| Author: |
LeighAnne Olsen, Eileen R. Choffnes,
& Alison Mack, Rapporteurs |
| Release at: | 2012 |
| Pages: | 633 |
| Edition: |
1st Edition
|
| File Size: | 68 MB |
| File Type: | |
| Language: | English |
Description of The Social Biology of Microbial Communities
The social biology of microbial communities written by LeighAnne Olsen is great for microbial community studies available in ebook (pdf) free download. 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, the National Institutes of Health (NIH) and Prevention (CDC). The purpose of the Forum is to provide structured opportunities for leaders from government, industry, and academia to regularly examine issues and meet of shared concern regarding research, detection, management, and prevention of emerging, reemerging, & novel infectious diseases in humans, animals, and plants.
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 identifying and knowledge points of agreement, & inform decision-makers about policy issues and science. The illuminate issues Forum seeks rather than resolve them. For this reason, it does not recommendations or provides advice on any specific policy initiative pending before any agency or organization. Its value derives instead from the diversity of its membership & from the contributions that individual members make throughout the activities of the Forum. The Forum changed its name to the Forum on Microbial Threats in September 2003.
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 identifying and knowledge points of agreement, & inform decision-makers about policy issues and science. The illuminate issues Forum seeks rather than resolve them. For this reason, it does not recommendations or provides advice on any specific policy initiative pending before any agency or organization. Its value derives instead from the diversity of its membership & from the contributions that individual members make throughout the activities of the Forum. The Forum changed its name to the Forum on Microbial Threats in September 2003.
Content of The Social Biology of Microbial Communities
The Social Biology of Microbial Communities 1
Introduction, 1
Statement of Task, 3
Organization of the Workshop Summary, 3
Glimpses of Microbial Community Dynamics, 4
Microbial Communities in Abiotic and Biotic Environments, 5
Biofilms, 5
Multicellular structures for migration and dispersal, 7
The bacterium and the squid, 7
Plant roots and their partners, 9
Microbial inhabitants of the human gut, 11
The Social Life of Microbes, 13
Microbial Communities: The Ultimate Social Network, 16
Microbial Communication, 16
Quorum sensing, 17
Interactions with Other Species: Marine Microbial Communities Bioluminescence, 20
Structure and Function of Microbial Communities 25
Factors Influencing Community Formation and Function, 28
The Role of Oxygen in the Function & Structure of Microbial Communities, 28
Source-Sink Dynamics: Free-Living & Host-Associated Chemosynthetic Symbionts, 30
Plant-Microbial Soil Communities, 33
Phylogenetic and Phylogenomic Approaches to Studies of Microbial Communities, 36
Microbial Community Dynamics and Assembly: From Acidophilic Biofilms to the Premature Infant Gut, 39
Genes and Ecology, 43
Dynamic Interactions of Microbial Communities 44
Communication and Information Processing, 45
Intraspecies Interaction: contact-dependent Communication, 45
Interkingdom Interactions: Symbiotic Microbes, Their Invading Pathogens, and Mammalian Host, 47
The Colony as a Community, 48
Swarming Bacteria as Agents of Microbial Dispersal, 49
The Fungal Gardens of the Ants Leaf-Cutter, 51
Gene Signals for Past Perturbations & Other Major Evolutionary Events Impacting Complex Gut Microbial Communities, 54
Evolution of Control and Cooperation of Cheating in the Social Amoeba, 57
Farming of bacteria, 58
Robustness and Emergence of Multicellular Behavior in Bacteria, 59
Evolutionary Transitions to Multicellularity, 60
Human-Microbe Mutualism, 62
Communities of microbes and genes, 63
Cooperative Survival Strategies, 66
The Expression and Community Cooperation of Virulence, 67
Cooperation, Cheating, and Coordinated Behaviors, 69
Multicellular behavior in bacteria, 69
Infectious cooperation, 69
Evolutionary Transitions Through Higher-Level Selection, 70
Looking Ahead: The Community Moving as the Unit of Study 71
Developing Theoretical and Experimental Frameworks, 71
Microbial Communities as Complex Adaptive Systems, 72
