National Academies Press: OpenBook
Suggested Citation:"Front Matter." National Research Council. 2007. The New Science of Metagenomics: Revealing the Secrets of Our Microbial Planet. Washington, DC: The National Academies Press. doi: 10.17226/11902.
×

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

THE NATIONAL ACADEMIES PRESS

Washington, DC
www.nap.edu

Suggested Citation:"Front Matter." National Research Council. 2007. The New Science of Metagenomics: Revealing the Secrets of Our Microbial Planet. Washington, DC: The National Academies Press. doi: 10.17226/11902.
×

THE NATIONAL ACADEMIES PRESS

500 Fifth Street, NW Washington, DC 20001

NOTICE: The project that is the subject of this report was approved by the Governing Board of the National Research Council, whose members are drawn from the councils of the National Academy of Sciences, the National Academy of Engineering, and the Institute of Medicine. The members of the committee responsible for the report were chosen for their special competences and with regard for appropriate balance.

This study was supported by Contract MCB—0544539 between the National Academy of Sciences and the National Science Foundation (NSF), Contract N01-OD-4-2139 between the National Academy of Sciences and the Department of Health and Human Services, National Institutes of Health (NIH), and Contract DE-AT01-05ER64072 between the National Academy of Sciences and the Department of Energy (DOE). The content of this publication does not necessarily reflect the views or policies of NIH, NSF, or DOE, nor does mention of trade names, commercial products, or organizations imply endorsement by the US Government.

International Standard Book Number-13: 978-0-309-10676-4

International Standard Book Number-10: 0-309-10676-1

Cover: Design by Francesca Moghari; artwork by Nicolle Rager Fuller (www.sayo-art.com).

Additional copies of this report are available from the

National Academies Press,

500 Fifth Street, NW, Lockbox 285, Washington, DC 20055; (800) 624-6242 or (202) 334-3313 (in the Washington metropolitan area); Internet, http://www.nap.edu.

Copyright 2007 by the National Academy of Sciences. All rights reserved.

Printed in the United States of America

Suggested Citation:"Front Matter." National Research Council. 2007. The New Science of Metagenomics: Revealing the Secrets of Our Microbial Planet. Washington, DC: The National Academies Press. doi: 10.17226/11902.
×

THE NATIONAL ACADEMIES

Advisers to the Nation on Science, Engineering, and Medicine


The National Academy of Sciences is a private, nonprofit, self-perpetuating society of distinguished scholars engaged in scientific and engineering research, dedicated to the furtherance of science and technology and to their use for the general welfare. Upon the authority of the charter granted to it by the Congress in 1863, the Academy has a mandate that requires it to advise the federal government on scientific and technical matters. Dr. Ralph J. Cicerone is president of the National Academy of Sciences.


The National Academy of Engineering was established in 1964, under the charter of the National Academy of Sciences, as a parallel organization of outstanding engineers. It is autonomous in its administration and in the selection of its members, sharing with the National Academy of Sciences the responsibility for advising the federal government. The National Academy of Engineering also sponsors engineering programs aimed at meeting national needs, encourages education and research, and recognizes the superior achievements of engineers. Dr. Wm. A. Wulf is president of the National Academy of Engineering.


The Institute of Medicine was established in 1970 by the National Academy of Sciences to secure the services of eminent members of appropriate professions in the examination of policy matters pertaining to the health of the public. The Institute acts under the responsibility given to the National Academy of Sciences by its congressional charter to be an adviser to the federal government and, upon its own initiative, to identify issues of medical care, research, and education. Dr. Harvey V. Fineberg is president of the Institute of Medicine.


