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Suggested Citation:"Front Matter." Institute of Medicine. 2013. The Science and Applications of Microbial Genomics: Workshop Summary. Washington, DC: The National Academies Press. doi: 10.17226/18261.
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THE SCIENCE AND APPLICATIONS OF
MICROBIAL GENOMICS

_________

WORKSHOP SUMMARY

Eileen R. Choffnes, LeighAnne Olsen, and Theresa Wizemann,
Rapporteurs

Forum on Microbial Threats

Board on Global Health

INSTITUTE OF MEDICINE
OF THE NATIONAL ACADEMIES

THE NATIONAL ACADEMIES PRESS

Washington, D.C.

www.nap.edu

Suggested Citation:"Front Matter." Institute of Medicine. 2013. The Science and Applications of Microbial Genomics: Workshop Summary. Washington, DC: The National Academies Press. doi: 10.17226/18261.
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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.

Financial support for this project was provided by the U.S. Department of Health and Human Services: National Institutes of Health, National Institute of Allergy and Infectious Diseases, Centers for Disease Control and Prevention, and the Food and Drug Administration; U.S. Department of Defense, Department of the Army: Global Emerging Infections Surveillance and Response System, Medical Research and Materiel Command, and the Defense Threat Reduction Agency; U.S. Department of Veterans Affairs; U.S. Department of Homeland Security; U.S. Agency for International Development; Uniformed Services University of the Health Sciences; the Alfred P. Sloan Foundation, American Society for Microbiology; sanofi pasteur; Burroughs Wellcome Fund; GlaxoSmithKline; Infectious Diseases Society of America; and the Merck Company Foundation. The views presented in this publication do not necessarily reflect the views of the organizations or agencies that provided support for this project.

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The serpent has been a symbol of long life, healing, and knowledge among almost all cultures and religions since the beginning of recorded history. The serpent adopted as a logotype by the Institute of Medicine is a relief carving from ancient Greece, now held by the Staatliche Museen in Berlin.

Cover image: Derivation of genome trees from the comparative analyses of complete genomes. (2005) PLoS Computational Biology Issue Image | Vol. 1(7) December 2005. PLoS Comput Biol 1(7): ev01.i07. doi:10.1371/image.pcbi.v01.i07. Genome graphic representation completed with GenomeViz software, provided by Rohit Ghai. Fractal tree obtained with the FractalTrees X software, provided by Simon Woodside. Compiled by Edouard Yeramian.

Suggested citation: IOM (Institute of Medicine). 2013. The Science and Applications of Microbial Genomics: Workshop Summary. Washington, DC: The National Academies Press.

Suggested Citation:"Front Matter." Institute of Medicine. 2013. The Science and Applications of Microbial Genomics: Workshop Summary. Washington, DC: The National Academies Press. doi: 10.17226/18261.
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Knowing is not enough; we must apply.
Willing is not enough; we must do.

—Goethe

image

INSTITUTE OF MEDICINE
OF THE NATIONAL ACADEMIES

Advising the Nation. Improving Health.

Suggested Citation:"Front Matter." Institute of Medicine. 2013. The Science and Applications of Microbial Genomics: Workshop Summary. Washington, DC: The National Academies Press. doi: 10.17226/18261.
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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. Charles M. Vest 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. Charles M. Vest are chair and vice chair, respectively, of the National Research Council.

www.national-academies.org

Suggested Citation:"Front Matter." Institute of Medicine. 2013. The Science and Applications of Microbial Genomics: Workshop Summary. Washington, DC: The National Academies Press. doi: 10.17226/18261.
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PLANNING COMMITTEE FOR A WORKSHOP ON THE
SCIENCE AND APPLICATIONS OF MICROBIAL GENOMICS1

BRUCE BUDOWLE, University of North Texas Health Science Center, Fort Worth, Texas

ARTURO CASADEVALL, Albert Einstein College of Medicine, Bronx, New York

JONATHAN EISEN, University of California, Davis, California

CLAIRE FRASER, University of Maryland School of Medicine, Baltimore, Maryland

PAUL KEIM, Northern Arizona University, Flagstaff, Arizona

DAVID RELMAN, Stanford University, Stanford, California

__________________

1 Institute of Medicine planning committees are solely responsible for organizing the workshop, identifying topics, and choosing speakers. The responsibility for the published workshop summary rests solely with the workshop rapporteurs and the institution.

