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Suggested Citation:"Front Matter." Institute of Medicine. 2012. The Social Biology of Microbial Communities: Workshop Summary. Washington, DC: The National Academies Press. doi: 10.17226/13500.
×

THE SOCIAL BIOLOGY
OF

MICROBIAL COMMUNITIES

WORKSHOP SUMMARY

LeighAnne Olsen, Eileen R. Choffnes,
and Alison Mack, 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. 2012. The Social Biology of Microbial Communities: Workshop Summary. Washington, DC: The National Academies Press. doi: 10.17226/13500.
×

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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.

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, Food and Drug Administration, and the Fogarty International Center; 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; 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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Cover images: (Front) Colony developed by the Gram-positive social bacteria Paenibacillus dendritiformis (chiral morphotype). The colony diameter is about 6 cm, and the number of cells is about the same as the number of people on Earth. For more information see http://star.tau.ac.il/~eshel. Photo credit: Eshel Ben-Jacob/Tel Aviv University. (Back) Bioluminescence offers undersea advantages to (clockwise from top left) a pelagic worm, squid, krill, scaleless black dragonfish, and deepwater jellyfish. Photo Credit: Edith Widder/Ocean Research and Conservation Association.

Suggested citation: IOM (Institute of Medicine). 2012. The Social Biology of Microbial Communities: Workshop Summary. Washington, DC: The National Academies Press.

Suggested Citation:"Front Matter." Institute of Medicine. 2012. The Social Biology of Microbial Communities: Workshop Summary. Washington, DC: The National Academies Press. doi: 10.17226/13500.
×

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. 2012. The Social Biology of Microbial Communities: Workshop Summary. Washington, DC: The National Academies Press. doi: 10.17226/13500.
×

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.

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Suggested Citation:"Front Matter." Institute of Medicine. 2012. The Social Biology of Microbial Communities: Workshop Summary. Washington, DC: The National Academies Press. doi: 10.17226/13500.
×

PLANNING COMMITTEE FOR A WORKSHOP ON
THE MICROBIOME IN HEALTH AND DISEASE1

BONNIE BASSLER, Princeton University, Princeton, New Jersey

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

JONATHAN EISEN, University of California, Davis, California

JO HANDELSMAN, Yale University, New Haven, Connecticut

CAROLE HEILMAN, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland

DAVID RELMAN, Stanford University and Veterans Affairs Palo Alto Health Care System, Palo Alto, California

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

___________

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. 2012. The Social Biology of Microbial Communities: Workshop Summary. Washington, DC: The National Academies Press. doi: 10.17226/13500.
×

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

DAVID BLAZES,2 Division of Global Emerging Infectious Surveillance, Armed Forces Health Surveillance Center, Silver Spring, Maryland

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

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

PAULA R. BRYANT, 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

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,3 Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, Maryland

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

___________

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 March 31, 2012.

3 Forum member since June 1, 2012.

Suggested Citation:"Front Matter." Institute of Medicine. 2012. The Social Biology of Microbial Communities: Workshop Summary. Washington, DC: The National Academies Press. doi: 10.17226/13500.
×

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

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,4 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

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

MARK A. MILLER,5 Fogarty International Center, Bethesda, Maryland

JULIE PAVLIN,6 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, 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, U.S. Agency for International Development, Washington, DC

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

___________

4 Forum member since June 1, 2012.

5 Forum member until August 31, 2012.

6 Forum member since April 1, 2012.

Page viii Cite
Suggested Citation:"Front Matter." Institute of Medicine. 2012. The Social Biology of Microbial Communities: Workshop Summary. Washington, DC: The National Academies Press. doi: 10.17226/13500.
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Staff

EILEEN CHOFFNES, Scholar and Director

LEIGHANNE OLSEN, Program Officer

KATHERINE McCLURE, Senior Program Associate

REBEKAH HUTTON, Research Associate

PAMELA BERTELSON, Senior Program Assistant

Suggested Citation:"Front Matter." Institute of Medicine. 2012. The Social Biology of Microbial Communities: Workshop Summary. Washington, DC: The National Academies Press. doi: 10.17226/13500.
×