The National Research Council was organized by the National Academy of Sciences in 1916 to associate the broad community of science and technology with the Academy’s purposes of furthering knowledge and advising the federal government. Functioning in accordance with general policies determined by the Academy, the Council has become the principal operating agency of both the National Academy of Sciences and the National Academy of Engineering in providing services to the government, the public, and the scientific and engineering communities. The Council is administered jointly by both Academies and the Institute of Medicine. Dr. Ralph J. Cicerone and Dr. Wm. A. Wulf are chair and vice chair, respectively, of the National Research Council.


www.national-academies.org

Suggested Citation:"Front Matter." National Research Council. 2007. The New Science of Metagenomics: Revealing the Secrets of Our Microbial Planet. Washington, DC: The National Academies Press. doi: 10.17226/11902.
×

This page intentionally left blank.

Suggested Citation:"Front Matter." National Research Council. 2007. The New Science of Metagenomics: Revealing the Secrets of Our Microbial Planet. Washington, DC: The National Academies Press. doi: 10.17226/11902.
×

COMMITTEE ON METAGENOMICS: CHALLENGES AND FUNCTIONAL APPLICATIONS

JO HANDELSMAN (Cochair),

University of Wisconsin, Madison

JAMES TIEDJE (Cochair),

Michigan State University, East Lansing

LISA ALVAREZ-COHEN,

University of California, Berkeley

MICHAEL ASHBURNER,

University of Cambridge, United Kingdom

ISAAC K. O. CANN,

University of Illinois, Urbana-Champaign

EDWARD F. DELONG,

Massachusetts Institute of Technology, Cambridge

W. FORD DOOLITTLE,

Dalhousie University, Halifax, Nova Scotia, Canada

CLAIRE M. FRASER-LIGGETT,

University of Maryland School of Medicine, Baltimore

ADAM GODZIK,

Burnham Institute for Medical Research, La Jolla, CA

JEFFREY I. GORDON,

Washington University School of Medicine, St. Louis, MO

MARGARET RILEY,

University of Massachusetts, Amherst

MOLLY B. SCHMID,

Keck Graduate Institute, Claremont, CA

Staff

ANN H. REID, Study Director

FRANCES E. SHARPLES, Director,

Board on Life Sciences

ANNE F. JURKOWSKI, Senior Program Assistant

MERC FOX, Program Assistant

NORMAN GROSSBLATT, Senior Editor

Suggested Citation:"Front Matter." National Research Council. 2007. The New Science of Metagenomics: Revealing the Secrets of Our Microbial Planet. Washington, DC: The National Academies Press. doi: 10.17226/11902.
×

BOARD ON LIFE SCIENCES

KEITH YAMAMOTO (Chair),

University of California, San Francisco

ANN M. ARVIN,

Stanford University School of Medicine, Stanford, CA

JEFFREY L. BENNETZEN,

University of Georgia, Athens

RUTH BERKELMAN,

Emory University, Atlanta, GA

DEBORAH BLUM,

University of Wisconsin, Madison

R. ALTA CHARO,

University of Wisconsin, Madison

JEFFREY L. DANGL,

University of North Carolina, Chapel Hill

PAUL R. EHRLICH,

Stanford University, Stanford, CA

MARK D. FITZSIMMONS,

John D. and Catherine T. MacArthur Foundation, Chicago, IL

JO HANDELSMAN,

University of Wisconsin, Madison

ED HARLOW,

Harvard Medical School, Boston, MA

KENNETH H. KELLER,

University of Minnesota, Minneapolis

RANDALL MURCH,

Virginia Polytechnic Institute and State University, Alexandria

GREGORY A. PETSKO,

Brandeis University, Waltham, MA

MURIEL E. POSTON,

Skidmore College, Saratoga Springs, NY

JAMES REICHMAN,

University of California, Santa Barbara

MARC T. TESSIER-LAVIGNE,

Genentech, Inc., South San Francisco, CA

JAMES TIEDJE,

Michigan State University, East Lansing

TERRY L. YATES,

University of New Mexico, Albuquerque

Staff

FRANCES E. SHARPLES, Director

KERRY A. BRENNER, Senior Program Officer

ANN H. REID, Senior Program Officer

MARILEE K. SHELTON-DAVENPORT, Senior Program Officer

EVONNE P. Y. TANG, Senior Program Officer

ROBERT T. YUAN, Senior Program Officer

ADAM P. FAGEN, Program Officer

ANNA FARRAR, Financial Associate

ANNE F. JURKOWSKI, Senior Program Assistant

TOVA JACOBOVITS, Senior Program Assistant

MERC FOX, Program Assistant

Suggested Citation:"Front Matter." National Research Council. 2007. The New Science of Metagenomics: Revealing the Secrets of Our Microbial Planet. Washington, DC: The National Academies Press. doi: 10.17226/11902.
×