Suggested Citation:"Front Matter." Institute of Medicine. 2013. The Science and Applications of Microbial Genomics: Workshop Summary. Washington, DC: The National Academies Press. doi: 10.17226/18261.
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FORUM ON MICROBIAL THREATS1

DAVID A. RELMAN (Chair), Stanford University, and Veterans Affairs Palo Alto Health Care System, Palo Alto, California

JAMES M. HUGHES (Vice-Chair), Global Infectious Diseases Program, Emory University, Atlanta, Georgia

LONNIE J. KING (Vice-Chair), The Ohio State University, Columbus, Ohio

KEVIN ANDERSON, Biological and Chemical Defense Division, Science and Technology Directorate, Department of Homeland Security, Washington, DC

ENRIQUETA C. BOND, Burroughs Wellcome Fund (Emeritus), QE Philanthropic Advisors, Marshall, Virginia

ROGER G. BREEZE, Lawrence Livermore National Laboratory, Livermore, California

PAULA R. BRYANT,2 Defense Threat Reduction Agency, Medical S&T Division, Fort Belvoir, Virginia

JOHN E. BURRIS, Burroughs Wellcome Fund, Research Triangle Park, North Carolina

ARTURO CASADEVALL, Albert Einstein College of Medicine, Bronx, New York

ANDREW CLEMENTS,3 U.S. Agency for International Development, Washington, DC

PETER DASZAK, EcoHealth Alliance, New York, New York

JEFFREY S. DUCHIN, Public Health–Seattle and King County, Seattle, Washington

JONATHAN EISEN, Genome Center, University of California, Davis, California

RALPH L. ERICKSON, Walter Reed Army Institute of Research, Silver Spring, Maryland

MARK B. FEINBERG, Merck Vaccine Division, Merck & Co., Inc., West Point, Pennsylvania

JACQUELINE FLETCHER, Oklahoma State University, Stillwater, Oklahoma

CLAIRE FRASER, Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, Maryland

JESSE L. GOODMAN, Food and Drug Administration, Rockville, Maryland

EDUARDO GOTUZZO, Instituto de Medicina Tropical–Alexander von Humbolt, Universidad Peruaña Cayetano Heredia, Lima, Peru

__________________

1 Institute of Medicine Forums and Roundtables do not issue, review, or approve individual documents. The responsibility for the published workshop summary rests with the workshop rapporteurs and the institution.

2 Forum member until February 8, 2013.

3 Forum member since January 1, 2013.

Suggested Citation:"Front Matter." Institute of Medicine. 2013. The Science and Applications of Microbial Genomics: Workshop Summary. Washington, DC: The National Academies Press. doi: 10.17226/18261.
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CAROLE A. HEILMAN, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland

DAVID L. HEYMANN, Health Protection Agency, London, United Kingdom

ZHI HONG, GlaxoSmithKline, Research Triangle Park, North Carolina

PHILIP HOSBACH, sanofi pasteur, Swiftwater, Pennsylvania

STEPHEN ALBERT JOHNSTON, Arizona BioDesign Institute, Arizona State University, Tempe, Arizona

KENT KESTER, Uniformed Services University of the Health Sciences, Bethesda, Maryland

GERALD T. KEUSCH, Boston University School of Medicine and Boston University School of Public Health, Boston, Massachusetts

RIMA F. KHABBAZ, Centers for Disease Control and Prevention, Atlanta, Georgia

STANLEY M. LEMON, School of Medicine, University of North Carolina, Chapel Hill, North Carolina

