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Metagenomics

Methods and Protocols

  • Book
  • © 2010

Overview

Editors:
  1. Wolfgang R. Streit

    1. Biocenter Klein Flottbek, Microbiology & Biotechnology, University of Hamburg, Hamburg, Germany

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  2. Rolf Daniel

    1. Institute of Microbiology and Genetics, Dept. of Genomic & Applied Microbiology, Georg August University, Göttingen, Germany

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  • Introduces basic methods commonly used in laboratories that have a strong background in microbial metagenomics -Provides a diverse range of screening protocols for metagenome libraries -Examines expert tips on troubleshooting and avoiding troublesome pitfalls -Covers a wide range of metagenome function- and sequence-based screening technologies
  • Includes supplementary material: sn.pub/extras

Part of the book series: Methods in Molecular Biology (MIMB, volume 668)

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Table of contents (24 protocols)

  1. Front Matter

    Pages i-xi
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  2. Molecular Methods to Study Complex Microbial Communities

    • JosĂ© M. Vieites, MarĂ­a-Eugenia Guazzaroni, Ana Beloqui, Peter N. Golyshin, Manuel Ferrer
    Pages 1-37

  3. Construction of Small-Insert and Large-Insert Metagenomic Libraries

    • Carola Simon, Rolf Daniel
    Pages 39-50

  4. Construction and Screening of Marine Metagenomic Libraries

    • Nancy Weiland, Carolin Löscher, Rebekka Metzger, Ruth Schmitz
    Pages 51-65

  5. Metagenomic Analysis of Isotopically Enriched DNA

    • Yin Chen, Josh D. Neufeld, Marc G. Dumont, Michael W. Friedrich, J. Colin Murrell
    Pages 67-75

  6. Wide Host-Range Cloning for Functional Metagenomics

    • Margaret Wexler, Andrew W. B. Johnston
    Pages 77-96

  7. Cloning and Expression Vectors for a Gram-Positive Host, Streptomyces lividans

    • Kristof Vrancken, Lieve Van Mellaert, Jozef AnnĂ©
    Pages 97-107

  8. Retracted Chapter: Heterologous Gene Expression in the Hyperthermophilic Archaeon Sulfolobus solfataricus

    • Angel Angelov, Wolfgang Liebl
    Pages 109-116

  9. Novel Tools for the Functional Expression of Metagenomic DNA

    • Sonja Christina Troeschel, Thomas Drepper, Christian Leggewie, Wolfgang R. Streit, Karl-Erich Jaeger
    Pages 117-139

  10. Screening of Functional Promoter from Metagenomic DNA for Practical Use in Expression Systems

    • So-Youn Park, Geun-Joong Kim
    Pages 141-152

  11. Substrate-Induced Gene Expression Screening: A Method for High-Throughput Screening of Metagenome Libraries

    • Taku Uchiyama, Kentaro Miyazaki
    Pages 153-168

  12. Screens for Active and Stereoselective Hydrolytic Enzymes

    • Dominique Böttcher, Marlen Schmidt, Uwe T. Bornscheuer
    Pages 169-176

  13. Screening for Cellulase-Encoding Clones in Metagenomic Libraries

    • Nele Ilmberger, Wolfgang R. Streit
    Pages 177-188

  14. Screening Metagenomic Libraries for Laccase Activities

    • Manuel Ferrer, Ana Beloqui, Peter N. Golyshin
    Pages 189-202

  15. Screening for N-AHSL-Based-Signaling Interfering Enzymes

    • Phil M. Oger, StĂ©phane Uroz
    Pages 203-217

  16. Identification of Molecular Markers to Follow Up the Bioremediation of Sites Contaminated with Chlorinated Compounds

    • Massimo Marzorati, Annalisa Balloi, Francesca De Ferra, Daniele Daffonchio
    Pages 219-234

  17. Methods for the Isolation of Genes Encoding Novel PHB Cycle Enzymes from Complex Microbial Communities

    • Ricardo F. Nordeste, Maria A. Trainer, Trevor C. Charles
    Pages 235-246

  18. Metagenomic Approaches to Identify and Isolate Bioactive Natural Products from Microbiota of Marine Sponges

    • Cristian Gurgui, Jörn Piel
    Pages 247-264

  19. Screening for Novel Antibiotic Resistance Genes

    • Mindy G. Brown, Elizabeth H. Mitchell, David L. Balkwill
    Pages 265-271

  20. Novel Metal Resistance Genes from Microorganisms: A Functional Metagenomic Approach

    • JosĂ© E. González-Pastor, Salvador Mirete
    Pages 273-285
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Keywords

About this book

Metagenomics has proven to be a powerful tool for exploring the ecology, metabolic profiling, and comparison of complex microbial communities as well as its important applications in the mining of metagenomes for genes encoding novel biocatalysts and drug molecules for bioindustries. In Metagenomics: Methods and Protocols, expert researches provide an overview and introduction to basic methods commonly used in laboratories that have a strong background in microbial metagenomics. The book attempts to address all of the working steps involved in this crucial field, beginning with DNA isolation from soils and marine samples and continuing with the construction and screening of libraries, along with key advise involving bioinformatic tools available to analyze large metagenomic sequence data sets. Written in the highly successful Methods in Molecular Biology™ series format, chapters include brief 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, Metagenomics: Methods and Protocols serves as a very complete guide to available screening protocols for all major biocatalysts in order to allow for the easy setup of these screens in any microbiology lab.

Editors and Affiliations

  • Biocenter Klein Flottbek, Microbiology & Biotechnology, University of Hamburg, Hamburg, Germany

    Wolfgang R. Streit

  • Institute of Microbiology and Genetics, Dept. of Genomic & Applied Microbiology, Georg August University, Göttingen, Germany

    Rolf Daniel

Bibliographic Information

  • Book Title: Metagenomics

  • Book Subtitle: Methods and Protocols

  • Editors: Wolfgang R. Streit, Rolf Daniel

  • Series Title: Methods in Molecular Biology

  • DOI: https://doi.org/10.1007/978-1-60761-823-2

  • Publisher: Humana Totowa, NJ

  • eBook Packages: Springer Protocols

  • Copyright Information: Springer Science+Business Media, LLC 2010

  • Hardcover ISBN: 978-1-60761-822-5Published: 21 September 2010

  • Softcover ISBN: 978-1-4939-6123-8Published: 23 August 2016

  • eBook ISBN: 978-1-60761-823-2Published: 10 September 2010

  • Series ISSN: 1064-3745

  • Series E-ISSN: 1940-6029

  • Edition Number: 1

  • Number of Pages: XI, 341

  • Topics: Human Genetics, Microbiology, Microbial Genetics and Genomics

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