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. 2012. The Social Biology of Microbial Communities: Workshop Summary. Washington, DC: The National Academies Press. doi: 10.17226/13500.
×

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

Staff

PATRICK KELLEY, Director

ANGELA CHRISTIAN, Program Associate

Suggested Citation:"Front Matter." Institute of Medicine. 2012. The Social Biology of Microbial Communities: Workshop Summary. Washington, DC: The National Academies Press. doi: 10.17226/13500.
×

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:

Eshel Ben-Jacob, School of Physics and Astronomy, Tel Aviv University, Tel Aviv, Israel

Steve Diggle, School of Molecular Medical Sciences, University of Nottingham, Nottingham, United Kingdom

David Rizzo, Department of Plant Pathology, University of California, Davis, 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

Suggested Citation:"Front Matter." Institute of Medicine. 2012. The Social Biology of Microbial Communities: Workshop Summary. Washington, DC: The National Academies Press. doi: 10.17226/13500.
×

before its release. The review of this workshop summary was overseen by Dr. Melvin Worth. Appointed by the Institue 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.

Page xiii Cite
Suggested Citation:"Front Matter." Institute of Medicine. 2012. The Social Biology of Microbial Communities: Workshop Summary. Washington, DC: The National Academies Press. doi: 10.17226/13500.
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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. 2012. The Social Biology of Microbial Communities: Workshop Summary. Washington, DC: The National Academies Press. doi: 10.17226/13500.
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The Forum gratefully acknowledges the contributions of the members of the planning committee1: Bonnie Bassler (Princeton University), Arturo Casadevall (Albert Einstein College of Medicine), Jonathan Eisen (University of California, Davis), Jo Handelsman (Yale University), Carole Heilman (National Institute of Allergy and Infectious Diseases, NIH), David Relman (Stanford University and Veterans Affairs Palo Alto Health Care System), and P. Fredrick Sparling (University of North Carolina, Chapel Hill).

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, 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, Alison Mack, Vilija Teel, 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, Food and Drug Administration, and the Fogarty International Center; 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; 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.

Suggested Citation:"Front Matter." Institute of Medicine. 2012. The Social Biology of Microbial Communities: Workshop Summary. Washington, DC: The National Academies Press. doi: 10.17226/13500.
×

Phylogenetic and Phylogenomic Approaches to Studies of Microbial Communities

Microbial Community Assembly and Dynamics: From Acidophilic Biofilms to the Premature Infant Gut

Genes and Ecology

Dynamic Interactions of Microbial Communities

Communication and Information Processing

Intraspecies Interaction: Contact-Dependent Communication

Interkingdom Interactions: Symbiotic Microbes, Their Mammalian Host, and Invading Pathogens

The Colony as a Community

Swarming Bacteria as Agents of Microbial Dispersal

The Fungal Gardens of the Leaf-Cutter Ants

Gene Signals for Past Perturbations and Other Major Evolutionary Events Impacting Complex Gut Microbial Communities

Evolution of Cooperation and Control of Cheating in the Social Amoeba

Farming of bacteria

Emergence and Robustness of Multicellular Behavior in Bacteria

Evolutionary Transitions to Multicellularity

Human-Microbe Mutualism

Communities of microbes and genes

Cooperative Survival Strategies

Community Cooperation and the Expression of Virulence

Cooperation, Cheating, and Coordinated Behaviors

Multicellular behavior in bacteria

Infectious cooperation

Evolutionary Transitions Through Higher-Level Selection

Looking Ahead: Moving to the Community as the Unit of Study

Developing Theoretical and Experimental Frameworks

Microbial Communities as Complex Adaptive Systems

Probing Resilience Through Perturbation

New Tools and Approaches for an Emerging Field of Inquiry

Statistical Tools for Integrating Community Networks and Spatial and Clinical Data

Transdisciplinarity

Semantics

Insights into Life on Earth and Other Worlds

Untapped Innovation and Functional Novelty

Genetic and Metabolic Diversity

Microbial Roles in Health

Page xvii Cite
Suggested Citation:"Front Matter." Institute of Medicine. 2012. The Social Biology of Microbial Communities: Workshop Summary. Washington, DC: The National Academies Press. doi: 10.17226/13500.
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Workshop Overview References