MARGARET McFALL-NGAI, University of Wisconsin, Madison, Wisconsin

EDWARD McSWEEGAN, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland

MARK A. MILLER,4 Fogarty International Center, Bethesda, Maryland

PAULA J. OLSIEWSKI,5 the Alfred P. Sloan Foundation, New York, New York

JULIE PAVLIN, Armed Forces Health Surveillance Center, Silver Spring, Maryland

GEORGE POSTE, Complex Adaptive Systems Initiative, Arizona State University, Tempe, Arizona

DAVID RIZZO, Department of Plant Pathology, University of California, Davis, California

GARY A. ROSELLE, Veterans Health Administration, Department of Veterans Affairs, Cincinnati, Ohio

ALAN S. RUDOLPH,6 Defense Threat Reduction Agency, Fort Belvoir, Virginia

KEVIN RUSSELL, Armed Forces Health Surveillance Center, Silver Spring, Maryland

JANET SHOEMAKER, American Society for Microbiology, Washington, DC

P. FREDERICK SPARLING, University of North Carolina, Chapel Hill, North Carolina

MURRAY TROSTLE,7 U.S. Agency for International Development, Washington, DC

MARY E. WILSON, Harvard School of Public Health, Harvard University, Boston, Massachusetts

__________________

4 Forum member until August 31, 2012.

5 Forum member since January 30, 2013.

6 Forum member until February 8, 2013.

7 Forum member until December 31, 2012.

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Suggested Citation:"Front Matter." Institute of Medicine. 2013. The Science and Applications of Microbial Genomics: Workshop Summary. Washington, DC: The National Academies Press. doi: 10.17226/18261.
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IOM Staff

EILEEN CHOFFNES, Scholar and Director

LEIGHANNE OLSEN, Program Officer

KATHERINE McCLURE, Senior Program Associate

REBEKAH HUTTON, Research Associate

PAMELA BERTELSON,8 Senior Program Assistant

__________________

8 Staff member until February 15, 2013.

Suggested Citation:"Front Matter." Institute of Medicine. 2013. The Science and Applications of Microbial Genomics: Workshop Summary. Washington, DC: The National Academies Press. doi: 10.17226/18261.
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BOARD ON GLOBAL HEALTH1

RICHARD GUERRANT (Chair), Thomas H. Hunter Professor of International Medicine and Director, Center for Global Health, University of Virginia School of Medicine, Charlottesville, Virginia

JO IVEY BOUFFORD (IOM Foreign Secretary), President, New York Academy of Medicine, New York, New York

CLAIRE V. BROOME, Adjunct Professor, Division of Global Health, Rollins School of Public Health, Emory University, Atlanta, Georgia

JACQUELYN C. CAMPBELL, Anna D. Wolf Chair, and Professor, Johns Hopkins University School of Nursing, Baltimore, Maryland

THOMAS J. COATES, Michael and Sue Steinberg Professor of Global AIDS, Research Co-Director, UC Global Health Institute, David Geffen School of Medicine, University of California, Los Angeles, California

GARY DARMSTADT, Director, Family Health Division, Global Health Program, Bill & Melinda Gates Foundation, Seattle, Washington

VALENTIN FUSTER, Director, Wiener Cardiovascular Institute Kravis Cardiovascular Health Center Professor, Cardiology, Mount Sinai School of Medicine, Mount Sinai Medical Center, New York, New York

JACOB A. GAYLE, Vice President, Community Affairs, Executive Director, Medtronic Foundation, Minneapolis, Minnesota

GLENDA E. GRAY, Executive Director, Perinatal HIV Research Unit, Chris Hani Baragwanath Hospital, University of the Witwatersrand, Diepkloof, South Africa

STEPHEN W. HARGARTEN, Professor and Chair, Emergency Medicine, Director, Medical College of Wisconsin, Milwaukee, Wisconsin

JAMES HOSPEDALES, Coordinator, Chronic Disease Project, Health Surveillance and Disease Management Area, Pan American Health Organization and World Health Organization, Washington, DC

PETER J. HOTEZ, Professor and Chair, Department of Microbiology, Immunology, and Tropical Medicine, The George Washington University, Washington, DC

CLARION JOHNSON, Global Medical Director, Medicine and Occupational Medicine Department, Exxon Mobil, Fairfax, Virginia

FITZHUGH MULLAN, Professor, Department of Health Policy, The George Washington University, Washington, DC

OLUFUNMILAYO F. OLOPADE, Walter L. Palmer Distinguished Service Professor of Medicine, The University of Chicago, Chicago, Illinois

__________________

1 Institute of Medicine boards do not review or approve individual workshop summaries. The responsibility for the content of the workshop summary rests with the workshop rapporteurs and the institution.