Probing Resilience Through Perturbation, 76
Approaches and New Tools for an Emerging Field of Inquiry, 77
Statistical Tools for Integrating Community Networks, Spatial and Clinical Data, 78
Transdisciplinarity, 79
Semantics, 80
Insights into Life on Earth & Other Worlds, 81
Untapped Innovation and Functional Novelty, 83
Genetics and Metabolic Diversity, 85
Microbial Roles in Health, 86
Workshop Overview References 87
Appendixes
A Contributed Manuscripts 97
A1 Strain-Resolved Community Genomic Analysis of Gut Microbial Colonization in a Premature Infant, 97
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, 115
Sam P. Brown, Daniel M. Cornforth, and Nicole Mideo
A3 Free-Living Tube Worm Endosymbionts Found at Deep-Sea Vents, 128
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, 137
Ainslie E. F. Little and Cameron R. Currie
A5 Metagenomic and Metaproteomic Insights into Bacterial Communities in Leaf-Cutter Ant Fungus Gardens, 153
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. Piechowski, 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, 180
Jonathan A. Eisen
A7 Sociomicrobiology and Quorum Sensing—Mediated Communication, 213
Josephine R. Chandler and E. Peter Greenberg
A8 Acyl-Homoserine Lactone-Dependent Eavesdropping Promotes Competition in a Laboratory Co-Culture Model, 223
Josephine R. Chandler, Silja Heilmann, John E. Mittler, and E. Peter Greenberg
A9 Rules of Engagement: Interspecies Interactions That Regulate Microbial Communities, 242
Ainslie E. F. Little, Courtney J. Robinson, S. Brook Peterson, Kenneth F. Raffa, and Jo Handelsman
A10 Statistical Data Analysis and Challenges from the Microbiome, 275
Susan Holmes and Paul J. McMurdie
A11 Dispersal of Cargo Microorganisms by Swarming Bacteria, 304
Colin J. Ingham
A12 Evidence for Cascades of Perturbation and Adaptation in the Metabolic Genes of Higher Termite Gut Symbionts, 323
Xinning Zhang and Jared R. Leadbetter
A13 Mathematical and Computational Challenges in the Study of Complex Adaptive Microbial Systems, 361
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), 385
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, 409
Paul B. Rainey and Benjamin Kerr
A16 An Ecological and Evolutionary Perspective on Human-Microbe Mutualism and Disease, 426
Les Dethlefsen, David A. Relman, and Margaret McFall-Ngai
A17 Incomplete Recovery and Individualized Responses of the Human Distal Gut Microbiota to Repeated Antibiotic Perturbation, 447
Les Dethlefsen and David A. Relman
A18 Studying the Enteric Microbiome in Inflammatory Bowel Diseases: Getting Through the Growing Pains and Moving Forward, 470
Vincent B. Young, Stacy A. Kahn, Thomas M. Schmidt, and Eugene B. Chang
A19 Inter-Kingdom Signalling: Communication Between Bacteria and Their Hosts, 484
David T. Hughes and Vanessa Sperandio
A20 Evolution of Cooperation and Control of Cheating in a Social Microbe, 509
Joan E. Strassmann and David C. Queller
A21 Glowing Corpses and Radiant Excrement: The Role of Bioluminescence in Microbial Communities, 533
Edith A. Widder
A22 Social Interaction, Noise and Antibiotic-Mediated Switches in the Intestinal Microbiota, 549
Vanni Bucci, Serena Braddy, Giulio Biroli, and Joao B. Xavier
B Agenda 581
C Acronyms 585
D Glossary 587
E Speaker Biographies 595
Introduction, 1
Statement of Task, 3
Organization of the Workshop Summary, 3
Glimpses of Microbial Community Dynamics, 4
Microbial Communities in Abiotic and Biotic Environments, 5
Biofilms, 5
Multicellular structures for migration and dispersal, 7
The bacterium and the squid, 7
Plant roots and their partners, 9
Microbial inhabitants of the human gut, 11
The Social Life of Microbes, 13
Microbial Communities: The Ultimate Social Network, 16
Microbial Communication, 16
Quorum sensing, 17
Interactions with Other Species: Marine Microbial Communities Bioluminescence, 20
Structure and Function of Microbial Communities 25
Factors Influencing Community Formation and Function, 28
The Role of Oxygen in the Function & Structure of Microbial Communities, 28
Source-Sink Dynamics: Free-Living & Host-Associated Chemosynthetic Symbionts, 30
Plant-Microbial Soil Communities, 33
Phylogenetic and Phylogenomic Approaches to Studies of Microbial Communities, 36
Microbial Community Dynamics and Assembly: From Acidophilic Biofilms to the Premature Infant Gut, 39
Genes and Ecology, 43
Dynamic Interactions of Microbial Communities 44
Communication and Information Processing, 45