Appendixes

A Contributed Manuscripts

A1    Strain-Resolved Community Genomic Analysis of Gut Microbial Colonization in a Premature Infant

Michael J. Morowitz, Vincent J. Denef, Elizabeth K. Costello, Brian C. Thomas, Valeriy Poroyko, David A. Relman, and Jillian F. Banfield

A2    Evolution of Virulence in Opportunistic Pathogens: Generalism, Plasticity, and Control

Sam P. Brown, Daniel M. Cornforth, and Nicole Mideo

A3    Free-Living Tube Worm Endosymbionts Found at Deep-Sea Vents

Tara L. Harmer, Randi D. Rotjan, Andrea D. Nussbaumer, Monika Bright, Andrew W. Ng, Eric G. DeChaine, and Colleen M. Cavanaugh

A4    Parasites May Help Stabilize Cooperative Relationships

Ainslie E. F. Little and Cameron R. Currie

A5    Metagenomic and Metaproteomic Insights into Bacterial Communities in Leaf-Cutter Ant Fungus Gardens

Frank O. Aylward, Kristin E. Burnum, Jarrod J. Scott, Garret Suen, Susannah G. Tringe, Sandra M. Adams, Kerrie W. Barry, Carrie D. Nicora, Paul D. Piehowski, Samuel O. Purvine, Gabriel J. Starrett, Lynne A. Goodwin, Richard D. Smith, Mary S. Lipton, and Cameron R. Currie

A6    Phylogenetic and Phylogenomic Approaches to Studies of Microbial Communities

Jonathan A. Eisen

A7    Sociomicrobiology and Quorum Sensing—Mediated Communication

Josephine R. Chandler and E. Peter Greenberg

A8    Acyl-Homoserine Lactone-Dependent Eavesdropping Promotes Competition in a Laboratory Co-Culture Model

Josephine R. Chandler, Silja Heilmann, John E. Mittler, and E. Peter Greenberg

A9    Rules of Engagement: Interspecies Interactions That Regulate Microbial Communities

Ainslie E. F. Little, Courtney J. Robinson, S. Brook Peterson, Kenneth F. Raffa, and Jo Handelsman

A10  Statistical Data Analysis Challenges from the Microbiome

Susan Holmes and Paul J. McMurdie

Page xviii Cite
Suggested Citation:"Front Matter." Institute of Medicine. 2012. The Social Biology of Microbial Communities: Workshop Summary. Washington, DC: The National Academies Press. doi: 10.17226/13500.
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A11  Dispersal of Cargo Microorganisms by Swarming Bacteria

Colin J. Ingham

A12  Evidence for Cascades of Perturbation and Adaptation in the Metabolic Genes of Higher Termite Gut Symbionts

Xinning Zhang and Jared R. Leadbetter

A13  Mathematical and Computational Challenges in the Study of Complex Adaptive Microbial Systems

Simon A. Levin, Juan A. Bonachela, and Carey D. Nadell

A14  Identification of a Target Cell Permissive Factor Required for Contact-Dependent Growth Inhibition (CDI)

Elie J. Diner, Christina M. Beck, Julia S. Webb, David A. Low, and Christopher S. Hayes

A15  Cheats as First Propagules: A New Hypothesis for the Evolution of Individuality During the Transition from Single Cells to Multicellularity

Paul B. Rainey and Benjamin Kerr

A16  An Ecological and Evolutionary Perspective on Human-Microbe Mutualism and Disease

Les Dethlefsen, Margaret McFall-Ngai, and David A. Relman

A17  Incomplete Recovery and Individualized Responses of the Human Distal Gut Microbiota to Repeated Antibiotic Perturbation

Les Dethlefsen and David A. Relman

A18  Studying the Enteric Microbiome in Inflammatory Bowel Diseases: Getting Through the Growing Pains and Moving Forward