Acknowledgments

This report has been reviewed in draft form by persons chosen for their diverse perspectives and technical expertise in accordance with procedures approved by the National Research Council’s Report Review Committee. The purpose of the independent review is to provide candid and critical comments that will assist the institution in making the published report as sound as possible and to ensure that the report meets institutional standards of objectivity, evidence, and responsiveness to the study charge. The review comments and draft manuscript remain confidential to protect the integrity of the deliberative process. We wish to thank the following for their review of the report:

Gary Anderson, Lawrence Berkeley National Laboratory, Berkeley, CA

Jeffrey Dangl, University of North Carolina, Chapel Hill

Julian E. Davies, University of British Columbia, Vancouver, BC, Canada

Jed Fuhrman, University of Southern California, Los Angeles

Dennis Mangan, University of Southern California School of Dentistry, Los Angeles

Victor Markowitz, Lawrence Berkeley National Laboratory, Berkeley, CA

Randall Murch, Virginia Polytechnic Institute and State University, Blacksburg

Norman R. Pace (NAS), University of Colorado, Boulder

David Relman, Stanford University, Stanford, CA

Edward Rubin, Lawrence Berkeley National Laboratory, Berkeley, CA

George Weinstock, Baylor College of Medicine, Houston, TX

Page viii Cite
Suggested Citation:"Front Matter." National Research Council. 2007. The New Science of Metagenomics: Revealing the Secrets of Our Microbial Planet. Washington, DC: The National Academies Press. doi: 10.17226/11902.
×

Although the reviewers listed above have provided constructive comments and suggestions, they were not asked to endorse the conclusions or recommendations, nor did they see the final draft of the report before its release. The review of the report was overseen by John Wooley, University of California, San Diego. Appointed by the National Research Council, he was responsible for making certain that an independent examination of this report was carried out in accordance with institutional procedures and that all review comments were carefully considered. Responsibility for the final content of the report rests entirely with the author committee and the institution.

The committee benefited from briefings provided by severalspeakers. At its second meeting, on May 2, 2006, the committee was briefed by: Michael Gray (by telephone), Professor and Department Head, Canada Research Chair in Genomics and Genome Evolution, Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, Nova Scotia, Canada; Mitchell Sogin, Senior Scientist and Director of the Josephine Bay Paul Center for Comparative Molecular Biology and Evolution, The Woods Hole Biological Laboratory, Woods Hole, MA; and Robert Edwards, San Diego State University and Burnham Institute, San Diego, CA. At its third meeting, on July 27, 2006, the committee was briefed by: David J. Lipman, Director, National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Rockville, MD; Rolf Apweiler, Head of Sequence Database Group, European Bioinformatics Institute, Cambridge, UK; Victor Markowitz, Head of Lawrence Berkeley National Lab’s Biological Data Management and Technology Center, Berkeley, CA; Paul Gilna, Executive Director, CAMERA, San Diego, CA; and Amaranth Gupta, Associate Research Scientist, Director Advanced Query Processing Lab, San Diego Supercomputer Center, University of California, San Diego.

The committee extends heartfelt thanks to Ann Reid who served as Study Director for this report. The product reflects both Ann’s attention to our charge and her ability to provoke us into addressing it thoroughly. Her outstanding editing contributed greatly to the clarity and logic of the report. We also thank Anne Jurkowski for her dedication to this report and its authors. Throughout the process, the committee relied on Anne’s administrative prowess and her willingness to do whatever was necessary to get the report done or the committee on track. Anne’s aesthetic intuition and visual acuity shaped the report as well as its derivative materials.

