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Front Matter i-xxvi
Workshop Overview 1-92
A1 Effector and memory T cell responses to commensal bacteria--Yasmine Belkaid, Nicolas Bouladoux, and Timothy W. Hand 93-109
A2 What are the consequences of the disappearing human microbiota?--Martin J. Blaser and Stanley Falkow 110-130
A3 Pathways in microbe-induced obesity--Laura M. Cox and Martin J. Blaser 131-152
A4 Microbial exposure during early life has persistent effects on natural killer T Cell function--Torsten Olszak, Dingding An, Sebastian Zeissig, Miguel Penilla Vera, Julia Richter, Andre Franke, Jonathan N. Glickman, Reiner Siebert, Rebecca M. Barron, Dennis L. Kasper, and Richard S. Blumberg 153-163
A5 The application of ecological theory toward an understanding of the human microbiome--Elizabeth K. Costello, Keaton Stagaman, Les Dethlefsen, Brendan J. M. Bohannan, and David A. Relman 164-183
A6 Seasonal restructuring of the ground squirrel gutmicrobiota over the annual hibernation cycle--Hannah V. Carey, William A. Walters, and Rob Knight 184-206
A7 Lessons from studying insect symbioses--Angela E. Douglas 207-223
A8 A new vision of immunity: homeostasis of the superorganism--Grard Eberl 224-248
A9 Host defense and immunomodulation of mucosal candidiasis--Paul L. Fidel, Jr., and Mairi C. Noverr 249-272
A10 Microbiota-targeted therapies: An ecological perspective--Katherine P. Lemon, Gary C. Armitage, David A. Relman, and Michael Fischbach 273-291
A11 Community ecology and the vaginal microbiome--Larry J. Forney and Jacques Ravel 292-322
A12 Investigating bacterial-animal symbioses with light sheet microscopy--Michael J. Taormina, Matthew Jemielita, W. Zac Stephens, Adam R. Burns, Joshua V. Troll, Raghuveer Parthasarathy, and Karen Guillemin 323-346
A13 Clinical application of fecal microbiota transplantation in Clostridium difficile infection and beyond--Josbert J. Keller and Els van Nood 347-355
A14 Consumption of human milk glycoconjugates by infant-associated bifidobacteria: Mechanisms and implications--Daniel Garrido, David C. Dallas, and David A. Mills 356-382
A15 Bacteriophage adhering to mucus providea nonhost-derived immunity--Jeremy J. Barr, Rita Auro, Mike Furlan, Katrine L. Whiteson, Marcella L. Erb, Joe Pogliano, Aleksandr Stotland, Roland Wolkowicz, Andrew S. Cutting, Kelly S. Doran, Peter Salamon, Merry Youle, and Forest Rohwer 383-400
A16 Topographic diversity of fungal and bacterial communities in human skin--Keisha Findley, Julia Oh, Joy Yang, Sean Conlan, Clayton Deming, Jennifer A. Meyer, Deborah Schoenfeld, Effie Nomicos, Morgan Park, NIH Intramural Sequencing Center Comparative Sequencing Program, Heidi H. Kong, and Julia A. Segre 401-411
A17 Distinct microbial communities within the endosphere and rhizosphere of Populus deltoides roots across contrasting soil types--Neil R. Gottel, Hector F. Castro, Marilyn Kerley, Zamin Yang, Dale A. Pelletier, Mircea Podar, Tatiana Karpinets, Ed Uberbacher, Gerald A. Tuskan, Rytas Vilgalys, Mitchel J. Doktycz, and Christopher W. Schadt 412-434
A18 Interactions between commensal fungi and the C-type lectin receptor Dectin-1 influence colitis--Iliyan D. Iliev, Vincent A. Funari, Kent D. Taylor, Quoclinh Nguyen, Christopher N. Reyes, Samuel P. Strom, Jordan Brown, Courtney A. Becker, Phillip R. Fleshner, Marla Dubinsky, Jerome I. Rotter, Hanlin L. Wang, Dermot P. B. McGovern, Gordon D. Brown, and David M. Underhill 435-444
A19 Metagenomics and personalized medicine--Herbert W. Virgin and John A. Todd 445-470
A20 From genetics of inflammatory bowel disease towards mechanistic insights--Daniel B. Graham and Ramnik J. Xavier 471-488
A21 Antimicrobial peptides and the microbiome--Michael Zasloff 489-496
Appendix B: Agenda 497-500
Appendix C: Acronyms 501-502
Appendix D: Glossary 503-512
Appendix E: Speaker Biographies 513-522

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	DAY ONE: MONDAY, MARCH 18, 2013