Suggested Citation:"Front Matter." Institute of Medicine. 2013. The Science and Applications of Microbial Genomics: Workshop Summary. Washington, DC: The National Academies Press. doi: 10.17226/18261.
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GUY PALMER, Regents Professor of Pathology and Infectious Diseases, Director of the School for Global Animal Health, Washington State University, Pullman, Washington

THOMAS C. QUINN, Associate Director for International Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Professor of Medicine, International Health, Epidemiology, and Molecular Biology and Immunology, Johns Hopkins University School of Medicine, Baltimore, Maryland

JENNIFER PRAH RUGER, Associate Professor, Division of Health Policy and Administration, Yale University School of Public Health, New Haven, Connecticut

IOM Staff

PATRICK KELLEY, Director

ANGELA CHRISTIAN, Program Associate

Suggested Citation:"Front Matter." Institute of Medicine. 2013. The Science and Applications of Microbial Genomics: Workshop Summary. Washington, DC: The National Academies Press. doi: 10.17226/18261.
×

Reviewers

This workshop summary has been reviewed in draft form by individuals 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 this independent review is to provide candid and critical comments that will assist the institution in making its published workshop summary as sound as possible and to ensure that the workshop summary meets institutional standards for objectivity, evidence, and responsiveness to the study charge. The review comments and draft manuscript remain confidential to protect the integrity of the process. We wish to thank the following individuals for their review of this workshop summary:

Roger G. Breeze, Lawrence Livermore National Laboratory, Livermore, California

James M. Hughes, Rollins School of Public Health, Emory University, Atlanta, Georgia

Tim Stearns, Department of Biology, Stanford University, Department of Genetics, Stanford School of Medicine, Stanford, California

Mary E. Wilson, Harvard School of Public Health, Harvard University, Boston, Massachusetts

Although the reviewers listed above have provided many constructive comments and suggestions, they did not see the final draft of the workshop summary before its release. The review of this workshop summary was overseen by Dr.

Suggested Citation:"Front Matter." Institute of Medicine. 2013. The Science and Applications of Microbial Genomics: Workshop Summary. Washington, DC: The National Academies Press. doi: 10.17226/18261.
×

Melvin Worth. Appointed by the Institute of Medicine, he was responsible for making certain that an independent examination of this workshop summary was carried out in accordance with institutional procedures and that all review comments were carefully considered. Responsibility for the final content of this workshop summary rests entirely with the rapporteurs and the institution.

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Suggested Citation:"Front Matter." Institute of Medicine. 2013. The Science and Applications of Microbial Genomics: Workshop Summary. Washington, DC: The National Academies Press. doi: 10.17226/18261.
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Acknowledgments

The Forum on Emerging Infections was created by the Institute of Medicine (IOM) in 1996 in response to a request from the Centers for Disease Control and Prevention (CDC) and the National Institutes of Health (NIH). The purpose of the Forum is to provide structured opportunities for leaders from government, academia, and industry to regularly meet and examine issues of shared concern regarding research, prevention, detection, and management of emerging, reemerging, and novel infectious diseases in humans, plants, and animals. In pursuing this task, the Forum provides a venue to foster the exchange of information and ideas, identify areas in need of greater attention, clarify policy issues by enhancing knowledge and identifying points of agreement, and inform decision makers about science and policy issues. The Forum seeks to illuminate issues rather than resolve them. For this reason, it does not provide advice or recommendations on any specific policy initiative pending before any agency or organization. Its value derives instead from the diversity of its membership and from the contributions that individual members make throughout the activities of the Forum. In September 2003, the Forum changed its name to the Forum on Microbial Threats.

