyses
      • Conclusion
    • Chapter 5: Computational Tools for Taxonomic Microbiome Profiling of Shotgun Metagenomes
      • Abstract
      • Introduction
      • Taxonomic profiling with shotgun metagenomics
      • Assembly-based taxonomic profiling of microbiome
      • Compositional approaches for metagenomic binning
      • Mapping-based recruitment of metagenomic reads
      • Marker-based taxonomic profiling
      • Profiling large metagenomic cohorts: a case study
      • Conclusions and outlook
      • Acknowledgments
    • Chapter 6: Hypothesis Testing of Metagenomic Data
      • Abstract
      • Introduction
      • Metagenomic data
      • Compare diversity across groups
      • Compare a taxon of interest across groups
      • Compare the frequency of all taxa across groups
      • Discussion and future research
    • Chapter 7: Longitudinal Microbiome Data Analysis
      • Abstract
      • Introduction
      • Examples
      • Computational methods for analyzing microbiome time-series data
      • Conclusion
    • Chapter 8: Metagenomics for Bacteriology
      • Abstract
      • Healthy hosts and microbiomes
      • What about disease?
      • Food, biotransformation, and life
      • Some practical usage of the microbiomes
      • Our societal choices influence the microbiomes
      • Diving into a detailed view of the scales involved
      • What would help to further the leap?
      • Acknowledgments
    • Chapter 9: Toward the Understanding of the Human Virome
      • Abstract
      • Introduction
      • Virome characterization workflow
      • Recent virome studies
      • Interaction of the virome with the human host
      • Concluding remarks
    • Chapter 10: Promises and Prospects of Microbiome Studies
      • Abstract
      • Microbiome during development and disease
      • Therapeutic potential of microbiota modifications
      • Challenges ahead: human microbiome information in the health care system
      • Ethical considerations of microbiome research
      • Citizen scientist, crowdsourced research, and the microbiome
      • Metagenomics, agriculture, and food microbiology
      • Summary
      • Acknowledgments
    • Glossary
    • Index

Product details

  • No. of pages: 188
  • Language: English
  • Copyright: © Academic Press 2014
  • Published: November 7, 2014
  • Imprint: Academic Press
  • Paperback ISBN: 9780124104723
  • eBook ISBN: 9780124105089

About the Editors

Jacques Izard

Affiliations and Expertise

The Forsyth Institute, Cambridge, Massachusetts, USA

Maria Rivera

Affiliations and Expertise

Virginia Commonwealth University, Department of Biology, Richmond, Virginia, USA

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