Handbook of Molecular Microbial Ecology II: Metagenomics in Different Habitats

Handbook of Molecular Microbial Ecology II: Metagenomics in Different Habitats

Editor(s): Frans J. de Bruijn

Published Online: 10 NOV 2011 08:42AM EST

Print ISBN: 9780470647196

Online ISBN: 9781118010549

DOI: 10.1002/9781118010549

About this Book

The premiere two-volume reference on revelations from studying complex microbial communities in many distinct habitats

Metagenomics is an emerging field that has changed the way microbiologists study microorganisms. It involves the genomic analysis of microorganisms by extraction and cloning of DNA from a group of microorganisms, or the direct use of the purified DNA or RNA for sequencing, which allows scientists to bypass the usual protocol of isolating and culturing individual microbial species. This method is now used in laboratories across the globe to study microorganism diversity and for isolating novel medical and industrial compounds.

Handbook of Molecular Microbial Ecology is the first comprehensive two-volume reference to cover unculturable microorganisms in a large variety of habitats, which could not previously have been analyzed without metagenomic methodology. It features review articles as well as a large number of case studies, based largely on original publications and written by international experts. This second volume, Metagenomics in Different Habitats, covers such topics as:

  • Viral genomes

  • Metagenomics studies in a variety of habitats, including marine environments and lakes, soil, and human and animal digestive tracts

  • Other habitats, including those involving microbiome diversity in human saliva and functional intestinal metagenomics; diversity of archaea in terrestrial hot springs; and microbial communities living at the surface of building stones

  • Biodegradation

  • Biocatalysts and natural products

A special feature of this book is the highlighting of the databases and computer programs used in each study; they are listed along with their sites in order to facilitate the computer-assisted analysis of the vast amount of data generated by metagenomic studies. Such studies in a variety of habitats are described here, which present a large number of different system-dependent approaches in greatly differing habitats.

Handbook of Molecular Microbial Ecology II is an invaluable reference for researchers in metagenomics, microbial ecology, microbiology, and environmental microbiology; those working on the Human Microbiome Project; microbial geneticists; and professionals in molecular microbiology and bioinformatics.

Table of contents

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  1. Part 1: Viral Genomes

    1. Chapter 4

      Metagenomic Contrasts of Viruses in Soil and Aquatic Environments (pages 25–36)

      K. Eric Wommack, Sharath Srinivasiah, Mark R. Liles, Jaysheel Bhavsar, Shellie Bench, Kurt E. Williamson and Shawn W. Polson

    2. Chapter 5

      Biodiversity and Biogeography of Phages in Modern Stromatolites and Thrombolites (pages 37–44)

      Christelle Desnues, Beltran Rodriguez-Brito, Steve Rayhawk, Scott Kelley, Tuong Tran, Matthew Haynes, Hong Liu, Mike Furlan, Linda Wegley, Betty Chau, Yijun Ruan, Dana Hall, Florent E. Angly, Robert A. Edwards, Linlin Li, Rebecca Vega Thurber, R. Pamela Reid, Janet Siefert, Valeria Souza, David L. Valentine, Brandon K. Swan, Mya Breitbart and Forest Rohwer

    3. Chapter 7

      Next-Generation Sequencing and Metagenomic Analysis: A Universal Diagnostic Tool in Plant Pathology (pages 63–72)

      Ian P. Adams, Rachel H. Glover, Wendy A. Monger, Richard Thwaites, Rick Mumford, Elena Jackeviciene, Meletele Navalinskiene, Marija Samuitiene and Neil Boonham

    4. Chapter 8

      Direct Metagenomic Detection of Viral Pathogens in Human Specimens Using an Unbiased High-Throughput Sequencing Approach (pages 73–80)

      Takaaki Nakaya, Shota Nakamura, Yoshiko Okamoto, Yoshiyuki Nagai, Jun Kawai, Yoshihide Hayashizaki, Tetsuya Iida and Toshihiro Horii

  2. Part 2: The Soil Habitat

    1. Chapter 13

      Actinobacterial Diversity Associated with Antarctic Dry Valley Mineral Soils (pages 125–133)

      Bronwyn M. Kirby, Marilize Le Roes-Hill, S. Craig Cary, Stephanie G. Burton, I. Marla Tuffin and Don A. Cowan

  3. Part 3: The Digestive Tract

    1. Chapter 18

      Functional Intestinal Metagenomics (pages 175–190)

      Bartholomeus van den Bogert, Milkha M. Leimena, Willem M. de Vos, Erwin G. Zoetendal and Michiel Kleerebezem

    2. Chapter 19

      Assessment and Improvement of Methods for Microbial DNA Preparation from Fecal Samples (pages 191–198)

      Mariko Ueno, Mami Kikuchi, Kenshiro Oshima, Seok-won Kim, Hidetoshi Morita and Masahira Hattori

    3. Chapter 21

      Culture-Independent Analysis of the Human Gut Microbiota and their Activities (pages 207–219)

      Jonathan Swann, Selena E. Richards, Qing Shen, Elaine Holmes, Julian R. Marchesi and Kieran Tuohy

  4. Part 4: Marines and Lakes

  5. Part 5: Other Habitats

    1. Chapter 36

      The Microbiome of Leaf-Cutter Ant Fungus Gardens (pages 367–379)

      Garret Suen, Jarrod J. Scott, Frank O. Aylward and Cameron R. Currie

    2. Chapter 39

      Analysis of the Metagenome from a Biogas-Producing Microbial Community by Means of Bioinformatics Methods (pages 403–414)

      Sebastian Jaenicke, Martha Zakrzewski, Sebastian Jünemann, Alfred Pühler, Alexander Goesmann and Andreas Schlüter

  6. Part 6: Biodegradation

  7. Part 7: Biocatalysts and Natural Products

    1. Chapter 48

      Carboxylesterases and Lipases from Metagenomes (pages 499–506)

      Jennifer Chow, Ulrich Krauss, Karl-Erich Jaeger and Wolfgang R. Streit

  8. Part 8: Summary

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