We thank Dr. Patrick Schloss for his assistance in building the meta- genomics bibliography and Dr. Luke Moe, Snow Brook Peterson, and Dr. Ainslie Little for helpful discussion and Christina Matta for assuring historical accuracy.

Suggested Citation:"Front Matter." National Research Council. 2007. The New Science of Metagenomics: Revealing the Secrets of Our Microbial Planet. Washington, DC: The National Academies Press. doi: 10.17226/11902.
×
   

 How Do Microbial Communities Work?,

 

40

   

 How Do Microbial Communities React to Change?,

 

43

   

 How 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

   

 The Human-Microbiome Project,

 

57

   

 Viral Metagenomics,

 

58

4

 

DESIGNING A SUCCESSFUL METAGENOMICS PROJECT: BEST PRACTICES AND FUTURE NEEDS

 

60

   

 Parallels with Traditional Microbial Genome Sequencing,

 

60

   

 Metagenomics Step by Step,

 

63

   

 Habitat Selection,

 

63

   

 Sampling Strategy,

 

64

   

 Macromolecule Recovery,

 

65

   

 Getting the Most Out of Metagenomics Studies,

 

67

   

 16S 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

   

 Function-Based Analyses of Microbial Communities,

 

76

   

 Advancing the Field,

 

77

   

 Sequencing Technology,

 

77

   

 Gene-Expression Systems,

 

79

   

 Single-Cell Analyses,

 

80

   

 Methods for Culturing Uncultured Species,

 

82

   

 Basic Microbiology,

 

83

   

 Understanding Microbial Habitats and Collecting Metadata,

 

83

   

 Downstream Development of Metagenomics,

 

84

Suggested Citation:"Front Matter." National Research Council. 2007. The New Science of Metagenomics: Revealing the Secrets of Our Microbial Planet. Washington, DC: The National Academies Press. doi: 10.17226/11902.
×

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

   

 Intellectual Property,

 

103

   

 Metagenomics and the Convention on Biological Diversity,

 

104

   

 Biosafety,

 

105

   

 Outreach,

 

106

7

 

A BALANCED PORTFOLIO: MULTI-SCALE PROJECTS IN THE “GLOBAL METAGENOMICS INITIATIVE”

 

107

   

 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 Genome Project,

 

117

   

 Lessons for Metagenomics,

 