Vincent B. Young, Stacy A. Kahn, Thomas M. Schmidt, and Eugene B. Chang

A19  Inter-Kingdom Signalling: Communication Between Bacteria and Their Hosts

David T. Hughes and Vanessa Sperandio

A20  Evolution of Cooperation and Control of Cheating in a Social Microbe

Joan E. Strassmann and David C. Queller

A21  Glowing Corpses and Radiant Excrement: The Role of Bioluminescence in Microbial Communities

Edith A. Widder

A22  Social Interaction, Noise and Antibiotic-Mediated Switches in the Intestinal Microbiota

Vanni Bucci, Serena Bradde, Giulio Biroli, and Joao B. Xavier

B Agenda

C Acronyms

D Glossary

E Speaker Biographies

Suggested Citation:"Front Matter." Institute of Medicine. 2012. The Social Biology of Microbial Communities: Workshop Summary. Washington, DC: The National Academies Press. doi: 10.17226/13500.
×

A8-1    Sensitivity of C. violaceum (Cv) Strains to B. thailandensis (Bt) culture fluid

A8-2    Sensitivity of B. thailandensis (Bt) Strains to C. violaceum (Cv) Culture Fluid

A8-3    Final Yields of B. thailandensis (Bt) and C. Violaceum (Cv) in a Pure Culture and Co-Culture

A10-1  Differentially Represented OTUs

A12-1  Characteristics of Higher Termites Examined in this Study

A12-2  fdhF Inventories Constructed in this Study

A12-3  Distribution of Higher Termite Inventory Sequences amongst Four Major FDHH Clades

A12-4  PCR Conditions for Clone Library Construction

A12-5  Detailed Composition of Higher Termite fdhF Inventories

A12-6  Sequences Used in Phylogenetic Analyses

A13-1  Exponents Measured in the Different Theoretical and Experimental Work Cited in the Text

A14-1  Proteins Identified in the Cdi-CT Activating Fraction

A16-1  Model Systems for Animal–Microbe Symbioses

A17-1  Pyrosequencing reads, refOTUs, and coverage

A19-1  Hormonal Signals, Receptors and Biological Functions

FIGURES

WO-1    Microbial biofims: Sticking together for success

WO-2    Myxobacteria build multicellular fruiting bodies

WO-3    The bacterium and the squid

WO-4    The winnowing

WO-5    An example of nitrogen-fixing symbiosis between legumes and rhizobia bacteria

WO-6    The microbiome of various anatomical locations of the human body

WO-7    Mechanism of quorum sensing in the luminescent bacterium Vibrio fischeri

WO-8    The chemical structures of the four best-known luciferins are as diverse as their phylogenetic distribution

Suggested Citation:"Front Matter." Institute of Medicine. 2012. The Social Biology of Microbial Communities: Workshop Summary. Washington, DC: The National Academies Press. doi: 10.17226/13500.
×

WO-9    The burglar alarm jellyfish lights up blue to call in predators of its attackers

WO-10  Progression from studies on the individual scale to studies on the community scale

WO-11  Oxygen gradients and microbial function

WO-12  Hydrothermal vent organisms and their bacterial symbionts

WO-13  Molecular communication networks between organisms in the Bacillus cereus biocontrol system

WO-14  Parts of a root tip and areas of the rhizosphere

WO-15  rRNA universal tree of life based on a comparison of nucleic acid sequences found in all cellular life (small subunit ribosomal RNA)

WO-16  Schematic illustrating important features that make the AMD system a good model for studying microbial communities

WO-17  Microbial community proteomics: Functional assays in situ

WO-18  The dynamic genetic repertoire of microbial communities

WO-19  Contact-dependent growth inhibition (CDI)

WO-20  Photograph showing the result of transporting Aspergillus fumigatus conidia by swarming Paenibacillus vortex

WO-21  Colored scanning electron micrograph showing transport of a single conidium of Aspergillus fumigatus transported by swarming Paenibacillus vortex

WO-22  Coevolved crypts and exocrine glands support mutualistic bacteria in fungus-growing ants

WO-23  Inferred evolutionary history for fdhF in the symbiotic gut microbial communities of lignocellulose-feeding insects

