Handbook of Molecular Microbial Ecology I: Metagenomics and Complementary Approaches

Handbook of Molecular Microbial Ecology I: Metagenomics and Complementary Approaches

Editor(s): Frans J. de Bruijn

Published Online: 3 MAY 2011 02:15PM EST

Print ISBN: 9780470644799

Online ISBN: 9781118010518

DOI: 10.1002/9781118010518

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 first volume, Metagenomics and Complementary Approaches, covers such topics as:

  • Background information on DNA reassociation and use of 16 rRNA and other DNA fingerprinting approaches

  • Species designation in microbiology

  • Metagenomics: Introduction to the basic tools with examples

  • Consortia and databases

  • Bioinformatics

  • Computer-assisted analysis

  • Complementary approaches-microarrays, metatranscriptomics, metaproteomics, metabolomics, and single cell analysis

A special feature of this volume 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.

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

Table of contents

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  1. Part 1: Background Chapters

    1. Chapter 3

      Diversity of 23S rRNA Genes within Individual Prokaryotic Genomes (pages 17–27)

      Anna Pei, William E. Oberdorf, Carlos W. Nossa, Pooja Chokshi, Martin J. Blaser, Liying Yang, David M. Rosmarin and Zhiheng Pei

  2. Part 2: The Species Concept

    1. Chapter 10

      The Microbial Pangenome: Implications for Vaccine Development (pages 83–87)

      Annalisa Nuccitelli, Claudio Donati, Michèle A. Barocchi and Rino Rappuoli

    2. Chapter 13

      Metagenomic Approaches for the Identification of Microbial Species (pages 105–109)

      David M. Ward, Melanie C. Melendrez, Eric D. Becraft, Christian G. Klatt, Jason M. Wood and Frederick M. Cohan

  3. Part 3: Metagenomics

  4. Part 4: Consortia and Databases

    1. Chapter 33

      Soil Metagenomic Exploration of the Rare Biosphere (pages 287–298)

      Tom O. Delmont, Laure Franqueville, Samuel Jacquiod, Pascal Simonet and Timothy M. Vogel

  5. Part 5: Computer-Assisted Analysis

    1. Chapter 41

      Gene Prediction in Metagenomic Fragments with Orphelia: A Large-Scale Machine Learning Approach (pages 359–367)

      Katharina H. Hoff, Maike Tech, Thomas Lingner, Rolf Daniel, Burkhard Morgenstern and Peter Meinicke

    2. Chapter 42

      Binning Metagenomic Sequences Using Seeded GSOM (pages 369–378)

      Ching-Hung Tseng, Chon-Kit Kenneth Chan, Arthur L. Hsu, Saman K. Halgamuge and Sen-Lin Tang

    3. Chapter 46

      ARB: A Software Environment for Sequence Data (pages 399–406)

      Ralf Westram, Kai Bader, Elmar Prüsse, Yadhu Kumar, Harald Meier, Frank Oliver Glöckner and Wolfgang Ludwig

    4. Chapter 48

      MetaSim: A Sequencing Simulator for Genomics and Metagenomics (pages 417–421)

      Daniel C. Richter, Felix Ott, Alexander F. Auch, Ramona Schmid and Daniel H. Huson

    5. Chapter 51

      Primers4clades: A Web Server to Design Lineage-Specific PCR Primers for Gene-Targeted Metagenomics (pages 441–452)

      Bernardo Sachman-Ruiz, Bruno Contreras-Moreira, Enrique Zozaya, Cristina Martínez-Garza and Pablo Vinuesa

  6. Part 6: Complementary Approaches

  7. Part 6A: Microarrays

  8. Part 6B: Metatranscriptomics

    1. Chapter 65

      Soil Eukaryotic Diversity: A Metatranscriptomic Approach (pages 597–602)

      Roland Marmeisse, Julie Bailly, Coralie Damon, Frédéric Lehembre, Marc Lemaire, Micheline Wésolowski-Louvel and Laurence Fraissinet-Tachet

  9. Part 6C: Metaproteomics

  10. Part 6D: Metabolomics

  11. Part 6E: Single-Cell Analysis

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