118

Suggested Citation:"Front Matter." National Research Council. 2007. The New Science of Metagenomics: Revealing the Secrets of Our Microbial Planet. Washington, DC: The National Academies Press. doi: 10.17226/11902.
×
Suggested Citation:"Front Matter." National Research Council. 2007. The New Science of Metagenomics: Revealing the Secrets of Our Microbial Planet. Washington, DC: The National Academies Press. doi: 10.17226/11902.
×
Page R1
Suggested Citation:"Front Matter." National Research Council. 2007. The New Science of Metagenomics: Revealing the Secrets of Our Microbial Planet. Washington, DC: The National Academies Press. doi: 10.17226/11902.
×
Page R2
Suggested Citation:"Front Matter." National Research Council. 2007. The New Science of Metagenomics: Revealing the Secrets of Our Microbial Planet. Washington, DC: The National Academies Press. doi: 10.17226/11902.
×
Page R3
Suggested Citation:"Front Matter." National Research Council. 2007. The New Science of Metagenomics: Revealing the Secrets of Our Microbial Planet. Washington, DC: The National Academies Press. doi: 10.17226/11902.
×
Page R4
Suggested Citation:"Front Matter." National Research Council. 2007. The New Science of Metagenomics: Revealing the Secrets of Our Microbial Planet. Washington, DC: The National Academies Press. doi: 10.17226/11902.
×
Page R5
Suggested Citation:"Front Matter." National Research Council. 2007. The New Science of Metagenomics: Revealing the Secrets of Our Microbial Planet. Washington, DC: The National Academies Press. doi: 10.17226/11902.
×
Page R6
Suggested Citation:"Front Matter." National Research Council. 2007. The New Science of Metagenomics: Revealing the Secrets of Our Microbial Planet. Washington, DC: The National Academies Press. doi: 10.17226/11902.
×
Page R7
Page viii Cite
Suggested Citation:"Front Matter." National Research Council. 2007. The New Science of Metagenomics: Revealing the Secrets of Our Microbial Planet. Washington, DC: The National Academies Press. doi: 10.17226/11902.
×
Page R8
Suggested Citation:"Front Matter." National Research Council. 2007. The New Science of Metagenomics: Revealing the Secrets of Our Microbial Planet. Washington, DC: The National Academies Press. doi: 10.17226/11902.
×
Page R9
Suggested Citation:"Front Matter." National Research Council. 2007. The New Science of Metagenomics: Revealing the Secrets of Our Microbial Planet. Washington, DC: The National Academies Press. doi: 10.17226/11902.
×
Page R10
Suggested Citation:"Front Matter." National Research Council. 2007. The New Science of Metagenomics: Revealing the Secrets of Our Microbial Planet. Washington, DC: The National Academies Press. doi: 10.17226/11902.
×
Page R11
Suggested Citation:"Front Matter." National Research Council. 2007. The New Science of Metagenomics: Revealing the Secrets of Our Microbial Planet. Washington, DC: The National Academies Press. doi: 10.17226/11902.
×
Page R12
Next: Summary »
The New Science of Metagenomics: Revealing the Secrets of Our Microbial Planet Get This Book
×
Buy Paperback | $54.00 Buy Ebook | $43.99
MyNAP members save 10% online.
Login or Register to save!
Download Free PDF

Although we can't usually see them, microbes are essential for every part of human life -- indeed all life on Earth. The emerging field of metagenomics offers a new way of exploring the microbial world that will transform modern microbiology and lead to practical applications in medicine, agriculture, alternative energy, environmental remediation, and many others areas. Metagenomics allows researchers to look at the genomes of all of the microbes in an environment at once, providing a "meta" view of the whole microbial community and the complex interactions within it. It's a quantum leap beyond traditional research techniques that rely on studying -- one at a time -- the few microbes that can be grown in the laboratory. At the request of the National Science Foundation, five Institutes of the National Institutes of Health, and the Department of Energy, the National Research Council organized a committee to address the current state of metagenomics and identify obstacles current researchers are facing in order to determine how to best support the field and encourage its success. The New Science of Metagenomics recommends the establishment of a "Global Metagenomics Initiative" comprising a small number of large-scale metagenomics projects as well as many medium- and small-scale projects to advance the technology and develop the standard practices needed to advance the field. The report also addresses database needs, methodological challenges, and the importance of interdisciplinary collaboration in supporting this new field.

  1. ×

    Welcome to OpenBook!

    You're looking at OpenBook, NAP.edu's online reading room since 1999. Based on feedback from you, our users, we've made some improvements that make it easier than ever to read thousands of publications on our website.

    Do you want to take a quick tour of the OpenBook's features?

    No Thanks Take a Tour »
  2. ×

    Show this book's table of contents, where you can jump to any chapter by name.

    « Back Next »
  3. ×

    ...or use these buttons to go back to the previous chapter or skip to the next one.

    « Back Next »
  4. ×

    Jump up to the previous page or down to the next one. Also, you can type in a page number and press Enter to go directly to that page in the book.

    « Back Next »
  5. ×

    Switch between the Original Pages, where you can read the report as it appeared in print, and Text Pages for the web version, where you can highlight and search the text.

    « Back Next »
  6. ×

    To search the entire text of this book, type in your search term here and press Enter.

    « Back Next »
  7. ×

    Share a link to this book page on your preferred social network or via email.

    « Back Next »
  8. ×

    View our suggested citation for this chapter.

    « Back Next »
  9. ×

    Ready to take your reading offline? Click here to buy this book in print or download it as a free PDF, if available.

    « Back Next »
Stay Connected!