WO-24  Cheating in low-relatedness studies

WO-25  rhlA regulation ensures metabolic prudence

WO-26  A putative life cycle for mat-forming bacteria

WO-27  The number of genes distributed among the human-associated microbiota far outnumbers the number of genes humans inherit from their parents

WO-28  Patterns emerge from individual interactions in bacterial communities

WO-29  The persistence of influenza A illustrates how robustness can result from flexibility

WO-30  Alternative stable states, disturbance, and loss of resilience

WO-31  In 1977, the deep-ocean submersible Alvin led scientists to discover tubeworms living at the edges of hydrothermal vents in the deep sea

A1-1      Multiple stable compositional states in the developing gut microbiota of the premature infant

A1-2      Population dynamics based on metagenomic profiling

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Suggested Citation:"Front Matter." Institute of Medicine. 2012. The Social Biology of Microbial Communities: Workshop Summary. Washington, DC: The National Academies Press. doi: 10.17226/13500.
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A1-3      Analyses of two ecologically divergent Citrobacter UC1CIT subpopulations

A1-4      Citrobacter UC1CIT genomic overview

A2-1      Ecological and evolutionary dynamics of virulence factors across two growth environments

A2-2      Adaptation to a benign environment A can pre-adapt an opportunistic pathogen for virulent growth in V if there is a significant positive association between the properties of environments A and V

A2-3      Adaptation to a benign environment A can reduce the capacity for virulent growth in V (and vice versa) if there is a significant negative association (trade-off) between growth rates g and r

A3-1      FISH detection of free-living vestimentiferan bacterial symbionts

A4-1      Cheating/infection experiments

A4-2      Prisoner’s Dilemma simulations

A4-3      Cooperation and conflict within the fungus-growing ant microbe symbiosis

A5-1      Leaf cutter ants forage on plant material that they use as manure for specialized fungus gardens

A5-2      Reconstruction of KEGG pathways recovered from phylogenetic bins generated from the leaf-cutter ant fungus-garden metagenomes

A5-3      Comparison of the COG category distributions of the three combined fungus-garden metagenomes

A5-4      Fragment recruitment analysis of genes phylogenetically binned to Enterobacter FGI 35 against the draft Enterobacter FGI 35 genome

A5-5      Example of overlap between field-collected and laboratory-reared fungus-garden samples for the glycoside hydrolase family 3 peptide N.AIADLLFGDVNPSGK.L

A6-1      Unrooted phylogenetic tree showing the position of the S. velum symbionts in relation to that of other Proteobacteria species on the basis of 16s rRNA gene sequences

A6-2      rRNA tree

A6-3      RecA tree

A6-4      Phylogenetic diversity of Sargasso Sea sequences using multiple phylogenetic markers

A6-5      A flow chart of the STAP pipeline

A6-6      A flow chart illustrating the major components of AMPHORA

A6-7      An unrooted maximum likelihood bacterial genome tree

Page xxiii Cite
Suggested Citation:"Front Matter." Institute of Medicine. 2012. The Social Biology of Microbial Communities: Workshop Summary. Washington, DC: The National Academies Press. doi: 10.17226/13500.
×

A6-8      Major phylotypes identified in Sargasso Sea metagenomic data

A6-9      Comparison of the phylotyping performance by AMPHORA and MEGAN

A6-10    Hypothetical multiple sequence alignment including full length “reference” sequences as well as fragmentary sequences from metagenomic data

A6-11    Hypothetical multiple sequence alignment showing one approach to carrying out phylogenetic analysis of metagenomic data—to extract a “core” region of the alignment and only analyze sequences that contain most of this core

A6-12    Hypothetical multiple sequence alignment showing an alternative strategy for phylogenetic analysis of metagenomic data—to analyze everything even if some sequences do not overlap with each other

A6-13    Computational processes are represented as squares and databases are represented as cylinders in this generalized workflow of PhylOTU

A6-14    Conceptual overview of approach to infer phylogenetic relationships among sequences from metagenomic data sets