The Forum on Microbial Threats and the IOM wish to express their warmest appreciation to the individuals and organizations who gave their valuable time to provide information and advice to the Forum through their participation in the planning and execution of this workshop. A full list of presenters, and their biographical information, may be found in Appendixes B and E, respectively.

Suggested Citation:"Front Matter." Institute of Medicine. 2013. The Science and Applications of Microbial Genomics: Workshop Summary. Washington, DC: The National Academies Press. doi: 10.17226/18261.
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The Forum gratefully acknowledges the contributions of the members of the planning committee1: Bruce Budowle (University of North Texas Health Science Center), Arturo Casadevall (Albert Einstein College of Medicine), Jonathan Eisen (University of California, Davis), Claire Fraser (University of Maryland School of Medicine, Baltimore), Paul Keim (Northern Arizona University), and David Relman (Stanford University).

The Forum is also indebted to the IOM staff who tirelessly contributed throughout the planning and execution of the workshop and the production of this workshop summary report. On behalf of the Forum, we gratefully acknowledge these efforts led by Dr. Eileen Choffnes, Scholar and Director of the Forum; Dr. LeighAnne Olsen, Program Officer; Katherine McClure, Senior Program Associate; Rebekah Hutton, Research Associate; and Pamela Bertelson,2 Senior Program Assistant, for dedicating much effort and time to developing this workshop’s agenda and for their thoughtful and insightful approach and skill in planning for the workshop and in translating the workshop’s proceedings and discussion into this workshop summary report. We would also like to thank the following IOM staff and consultants for their valuable contributions to this activity: Daniel Bethea, Laura Harbold DeStefano, Julie Wiltshire, Theresa Wizemann, and Sarah Ziegenhorn.

Finally, the Forum wishes to recognize the sponsors that supported this activity. Financial support for this project was provided by the U.S. Department of Health and Human Services: National Institutes of Health, National Institute of Allergy and Infectious Diseases, Centers for Disease Control and Prevention, and the Food and Drug Administration; U.S. Department of Defense, Department of the Army: Global Emerging Infections Surveillance and Response System, Medical Research and Materiel Command, and the Defense Threat Reduction Agency; U.S. Department of Veterans Affairs; U.S. Department of Homeland Security; U.S. Agency for International Development; Uniformed Services University of the Health Sciences; the Alfred P. Sloan Foundation; American Society for Microbiology; sanofi pasteur; Burroughs Wellcome Fund; GlaxoSmithKline; Infectious Diseases Society of America; and the Merck Company Foundation. The views presented in this workshop summary are those of the workshop participants and have been summarized by the rapporteurs. They do not necessarily reflect the views of the Forum on Microbial Threats, its sponsors, or the IOM.

__________________

1 Institute of Medicine planning committees are solely responsible for organizing the workshop, identifying topics, and choosing speakers. The responsibility for the published workshop summary rests solely with the workshop rapporteurs and the institution.

2 Staff member until February 15, 2013.

Suggested Citation:"Front Matter." Institute of Medicine. 2013. The Science and Applications of Microbial Genomics: Workshop Summary. Washington, DC: The National Academies Press. doi: 10.17226/18261.
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A6   Sequencing Errors, Diversity Estimates, and the Rare Biosphere

Susan M. Huse, David B. Mark Welch, and Mitchell L. Sogin

A7   Phylogeography and Molecular Epidemiology of Yersinia pestis in Madagascar

Amy J. Vogler, Fabien Chan, David M. Wagner, Philippe Roumagnac, Judy Lee, Roxanne Nera, Mark Eppinger, Jacques Ravel, Lila Rahalison, Bruno W. Rasoamanana, Stephen M. Beckstrom-Sternberg, Mark Achtman, Suzanne Chanteau, and Paul Keim

A8   Big Data in Biology: Pitfalls When Using Shotgun Metagenomics to Define Hypotheses About Microbial Communities