Intraspecies Interaction: contact-dependent Communication, 45
Interkingdom Interactions: Symbiotic Microbes, Their Invading Pathogens, and Mammalian Host, 47
The Colony as a Community, 48
Swarming Bacteria as Agents of Microbial Dispersal, 49
The Fungal Gardens of the Ants Leaf-Cutter, 51
Gene Signals for Past Perturbations & Other Major Evolutionary Events Impacting Complex Gut Microbial Communities, 54
Evolution of Control and Cooperation of Cheating in the Social Amoeba, 57
Farming of bacteria, 58
Robustness and Emergence of Multicellular Behavior in Bacteria, 59
Evolutionary Transitions to Multicellularity, 60
Human-Microbe Mutualism, 62
Communities of microbes and genes, 63
Cooperative Survival Strategies, 66
The Expression and Community Cooperation of Virulence, 67
Cooperation, Cheating, and Coordinated Behaviors, 69
Multicellular behavior in bacteria, 69
Infectious cooperation, 69
Evolutionary Transitions Through Higher-Level Selection, 70
Looking Ahead: The Community Moving as the Unit of Study 71
Developing Theoretical and Experimental Frameworks, 71
Microbial Communities as Complex Adaptive Systems, 72
Probing Resilience Through Perturbation, 76
Approaches and New Tools for an Emerging Field of Inquiry, 77
Statistical Tools for Integrating Community Networks, Spatial and Clinical Data, 78
Transdisciplinarity, 79
Semantics, 80
Insights into Life on Earth & Other Worlds, 81
Untapped Innovation and Functional Novelty, 83
Genetics and Metabolic Diversity, 85
Microbial Roles in Health, 86
Workshop Overview References 87
Appendixes
A Contributed Manuscripts 97
A1 Strain-Resolved Community Genomic Analysis of Gut Microbial Colonization in a Premature Infant, 97
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, 115
Sam P. Brown, Daniel M. Cornforth, and Nicole Mideo
A3 Free-Living Tube Worm Endosymbionts Found at Deep-Sea Vents, 128
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, 137
Ainslie E. F. Little and Cameron R. Currie
A5 Metagenomic and Metaproteomic Insights into Bacterial Communities in Leaf-Cutter Ant Fungus Gardens, 153
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. Piechowski, 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, 180
Jonathan A. Eisen
A7 Sociomicrobiology and Quorum Sensing—Mediated Communication, 213
Josephine R. Chandler and E. Peter Greenberg
A8 Acyl-Homoserine Lactone-Dependent Eavesdropping Promotes Competition in a Laboratory Co-Culture Model, 223
Josephine R. Chandler, Silja Heilmann, John E. Mittler, and E. Peter Greenberg
A9 Rules of Engagement: Interspecies Interactions That Regulate Microbial Communities, 242
Ainslie E. F. Little, Courtney J. Robinson, S. Brook Peterson, Kenneth F. Raffa, and Jo Handelsman
A10 Statistical Data Analysis and Challenges from the Microbiome, 275
Susan Holmes and Paul J. McMurdie
A11 Dispersal of Cargo Microorganisms by Swarming Bacteria, 304
Colin J. Ingham
A12 Evidence for Cascades of Perturbation and Adaptation in the Metabolic Genes of Higher Termite Gut Symbionts, 323
Xinning Zhang and Jared R. Leadbetter
A13 Mathematical and Computational Challenges in the Study of Complex Adaptive Microbial Systems, 361
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), 385
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, 409
Paul B. Rainey and Benjamin Kerr
A16 An Ecological and Evolutionary Perspective on Human-Microbe Mutualism and Disease, 426
Les Dethlefsen, David A. Relman, and Margaret McFall-Ngai
A17 Incomplete Recovery and Individualized Responses of the Human Distal Gut Microbiota to Repeated Antibiotic Perturbation, 447
Les Dethlefsen and David A. Relman
A18 Studying the Enteric Microbiome in Inflammatory Bowel Diseases: Getting Through the Growing Pains and Moving Forward, 470
Vincent B. Young, Stacy A. Kahn, Thomas M. Schmidt, and Eugene B. Chang
A19 Inter-Kingdom Signalling: Communication Between Bacteria and Their Hosts, 484
David T. Hughes and Vanessa Sperandio
A20 Evolution of Cooperation and Control of Cheating in a Social Microbe, 509
Joan E. Strassmann and David C. Queller
A21 Glowing Corpses and Radiant Excrement: The Role of Bioluminescence in Microbial Communities, 533
Edith A. Widder
A22 Social Interaction, Noise and Antibiotic-Mediated Switches in the Intestinal Microbiota, 549
Vanni Bucci, Serena Braddy, Giulio Biroli, and Joao B. Xavier
B Agenda 581
C Acronyms 585
D Glossary 587
E Speaker Biographies 595
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