A6-15    Phylogenetic tree linking metagenomic sequences from 31 gene families along an oceanic depth gradient at the HOT ALOHA site

A6-16    Taxonomic diversity and standardized phylogenetic diversity versus depth in environmental samples along an oceanic depth gradient at the HOT ALOHA site

A6-17    Searching for novel phylogenetic lineages

A6-18    Phylogenetic tree of the RecA superfamily

A6-19    Phylogenetic tree of the RpoB superfamily

A6-20    Outline of a phylogenomic methodology

A6-21    Phylogenomic functional prediction is based on the concept of phylotyping

A6-22    Phylogenetically biased genome sequencing

A6-23    For each of four groupings (species, different strains of Streptococcus agalactiae; family, Enterobacteriaceae; phylum, Actinobacteria; domain, GEBA bacteria), all proteins from that group were compared to each other to identify protein families

A6-24    Using a phylogenetic tree of unique SSU rRNA gene sequences7, phylogenetic diversity was measured for four subsets of this tree: organisms with sequenced genomes pre-GEBA (blue), the GEBA organisms (red), all cultured organisms (dark grey), and all available SSU rRNA genes (light grey)

A7-1      Some examples of acyl-HSL quorum-sensing signals

A7-2      Acyl-HSL signaling in V. fischeri and P. aeruginosa

A7-3      The quorum-sensing circuits of B. thailandensis, B. pseudomallei, and B. mallei

Page xxiv Cite
Suggested Citation:"Front Matter." Institute of Medicine. 2012. The Social Biology of Microbial Communities: Workshop Summary. Washington, DC: The National Academies Press. doi: 10.17226/13500.
×

A8-1      B. thailandensisC. violaceum competition

A8-2      Competition in co-cultures of wild-type C. violaceum (Cv) and wild-type or mutant B. thailandensis (Bt) strains

A8-3      Co-cultures of the C. violaceum (Cv) wild-type Cv017 or the AHL mutant Cv026 and the B. thailandensis (Bt) competition-impaired AHL, bactobolin double mutant JBT125

A8-4      C. violaceum (Cv) quorum sensing is activated by B. thailandensis (Bt) AHLs

A8-5      Eavesdropping promotes competitiveness of Cv in co-cultures with a B. Bt bactobolin mutant

A8-6      In silico modeling

A9-1      Continuum of interspecific interactions that occur in microbial communities

A9-2      Progression from studies on the individual scale to studies on the community scale

A9-3      Four groups of questions in microbial ecology and some techniques to address them

A10-1    1985: A dripping tap. 1998: A fire hydrant. 2012: A perfect storm

A10-2    A) Heatmap of abundance reads. B) Volcano plot for expressions with transparency

A10-3    Global patterns global data mapped onto the OTU reference tree

A10-4    Plotting the values of gPCA variables with a tree using R

A10-5    Multicomponent class typical to R

A10-6    Initial analysis with only two batches; on the right we see the addition of a third set of data

A10-7    A PCA flowchart, with choice levels highlighted

A10-8    Network of enterotype groups among samples as defined by patients having 70 percent shared OTUs

A10-9    Network of enterotype taxa co-occurring in at least 85 percent of the samples

A10-10  Procrustes and co-inertia analysis of Cipro patients seen in their compromise common projection (the large scatterplot) and the taxa and mass spec feature projections on the left of the plot

A11-1    Swarming by Proteus mirabilis

A11-2    Microscopy of P. vortex cells and microcolonies

A11-3    Pattern formation by swarming P. vortex

A11-4    Transport of A. fumigatus conidia by P. vortex

A11-5    Transport of conidia by P. vortex

A11-6    Examples of motile microorganisms moving other objects within microengineered environments

Suggested Citation:"Front Matter." Institute of Medicine. 2012. The Social Biology of Microbial Communities: Workshop Summary. Washington, DC: The National Academies Press. doi: 10.17226/13500.
×

A11-7    Simple diagram of soil composed of manifold microniches separated by barriers that include air gaps and aqueous environments

