THE NEW SCIENCE OF METAGENOMICS
Revealing the Secrets of Our Microbial Planet
THE NATIONAL ACADEMIES PRESS
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www.nap.edu
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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
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THE NATIONAL ACADEMIES
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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
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
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
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.