Functional Metagenomics: Tools and Applications

1. Front Matter

   Pages i-viii

   PDF

2. Metagenomic Cosmid Libraries Suitable for Functional Screening in Proteobacteria

   • Jiujun Cheng, Kathy N. Lam, Katja Engel, Michael Hall, Josh D. Neufeld, Trevor C. Charles

   Pages 1-11

3. Expression Platforms for Functional Metagenomics: Emerging Technology Options Beyond Escherichia coli

   • Anna Lewin, Rahmi Lale, Alexander Wentzel

   Pages 13-44

4. Engineering of E. coli for Heterologous Expression of Secondary Metabolite Biosynthesis Pathways Recovered from Metagenomics Libraries

   • Lei Fang, Guojian Zhang, Blaine A. Pfeifer

   Pages 45-63

5. Functional Analysis in Metagenomics Using MEGAN 6

   • Sina Beier, Rewati Tappu, Daniel H. Huson

   Pages 65-74

6. Enhancing Metagenomic Approaches Through Synthetic Biology

   • Luana de Fátima Alves, Rafael Silva-Rocha, María-Eugenia Guazzaroni

   Pages 75-94

7. Metagenomics for the Discovery of Novel Biosurfactants

   • Wesley Williams, Marla Trindade

   Pages 95-117

8. Challenges and Opportunities in Discovery of Secondary Metabolites Using a Functional Metagenomic Approach

   • Alinne L. R. Santana-Pereira, Mark R. Liles

   Pages 119-138

9. Enhancing Functional Metagenomics of Complex Microbial Communities Using Stable Isotopes

   • Marcela Hernández, Josh D. Neufeld, Marc G. Dumont

   Pages 139-150

10. Metagenome Assembly and Functional Annotation

    • Adina Howe, Fan Yang, Qingpeng Zhang

    Pages 151-159

11. Human Gut Metagenomics: Success and Limits of the Activity-Based Approaches

    • Alexandra S. Tauzin, Elisabeth Laville, Davide Cecchini, Hervé M. Blottière, Marion Leclerc, Joël Doré et al.

    Pages 161-178

12. Metagenomics of Plant Microbiomes

    • G. Brader, E. Corretto, A. Sessitsch

    Pages 179-200

13. Metagenome Analyses of Multispecies Microbial Biofilms: First Steps Toward Understanding Diverse Microbial Systems on Surfaces

    • Christel Schmeisser, Ines Krohn-Molt, Wolfgang R. Streit

    Pages 201-215

14. Functional Metagenomics of a Replicase from a Novel Hyperthermophilic Aquificales Virus

    • David A. Mead, Scott Monsma, Baigen Mei, Krishne Gowda, Michael Lodes, Thomas W. Schoenfeld

    Pages 217-242

15. Functional Metagenomics and Antimicrobial Resistance

    • Fiona Walsh

    Pages 243-253

In this book, the latest tools available for functional metagenomics research are described.This research enables scientists to directly access the genomes from diverse microbial genomes at one time and study these “metagenomes”. Using the modern tools of genome sequencing and cloning, researchers have now been able to harness this astounding metagenomic diversity to understand and exploit the diverse functions of microorganisms. Leading scientists from around the world demonstrate how these approaches have been applied in many different settings, including aquatic and terrestrial habitats, microbiomes, and many more environments. This is a highly informative and carefully presented book, providing microbiologists with a summary of the latest functional metagenomics literature on all specific habitats.

• environmental genomics
• metagenome
• metagenomics
• microbiome
• industrial microbiology

• Department of Biology, University of Waterloo , Waterloo, Canada

  Trevor C. Charles

• Department of Biological Sciences, Auburn University , Auburn, USA

  Mark R. Liles

• Biorescources, AIT Austrian Institute of Technology Biorescources, Tulln, Austria

  Angela Sessitsch

Trevor C. Charles is a Professor in the Department of Biology at the University of Waterloo, Ontario, Canada. His general research area is bacterial molecular genetics. He has a particular interest in members of the Rhizobiales order of the Alphaproteobacteria. His research on microbial communities is directed towards functional metagenomics, which includes the design and implementation of metagenomic library screens for metabolic functions of interest. Some of the metagenome derived genes are being used to develop bacterial strains for bioproducts such as polyhydroxyalkanoate bioplastics. Dr. Charles has published over 80 peer-reviewed papers. 



Mark R. Liles is a Professor in the Department of Biological Sciences at Auburn University. As a postdoctoral scientist, Liles worked with Profs. Jo Handelsman and Robert Goodman at the University of Wisconsin-Madison on developing technology for soil metagenomic research. Ongoing research in Liles’ laboratory focuses on the use of functional metagenomics for the discovery of natural products, and the use of microorganisms for the prevention of disease in aquaculture and agriculture. He has published over 90 peer-reviewed manuscripts.



Angela Sessitsch heads the Bioresources Unit of the AIT Austrian Institute of Technology, Austria’s largest non-university research centre. She is an expert in plant-microbe interactions and microbiome research and ongoing research makes use of metagenomic approaches to obtain functional information of plant microbiomes. A. Sessitsch has published about 150 peer-reviewed papers.

Policies and ethics