A11-8    Dispersal of motile bacteria facilitated by fungal mycelia

A11-9    Example of dispersal of motile bacteria facilitated by fungal pseudomycelia mycelia

A11-10  Dispersal of Streptomyces coelicolor spores facilitated by swarming P. vortex

A12-1    Mitochondrial cytochrome oxidase II (COII) phylogeny of termites and related roaches

A12-2    Schematic cladogram of major termite families and higher termite subfamilies showing major events in gut habitat evolution

A12-3    Protein phylogeny of hydrogenase-linked formate dehydrogenases (FDHH)

A12-4    Protein phylogeny of Sec and Cys clade sequences within the “Gut spirochete group” of FDHH

A12-5    Targeted PCR assays on termite and roach gut DNA using Cys clade specific fdhF primers (Cys499F1b, 1045R), which yield a ca. 600 bp product (ladder left lane: NEB 2-log)

A12-6    Protein phylogeny of Higher Termite Spirochete group sequences

A12-7    Protein phylogeny and amino acid character analysis of AGR group sequences

A12-8    Products from nested PCR reactions using universal fdhF primers followed by Amitermes-Gnathamitermes-Rhychotermes clade specific primers on gut templates

A12-9    UniFrac principal component analysis of FDHH phylogeny associated with the gut microbial communities of termites and related insects

A12-10  Inferred evolutionary history for fdhF in the symbiotic gut microbial communities of lignocellulose-feeding insects

A13-1    Morphological phase diagram depicting the five different qualitative behaviors shown by bacterial colonies growing under different agar concentration (CA) and nutrient concentration (C)

A13-2    Snapshots of the bacterial colonies obtained, with the detailed simulation framework described in the text

A13-3    Bacterial fronts obtained, with the simulation framework using mid-to-low nutrient concentrations, with an elapse of time of 8 hours

A13-4    A time-series of polymer-producing cells (red) growing in a biofilm with non-producing cells (blue)

A14-1    CdiA-CT tRNase activity requires a cofactor

A14-2    CysK is necessary and sufficient for tRNase activity

Page xxvi Cite
Suggested Citation:"Front Matter." Institute of Medicine. 2012. The Social Biology of Microbial Communities: Workshop Summary. Washington, DC: The National Academies Press. doi: 10.17226/13500.
×

A14-3    CdiA-CT is an intrinsic tRNase

A14-4    CdiA-CT and CysK form a stable complex in vitro

A14-5    Activation of CdiA-CT in E. coli cells results in growth arrest and tRNA degradation

A14-6    CysK is required for CdiA-CT-mediated growth inhibition and tRNase activity in vivo

A14-7    CysK is required for growth inhibition during CDIUPEC536

A15-1    The role of group reproduction in group adaptation

A15-2    The rise, fall, and destruction of a simple undifferentiated group

A15-3    A putative life cycle for mat-forming bacteria

A16-1    Site-specific distributions of bacterial phyla in healthy humans

A16-2    Patterns of human-associated microbial diversity

A16-3    Relationships between bacterial 16S rRNA gene sequences from the intestinal microbiota of animals

A16-4    Adaptive landscapes

A17-1    Heat map displaying the relative abundance of refOTUs in three prominent clades of bacteria

A17-2    Three measures of biological diversity for samples

A17-3    PCoA of unweighted UniFrac distances, a phylogenetically aware measure of intersample (β) diversity

A17-4    Distance-based redundancy analysis of Bray–Curtis intersample distances calculated with log2-transformed abundance data

A19-1    Chemical structures of bacterial and host signals

A19-2    Mammalian signalling through membrane receptors

A19-3    Adrenergic sensing in enterohaemorrhagic Escherichia coli

A19-4    AHL inter-kingdom signalling

A20-1    D. discoideum fruiting bodies on an agar plate

A20-2    Colony cycles of D. discoideum

A20-3    In the social stage, clones may take advantage of their partner in three different ways

A20-4    Conflict is manifested in chimeras in the form of shorter stalk lengths, shorter migration distances, and unequal spore/stalk ratios

A20-5    Cheating can be controlled in the social stage if fruiting bodies are clonal, as might happen if they arise from different patches