Folker Meyer and Elizabeth M. Glass

A9   High-Throughput Bacterial Genome Sequencing: An Embarrassment of Choice, A World of Opportunity

Nicholas J. Loman, Chrystala Constantinidou, Jacqueline Z. M. Chan, Mihail Halachev, Martin Sergeant, Charles W. Penn, Esther R. Robinson, and Mark J. Pallen

A10 Evidence for Several Waves of Global Transmission in the Seventh Cholera Pandemic

Ankur Mutreja, Dong Wook Kim, Nicholas R. Thomson, Thomas R. Connor, Je Hee Lee, Samuel Kariuki, Nicholas J. Croucher, Seon Young Choi, Simon R. Harris, Michael Lebens, Swapan Kumar Niyogi, Eun Jin Kim, T. Ramamurthy, Jongsik Chun, James L. N. Wood, John D. Clemens, Cecil Czerkinsky, G. Balakrish Nair, Jan Holmgren, Julian Parkhill, and Gordon Dougan

A11 Multi-Partner Interactions in Corals in the Face of Climate Change

Koty H. Sharp and Kim B. Ritchie

A12 Genomic Transition to Pathogenicity in Chytrid Fungi

Suzanne Joneson, Jason E. Stahich, Shin-Han Shiu, and Erica Bree Rosenblum

A13 Natural and Experimental Infection of Caenorhabditis Nematodes by Novel Viruses Related to Nodaviruses

Marie-Anne Félix, Alyson Ashe, Joséphine Piffaretti, Guang Wu, Isabelle Nuez, Tony Békucard, Yanfang Jiang, Guoyan Zhao, Carl J. Franz, Leonard D. Goldstein, Mabel Sanroman, Eric A. Miska, and David Wang

A14 Genomic Approaches to Studying the Human Microbiota

George M. Weinstock

A15 Sequence Analysis of the Human Virome in Febrile and Afebrile Children

Kristine M. Wylie, Kathie A. Mihindukulasuriya, Erica Sodergren, George M. Weinstock, and Gregory A. Storch

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Suggested Citation:"Front Matter." Institute of Medicine. 2013. The Science and Applications of Microbial Genomics: Workshop Summary. Washington, DC: The National Academies Press. doi: 10.17226/18261.
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A14-1

DNA Sequencing Platforms Used for Microbiome Analysis

A14-2

Characteristics of Bacteria, Microbial Eukaryotes, and Viruses in the Human Microbiome

A15-1

Detection of Viruses with Next Generation Sequencing

A15-2

Samples

A15-3

Virus Genera Screened by PCR

A15-4

Illumina Sequences with Remote Homologies to Astroviruses

A15-5

Genome Coverage

FIGURES

WO-1

Universal tree of life based on a comparison of nucleic acid (RNA) sequences found in all cellular life (small subunit ribosomal RNA)

WO-2

First glimpses of the microbial world

WO-3

The great plate count anomaly

WO-4

The improvements in DNA sequencing efficiency over time

WO-5

Genome projects and complete genomes since 1995

WO-6

Growth of the viral sequence database mapped to seminal discoveries and improvements in sequencing technology

WO-7

Postulated routes of spread

WO-8

Plague ecology

WO-9

Fully parsimonious minimal spanning tree of 933 SNPs for 282 isolates of Y. pestis colored by location

WO-10

Microbiological identification of morphological variants of B. anthracis Ames

WO-11

Bacterial genome dynamics

WO-12

Molecular evolutionary mechanisms that shape bacterial species diversity

WO-13

Damage-response framework and the case of S. cerevisiae

WO-14

Six distinct pathogenic variants of diarrheagenic E. coli

WO-15

Inconsistency of typing with whole genomes or MLST

WO-16

Algorithm for the identification of attaching and effacing E. coli (AEEC) pathogens

WO-17

Time dependence of dN/dS in the core and non-core genome

WO-18

V. cholerae—repeated global transmission

WO-19

Next generation sequencing and new methodologies will help to capture intrahost diversity

