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Metagenomics

Methods and Protocols

  • Book
  • © 2023

Overview

Editors:
  1. Wolfgang R. Streit

    1. Department of Microbiology and Biotechnology, University of Hamburg, Hamburg, Germany

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  2. Rolf Daniel

    1. Institut für Mikrobiologie und Genetik, Georg-August-Universität Göttingen, Göttingen, Germany

    View editor publications

    You can also search for this editor in PubMed   Google Scholar

  • Includes cutting-edge techniques
  • Provides step-by-step detail essential for reproducible results
  • Contains key implementation advice from the experts

Part of the book series: Methods in Molecular Biology (MIMB, volume 2555)

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Table of contents (17 protocols)

  1. Front Matter

    Pages i-xi
    Download chapter PDF

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

    • Carola Simon, Rolf Daniel
    Pages 1-12

  3. Extraction of Total DNA and RNA from Marine Filter Samples and Generation of a Universal cDNA as Universal Template for Marker Gene Studies

    • Jacqueline Hollensteiner, Franziska Wemheuer, Dominik Schneider, Birgit Pfeiffer, Bernd Wemheuer
    Pages 13-21

  4. Functional Metagenomics as a Tool to Tap into Natural Diversity of Valuable Biotechnological Compounds

    • Nancy Weiland-Bräuer, Livía Saleh, Ruth A. Schmitz
    Pages 23-49

  5. Functional and Sequence-Specific Screening Protocols for the Detection of Novel Antimicrobial Resistance Genes in Metagenomic DNA

    • Supathep Tansirichaiya, William Hutton, Adam P. Roberts
    Pages 51-72

  6. Identification of PKS Gene Clusters from Metagenomic Libraries Using a Next-Generation Sequencing Approach

    • Alinne L. R. Santana-Pereira
    Pages 73-90

  7. Activity-Based Screening of Metagenomic Fosmid Libraries for Hydrogen-Uptake Enzymes

    • Nicole Adam-Beyer, Mirjam Perner
    Pages 91-101

  8. Functional Metagenomics Approach for the Discovery of Novel Genes Encoding Phosphatase Activity

    • Genis A. Castillo Villamizar, Heiko Nacke, Rolf Daniel
    Pages 103-114

  9. Isolation of Genes Encoding Carbon Metabolism Pathways from Complex Microbial Communities

    • Aranksha Thakor, Jiujun Cheng, Trevor C. Charles
    Pages 115-123

  10. Screening Metagenomes for Algae Cell Wall Carbohydrates Degrading Hydrolases in Enrichment Cultures

    • Jascha F. H. Macdonald, Ines Krohn, Wolfgang R. Streit
    Pages 125-137

  11. The PET-Degrading Potential of Global Metagenomes: From In Silico Mining to Active Enzymes

    • Jennifer Chow, Pablo Pérez-García, Robert F. Dierkes, Hongli Zhang, Wolfgang R. Streit
    Pages 139-151

  12. High-Throughput Screening for Thermostable Polyester Hydrolases

    • Yannick Branson, Christoffel P. S. Badenhorst, Lara Pfaff, Carolin Buchmann, Ren Wei, Uwe T. Bornscheuer
    Pages 153-165

  13. Metagenomic Screening of a Novel PET Esterase via In Vitro Expression System

    • Yuchen Han, Robert F. Dierkes, Wolfgang R. Streit
    Pages 167-179

  14. Assigning Functions of Unknown Enzymes by High-Throughput Enzyme Characterization

    • Patricia Molina-Espeja, Laura Fernandez-Lopez, Peter N. Golyshin, Manuel Ferrer
    Pages 181-194

  15. Isolation of a Host-Confined Phage Metagenome Allows the Detection of Phages Both Capable and Incapable of Plaque Formation

    • Ines Friedrich, Robert Hertel
    Pages 195-203

  16. CRISPR-Cas9 Shaped Viral Metagenomes Associated with Bacillus subtilis

    • Katharina Kohm, Veronika Theresa Lutz, Ines Friedrich, Robert Hertel
    Pages 205-212

  17. Cloning and Expression of Metagenomic DNA in Streptomyces lividans and Its Subsequent Fermentation for Optimized Production

    • Yuriy Rebets, Jan Kormanec, Andriy Lutzhetskyy, Kristel Bernaerts, Jozef Anné
    Pages 213-260

  18. DNA-, RNA-, and Protein-Based Stable-Isotope Probing for High-Throughput Biomarker Analysis of Active Microorganisms

    • Eleanor Jameson, Martin Taubert, Roey Angel, Sara Coyotzi, Yin Chen, Özge Eyice et al.
    Pages 261-282

  19. Back Matter

    Pages 283-287
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Keywords

About this book

This volume provides up-to-date and novel techniques for various screening technologies currently used in metagenomics and related areas. Starting with DNA/RNA isolation from environmental samples, the book continues by delving into areas such as current methods used to isolate DNA and construct metagenomic libraries, establishment of metagenome libraries in non-E. coli hosts, and topics like function-driven mining of metagenomic DNA, screening and analyzing protocols for a wide array of different genes encoding enzymes, bacterial viruses and much more. Written for the highly successful Methods in Molecular Biology series, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step and readily reproducible protocols, and tips on troubleshooting and avoiding known pitfalls. 

Authoritative and practical, Metagenomics: Methods and Protocols, Third Edition provides a comprehensive collection of up-to-date metagenome protocols and tools for the recovery of many major types of biocatalysts and allows for the easy setup of these screens in microbiology laboratories.

Editors and Affiliations

  • Department of Microbiology and Biotechnology, University of Hamburg, Hamburg, Germany

    Wolfgang R. Streit

  • Institut für Mikrobiologie und Genetik, Georg-August-Universität Göttingen, 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/10.1007/978-1-0716-2795-2

  • Publisher: Humana New York, NY

  • eBook Packages: Springer Protocols

  • Copyright Information: The Editor(s) (if applicable) and The Author(s), under exclusive license to Springer Science+Business Media, LLC, part of Springer Nature 2023

  • Hardcover ISBN: 978-1-0716-2794-5Published: 29 October 2022

  • Softcover ISBN: 978-1-0716-2797-6Published: 29 October 2023

  • eBook ISBN: 978-1-0716-2795-2Published: 28 October 2022

  • Series ISSN: 1064-3745

  • Series E-ISSN: 1940-6029

  • Edition Number: 3

  • Number of Pages: XI, 287

  • Number of Illustrations: 8 b/w illustrations, 34 illustrations in colour

  • Topics: Genetics and Genomics, Microbial Genetics and Genomics, Enzymology

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