Table of contents for The new science of metagenomics : revealing the secrets of our microbial planet / Committee On Metagenomics: Challenges and Functional Applications, Board on Life Sciences, Division on Earth and Life Studies, National Research Council of the National Academies.


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I  WHY METAGENOMICS?                                        12
What Is Metagenomics?, 13
"What Microbes Can Do: Four Examples, 15
Microbes Modulate and Maintain the Atmosphere, 15
Microbes Keep Us Healthy, 17
Microbes SIpport Plant Growth and Suppress Plant Disease, 18
Microbes Clean Up Fuel Leaks, 19
Invisible Communities: Global Impact, 19
Understanding Microbial Communities, 21
The Limits of Pure Culture, 21
The Genomics Promise, 23
Why Genomics i Not Enough, 25
Most Microbes Cannot Be Cultured, 25
Microbial Diversity and Variation Have No Limits, 27
Metagenomics Offers a Way Forward, 29
Metagenomics Can Contribute to Advances in Many Fields, 31
2   A NEW LIGHT ON BIOLOGY                                  33
What Is a Genome?, 33
What Is a Species?, 35
What Is the Role of Microbes in Maintaining the Health of
Their Hosts?, 37
How Diverse is Life?, 38
How Do Microbial Communities Work?, 40
How Do Microbial Communities React to Change?, 43
Flow Do Microbes Evolve?, 44
What Ecological and Evolutionary Roles Do Viruses Play?, 46
3  FROM GENOMICS TO METAGENOMICS: FIRST STEPS             47
Sequencing Is Just One Kind of Metagenomics, 48
Pioneering Projects in Metagenomics, 50
The Acid Mine Drainage Project, 50
The Sargasso Sea Metagenomic Survey and Community
Profiling, 53
The Soil-Resistome Project, 55
T he Hiuman-Microbiorne Project, 57
Viral Metagenomics, 58
4  DESIGNING A SUCCESSFUL METAGENOMICS PROJECT:
BEST PRACTICES AND FUTURE NEEDS                         60
Paralle!s with Traditional Microbial Genome Sequencing, 60
Metagenomics Step by Step, 63
Flabitat Selection, 63
Samp ing Strategy, 64
Macromolecule Recovery, 65
Getting the Most Out of Metagenomics Studies, 67
[,OS rRNA-Based Surveys, 67
16S rRNA Phylogenetic and Functional Anchors: A Hybrid
Approach, 70
Generation of Large-Scale DNA Sequence, 70
Assembling Whole Genomes, 71
Gene-Centric Analyses, 73
Hybridization- and Array-Based Analyses, 74
Flnction Based Analyses of Microbial Communities, 76
Advancing the Field, 77
Sequencing Technology, 77
Gene-Expression Systems, 79
Single-Ceii Analyses, 80
Methods for Culturing Uncultured Species, 82
Basic Microbiology, 83
Understanding Microbial Habitats and Collecting Metadata, 83
Dowrstream Development of Metagenomics, 84
5  DATA MANAGEMENT AND BIOINFORMATICS
CHALLENGES OF METAGENOMICS                              85
Genomic Data, 85
Metagenomic Data, 88
The Importance of Metadata, 90
Databases for Metagenomic Data, 92
Software, 94
Analysis of Metagenomic Sequence Data, 95
6  THE INSTITUTIONAL LANDSCAPE FOR METAGENOMICS:
NEW SCIENCE, NEW CHALLENGES                             98
Major Stakeholders in Metagenomics, 98
The Scientific Community, 98
Funding Agencies, 98
international Coordination, 99
Education and Training, 100
Other Institutional Issues, 102
Data Release, 102
Intellectua Property, 103
Metagenomics and the Convention on Biological Diversity, 104
Biosafety, 105
Outreach, 106
A BALANCED PORTFOLIO: MULTI-SCALE PROJECTS IN THE
"'GLOBAL METAGENOMICS INITIATIVE"                      1 07
The Vision, 107
Characteristics of Successful Large-Scale Projects, 108
Why Metagenomics Needs a "Big Science" Component, 109
What Kind of Large-Scale Projects in the Global Metagenomics
Initiative and How Many?, 112
Expected Benefits of Large-Scale Metagenomics Projects, 113
Theory and Principles, 113
Understanding Specific Habitats, 114
Technical Advancement of the Field, 114
International Collaboration and Training, 115
Learning from Previous Large-Scale Genomics Projects, 115
The Human Genome Project, 116
The Arabidopsis Genomne Project, 117
Lessons for Metagenomics, 118
A Preliminary Road Map, 118
Phase 1: Choosing Model Communities, 118
Phase II: Planning and Initial Data-Gathering, 120
Phase II: Implementation, 122
Conclusion, 122



Library of Congress subject headings for this publication: Microbial genomics, Microbial genetics