WO-20

Novelty of Bd at the phylogenetic level

WO-21

Interactions within coral reef communities

WO-22

Microbial biofilms are necessary for larval settlement

Suggested Citation:"Front Matter." Institute of Medicine. 2013. The Science and Applications of Microbial Genomics: Workshop Summary. Washington, DC: The National Academies Press. doi: 10.17226/18261.
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WO-23

Timeline of sequence-based metagenomic projects showing the variety of environments sampled since 2002

WO-24

Novel taxa are found in three of the major phyla associated with human stool samples

WO-25

P. acnes is dominant in pilosebaceous units in both acne patients and individuals with normal skin

WO-26

Genomic differences at the subspecies level (P. acnes)

WO-27

Overdispersion of 22 sample types from Dirichlet-multinomial distribution showing similarity between subjects

WO-28

Change in HIV communities with HAART

WO-29

Hydrothermal vents host substantial endolithic microbial communities

WO-30

Electrical continuity yields diverse representative community

WO-31

HGT is ecologically structured by functional class and at multiple spatial scales

WO-32

Season and size fraction distributions and habitat predictions mapped onto Vibrionaceae isolate phylogeny inferred by maximum likelihood analysis of partial hsp60 gene sequences

WO-33

Ecological differentiation in recombining microbial populations

WO-34

Metagenomic approach to studying the Earth’s microbiome

WO-35

Extrapolating microbial community structure

WO-36

We change the microbial community of a house

WO-37

Microbial genomics and tool development

WO-38

Putative transmission on networks constructed from genotyping data versus whole genome data for 32 patients

WO-39

Phylogenetic analysis of novel astrovirus VA1 identified in an outbreak of gastroenteritis

WO-40

Distribution of OTU relative abundances across 210 Human Microbiome Project stool samples

WO-41

Two Acinetobacter v6 tags differing by a single nucleotide and demonstrating a seasonally balanced abundance

WO-42

Principal coordinates analysis of 1,606 Human Microbiome Project shotgun metagenomes

WO-43

Principal coordinates analysis of 1,606 Human Microbiome Project shotgun metagenomes painted by sequencing technology

WO-44

The costs associated with data analysis are becoming the bottleneck for metagenomic analyses

WO-45

Changes in instrument capacity over the past decade, and the timing of major sequencing projects

WO-46

Prototype of a nanopore sequencing technology currently under development

WO-47

Phylogenetic “dark matter” left to be sampled

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Suggested Citation:"Front Matter." Institute of Medicine. 2013. The Science and Applications of Microbial Genomics: Workshop Summary. Washington, DC: The National Academies Press. doi: 10.17226/18261.
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A1-1

The microbial forensics attribution continuum

A1-2

A general overview of the work and information flow from sample to analysis to information developed based on use of second-generation sequencing technology

A3-1

An example demonstrating how the limitations of field and molecular epidemiology complicate outbreak reconstructions

A3-2

The dense social network in the outbreak community complicated outbreak reconstruction attempts

A3-3

The number of bacterial genome projects recorded in the Genomes Online Database (GOLD) increased exponentially with the introduction of next-generation sequencing methods in the mid-2000s

A3-4

Using microevolutionary events to track person-to-person spread of a pathogen over a social network

A4-1

Outline of studies indicating day of onset, day when oseltamivir treatment was started, and sampling timeline

A4-2

Longitudinal study of variant codon prevalence across multiple time-points in an infected immunocompromised child

A4-3

Transmission study of variant codon prevalence compared between son and father specimens

A6-1

An example rank abundance curve with a long-tail distribution

A6-2

Rarefaction curve for OTUs generated from Human Microbiome Project stool samples using the V3-V5 region

A6-3

We calculated alpha diversity (richness) using both ACE and Chao estimators with clusters based on complete linkage and average linkage algorithms

A6-4

Selecting multiple random subsamples of 5,000 reads from a larger data set of 50,000 reads, we created a set of pseudo-replicate samples

A6-5

The rank abundance curve shows only minor reductions in the long tail even assuming that as many as 1 in 500 reads generates a spurious OUT

