Metagenomics and its Applications in Agriculture, Biomedicine and Environmental Studies

Robert W. Li (Editor)
Agricultural Research Service, USA

Series: Genetics – Research and Issues
BISAC: MED107000

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Volume 10

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Special issue: Resilience in breaking the cycle of children’s environmental health disparities
Edited by I Leslie Rubin, Robert J Geller, Abby Mutic, Benjamin A Gitterman, Nathan Mutic, Wayne Garfinkel, Claire D Coles, Kurt Martinuzzi, and Joav Merrick

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Metagenomics is the study of microbial communities sampled directly from their natural environment, without prior culturing. DNA sequencing (or alternatively, an assay of functional properties) is applied to the culture-independent analyses of complex and diverse (“meta”) populations of microbes. The rapid growth of metagenomics entails an expanded focus on microbes in a wide range of basic and applied research fields, ranging from microbiology to agriculture, biomedicine to bioenergy, and from veterinary to clinical medicine. This new book is an insightful and inclusive study on metagenomics and its applications.
(Imprint: Nova Biomedical )

Foreword pp.i-xii
(John Wooley)

Chapter 1. Metagenomics: Methods & Challenges
(Martina Ederer) pp.1-32

Chapter 2. Towards a More Complete Metagenomics Toolkit
(Michael E. Sparks and Robert W. Li)pp.33-46

Chapter 3. Analyzing Metagenomic Data: Inferring Microbial Community Function with MG-RAST
(Dionysios A. Antonopoulos, Elizabeth M. Glass, and Folker Meyer)pp.47-60

Chapter 4. Automatic Annotation of Microbial Genomes and Metagenomic Sequences
(Victor Solovyev and Asaf Salamov) pp.61-78

Chapter 5. Next-Generation and Future DNA Sequencing Technologies and Metagenomics
(Peiming Zhang, Jian Gu, Jin He, Weimin Gao, et al.)pp.79-106

Chapter 6. Comparison of De Novo Short Read Assemblers on Simulated Metagenomic Data
(Ying Huang, Weizhong Li, David Perkins, and Robert W. Li)pp.107-120

Chapter 7. Submetagenomics: Selective Sampling of Metagenomic Subsets of Interest
(Yi Vee Chew and Andrew J. Holmes)pp.121-134

Chapter 8. Dynamics of the Rumen Microbiota
(Robert W. Li, Michael E. Sparks, and Erin E. Connor)pp.135-164

Chapter 9. Detection of Functional Shifts in the Rumen Microbiota in Response to Propionate Intake in Cattle
(Michael E. Sparks, Ying Huang, Ransom L. Baldwin, et al.)pp.165-184

Chapter 10. Carbohydrate Actives Enzymes Derived from Metagenomes: From Microbial Ecology to Enzymology
(Renaud Berlemont and Moreno Galleni)pp.185-210

Chapter 11. An Evolutionary Ecology Perspective on Comparative Metagenomics
(Dieter Ebert and Weihong Qi)pp.211-236

Chapter 12. Interactions of the Gut Microbiota and its Host in the Context of Gastrointestinal and Metabolic Diseases
(Rodrigo Bibiloni, Lutz Krause, and Chieh J. Chou)pp.237-254

Chapter 13. Metagenomic Analysis of Human Gut Microbiota
(Volker Mai, Mihai Pop, and Mark Schell)pp.255-276

Chapter 14. Emerging Relevance of Metagenomics in Medicine
(Vasuki Venkat, Ying Huang, Patricia Finn, and David Perkins)pp.277-286

Chapter 15. Metagenomic Gene Discovery
Moola S. Mutondo, Robert J. Huddy, Rolene Bauer, et al.)pp.287-320

Chapter 16. Emerging Techniques for Metagenome Screening
(Takefumi Shimoyama and Kazuya Watanabe)pp.321-336

Chapter 17. Viral Metagenomics: From Fish Slime to the World
(Dana Willner, Christelle Desnues, and Forest Rohwer)pp.337-366

Chapter 18. Exploration of a Microbial Community for Novel Genetic Resources using Activity-Based Screening of a Metagenomic Library
(Hikaru Suenaga and Kentaro Miyazaki)pp.367-380

Chapter 19. Microbial Communities in Crude Petroleum Oils and Metagenomics
(Kunio Yamane, Hideaki Maki, Shigeru Matsuyama, and Hiroo Uchiyama)pp.381-406

Chapter 20. Environmental Metaproteomics: Identifying the Protein Machinery that Impact the Activities and Interactions of Microbes in Isolation or Communities
(Richard J. Giannone, Martin Keller, and Robert Hettich)pp.407-436

Index pp.441-457

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