A21-1    The chemical structures of known luciferins

A21-2    The bacterial bioluminescence reaction

Page xxvii Cite
Suggested Citation:"Front Matter." Institute of Medicine. 2012. The Social Biology of Microbial Communities: Workshop Summary. Washington, DC: The National Academies Press. doi: 10.17226/13500.
×

A21-3    Pinecone fish

A21-4    Female anglerfish with attached male

A21-5    Fire shooter squid

A21-6    The life-cycle of the nematode host of the bioluminescent bacterium Photorhabdus luminescens

A22-1    The two-group model of the intestinal microbiota with antibiotic-sensitive and antibiotic-tolerant bacteria

A22-2    Multistability and hysteresis in a simple model of the intestinal microbiota

A22-3    Most probable microbiota states change from bistable scenario to mono-stable coexistence with increasing noise

A22-4    Microbiota resident time in antibiotic-tolerant domination as a function of the: antibiotic action (ε) and social interaction (ψ) parameters

A22-5    Analysis of microbiota response to the antibiotic ciprofloxacin from three subjects using singular value decomposition identifies antibiotic-sensitive and antibiotic-tolerant bacteria

A22-S1  Vectorial field of forces and the phase-plane analysis for bistable conditions

A22-S2  Model nullclines analysis in the absence of noise

A22-S3  Normalized-to-one areas of the basins of attraction, corresponding to sensitives (green curve) and tolerants (red curve), versus the antibiotic-killing y (A) or the social interaction e (B)

A22-S4  Time evolution of the sensitive (green) and tolerant (red) densities obtained by solving the Langevin equations for f = 1.1, y = 0.7, e variable with time (see Panel A) and three different noise regimes

A22-S5  A: most probable bacterial density r change with respect the noise parameter D when the boundary condition are fixed at negative values far enough from the location of the stable states; B: plot of four different stationary distributions

A22-S6  Stationary path connecting the stable points 1 and 2

A22-S7  Plot of the correlation with principal component 2 (PC2) versus correlation with principal component 1 (PC1) for all the phylotypes detected in each subjects (A-C)

A22-S8  Log2 abundance versus samples for all the phylotypes detected in each subject (A-C)

A22-S9  Ordination plot of the time samples based on their first two principal components

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Beginning with the germ theory of disease in the 19th century and extending through most of the 20th century, microbes were believed to live their lives as solitary, unicellular, disease-causing organisms . This perception stemmed from the focus of most investigators on organisms that could be grown in the laboratory as cellular monocultures, often dispersed in liquid, and under ambient conditions of temperature, lighting, and humidity. Most such inquiries were designed to identify microbial pathogens by satisfying Koch's postulates.3 This pathogen-centric approach to the study of microorganisms produced a metaphorical "war" against these microbial invaders waged with antibiotic therapies, while simultaneously obscuring the dynamic relationships that exist among and between host organisms and their associated microorganisms—only a tiny fraction of which act as pathogens.

Despite their obvious importance, very little is actually known about the processes and factors that influence the assembly, function, and stability of microbial communities. Gaining this knowledge will require a seismic shift away from the study of individual microbes in isolation to inquiries into the nature of diverse and often complex microbial communities, the forces that shape them, and their relationships with other communities and organisms, including their multicellular hosts.

On March 6 and 7, 2012, the Institute of Medicine's (IOM's) Forum on Microbial Threats hosted a public workshop to explore the emerging science of the "social biology" of microbial communities. Workshop presentations and discussions embraced a wide spectrum of topics, experimental systems, and theoretical perspectives representative of the current, multifaceted exploration of the microbial frontier. Participants discussed ecological, evolutionary, and genetic factors contributing to the assembly, function, and stability of microbial communities; how microbial communities adapt and respond to environmental stimuli; theoretical and experimental approaches to advance this nascent field; and potential applications of knowledge gained from the study of microbial communities for the improvement of human, animal, plant, and ecosystem health and toward a deeper understanding of microbial diversity and evolution. The Social Biology of Microbial Communities: Workshop Summary further explains the happenings of the workshop.

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