A7-1

SNP phylogeny of 262 Malagasy isolates

A7-2

Neighbor-joining dendrograms based upon MLVA data

A7-3

Geographic distribution of MLVA subclades in Madagascar

A7-4

Geographic distribution of SNP-defined nodes in the strain MG05-1020 lineage

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Suggested Citation:"Front Matter." Institute of Medicine. 2013. The Science and Applications of Microbial Genomics: Workshop Summary. Washington, DC: The National Academies Press. doi: 10.17226/18261.
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A8-1

The MG-RAST system has more than 58,000 metagenomic data sets totaling over 16.5 terabase pairs of information

A8-2

The DRISEE error profiles for two anonymous projects with three shotgun libraries

A8-3

A simple representation of average base abundance per base demonstrates that data is not distributed randomly

A9-1

High-throughput sequencing platforms

A10-1

A maximum-likelihood phylogenetic tree of the seventh pandemic lineage of V. cholerae based on SNP differences across the whole core genome, excluding probable recombination events

A10-2

Transmission events inferred for the seventh-pandemic phylogenetic tree, drawn on a global map

A11-1

Schematic of coral surfaces and associated microbes

A12-1

Phylogenetic relationships among the 19 taxa used in comparative genomics analyses

A12-2

Chytrid growth on cane-toad skin

A12-3

Gene family copy numbers for metalloproteases (M36), serine-type proteases (S41), aspartyl proteases (ASP), and CRN-like proteins (CRN) in the Chytridiomycota (Bd, Hp and S. punctatus), and a Blastocladiomycota outgroup (A. macrogynus)

A12-4

Maximum likelihood phylogenies of gene families containing (A) M36, (B) S41, and (C) Asp Pfam domains

A12-5

Left panel (paralog rates) shows box plots of synonymous substitution rates (Ks) for Bd lineage-specific duplicates in three protease families

A13-1

Intestinal cell infection phenotypes in wild Caenorhabditis isolates

A13-2

Transmission electron micrographs of intestinal cells of C. elegans JU1580 adult hermaphrodites

A13-3

Genomic organization and phylogenetic analysis of novel viruses

A13-4

Molecular evidence of viral infection

A13-5

Specificity of infection by the Orsay and Santeuil viruses

A13-6

Small RNAs produced upon viral infection

A13-7

RNAi-deficient mutants of C. elegans can be infected by the Orsay virus

A13-8

Natural variation in somatic RNAi efficacy in C. elegans

A14-1

Data and analysis workflow for microbiome analysis

Suggested Citation:"Front Matter." Institute of Medicine. 2013. The Science and Applications of Microbial Genomics: Workshop Summary. Washington, DC: The National Academies Press. doi: 10.17226/18261.
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Over the past several decades, new scientific tools and approaches for detecting microbial species have dramatically enhanced our appreciation of the diversity and abundance of the microbiota and its dynamic interactions with the environments within which these microorganisms reside. The first bacterial genome was sequenced in 1995 and took more than 13 months of work to complete. Today, a microorganism's entire genome can be sequenced in a few days. Much as our view of the cosmos was forever altered in the 17th century with the invention of the telescope, these genomic technologies, and the observations derived from them, have fundamentally transformed our appreciation of the microbial world around us.

On June 12 and 13, 2012, the Institute of Medicine's (IOM's) Forum on Microbial Threats convened a public workshop in Washington, DC, to discuss the scientific tools and approaches being used for detecting and characterizing microbial species, and the roles of microbial genomics and metagenomics to better understand the culturable and unculturable microbial world around us. Through invited presentations and discussions, participants examined the use of microbial genomics to explore the diversity, evolution, and adaptation of microorganisms in a wide variety of environments; the molecular mechanisms of disease emergence and epidemiology; and the ways that genomic technologies are being applied to disease outbreak trace back and microbial surveillance. Points that were emphasized by many participants included the need to develop robust standardized sampling protocols, the importance of having the appropriate metadata, data analysis and data management challenges, and information sharing in real time. The Science and Applications of Microbial Genomics summarizes this workshop.

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