Metagenomics: Methods and Protocols

ISBN-13: 9781071627945 / Angielski / Twarda / 2022 / 287 str.

Wolfgang R. Streit; Rolf Daniel

Opis

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.

Spis treści

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

            Carola Simon and Rolf Daniel

 

2. 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, and Bernd Wemheuer

 

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

            Nancy Weiland-Bräuer, Livia Saleh, and Ruth A. Schmitz

 

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

            Supathep Tansirichaiya, William Hutton, and Adam P. Roberts

 

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

            Alinne L.R. Santana-Pereira

 

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

            Nicole Adam-Beyer and Mirjam Perner

 

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

            Genis A. Castillo Villamizar, Heiko Nacke, and Rolf Daniel

 

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

            Aranksha Thakor, Jiujun Cheng, and Trevor C. Charles

 

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

            Jascha F.H. Macdonald, Ines Krohn, and Wolfgang R. Streit

 

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

            Jennifer Chow, Pablo Pérez-García, Robert F. Dierkes, Hongli Zhang, and Wolfgang R. Streit

 

11. High-Throughput Screening for Thermostable Polyester Hydrolases

            Yannick Branson, Christoffel P. S. Badenhorst, Lara Pfaff, Carolin Buchmann, Ren Wei, and Uwe T. Bornscheuer

 

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

            Yuchen Han, Robert F. Dierkes, and Wolfgang R. Streit

 

13. Assigning Functions of Unknown Enzymes by High Throughput Enzyme Characterization

            Patricia Molina, Laura Fernandez-Lopez, Peter N. Golyshin, and Manuel Ferrer

 

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

            Ines Friedrich and Robert Hertel

 

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

            Katharina Kohm, Veronika Theresa Lutz, Ines Friedrich, and Robert Hertel

 

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

            Yuriy Rebets, Jan Kormanec, Andriy Lutzhetskyy, Kristel Bernaerts, and Jozef Anné

 

17. 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, Hendrik Schäfer, J. Colin Murrell, Josh D. Neufeld, and Marc G. Dumont