7:30–8:00:	Registration and Continental Breakfast

8:00–8:15:	Welcoming Remarks: David Relman, James Hughes, and Lonnie King

8:15–9:00:	KEYNOTE: Indigenous microbes and the ecology of chronic diseases
	Martin Blaser, New York University

9:00–9:15:	Discussion

9:15–9:30:	BREAK


SESSION I: HOST–MICROBE INTERACTIONS IN HUMANS, ANIMALS, AND PLANTS

Moderator: Rima Khabbaz, Centers for Disease Control and Prevention

9:30–10:00:	Plant–microbe interactions in root endophyte and rhizosphere communities of Populus
	Gerald Tuskan, Oak Ridge National Laboratory

10:00–10:30:	Origins and maintenance of host–microbe interactions
	Angela Douglas, Cornell University

10:30–11:00:	Annual cycles of extreme dietary change shape gut microbiota and their hibernator hosts
	Hannah Carey, University of Wisconsin, Madison

11:00–11:30:	Symbiont microbiota and the development and maturation of the mammalian immune system
	Gérard Eberl, Pasteur Institute

11:30–12:00:	Discussion

12:00–1:00:	LUNCH

SESSION II: EMERGING INSIGHTS INTO HOST–MICROBE INTERACTIONS

Moderator: David Relman, Stanford University

1:00–1:30:	Community ecology and the human vaginal microbiome
	Larry Forney, University of Idaho

1:30–2:00:	Host defense and immunomodulation of mucosal candidiasis
	Paul Fidel, Jr., Louisiana State University

2:00–2:30:	Interactions between the mammalian virome, disease susceptibility genes, and the phenome
	Herbert “Skip” Virgin, Washington University

2:30–3:00:	BREAK

3:00–3:30:	Microbial community dynamics and disruption—Health and disease in coral reefs and the human lung
	Forest Rohwer, San Diego State University


3:30–4:00:	Interactions and functions of the gut microbiota in a model vertebrate host
	Karen Guillemin, University of Oregon

4:00–4:30:	The influence of the mucosal immune system and gut microbiota on inflammatory bowel diseases (IBDs)
	Richard Blumberg, Harvard Medical School

4:30–5:30:	Discussion

5:30–6:00:	Concluding Remarks

6:00:	ADJOURN DAY ONE

	DAY TWO: TUESDAY, MARCH 19, 2013

8:00–8:30:	Registration and Continental Breakfast

8:30–8:45:	Welcoming Remarks and Summary of Day One: David Relman

SESSION III: STRUCTURE AND FUNCTION OF HOSTASSOCIATED MICROBIAL COMMUNITIES

Moderator: Queta Bond, Burroughs Wellcome Fund

8:45–9:15:	The application of ecological concepts to host-associated microbial communities
	Brendan Bohannan, University of Oregon

9:15–9:45:	Nutrition and the infant gut microbiota—Health and disease in the first 1,000 days
	David Mills, University of California, Davis

9:45–10:15:	Roles of the microbiota in the control and pathogenesis of infections
	Yasmine Belkaid, National Institute of Allergy and Infectious Diseases

10:15–10:45:	BREAK

10:45–11:15:	Host–microbe interactions and the genetic architecture of IBD and other complex diseases
	Ramnik Xavier, Massachusetts General Hospital


11:15–11:45:	Host–mycobiome interactions in gut homeostasis and pathogenesis
	David Underhill, Cedars-Sinai Medical Center

11:45–12:15:	Discussion

12:15–1:15:	LUNCH

SESSION IV: RESEARCH CHALLENGES AND OPPORTUNITIES

Moderator: Jesse Goodman, Food and Drug Administration

1:15–1:45:	Metabolism, interspecies interactions, and novel approaches to disease diagnostics and treatment
	Michael Fischbach, University of California, San Francisco

1:45–2:15:	Fecal transplantation as a treatment option for recurrent Clostridium difficile infection
	Josbert J. Keller, University of Amsterdam

2:15–2:45:	BREAK

2:45–3:15:	Innate antimicrobial mechanisms in disease prevention and treatment
	Michael Zasloff, Georgetown University

3:15–3:45:	The skin microbiome and chronic disease states
	Julie Segre, National Human Genome Research Institute

3:45–4:30:	Discussion

4:30–4:45:	Concluding Remarks

4:45:	ADJOURN

Microbial Ecology in States of Health and Disease: Workshop Summary (2014)

Chapter: Appendix B: Agenda

My Academies

Microbial Ecology in States of Health and Disease: Workshop Summary (2014)

Chapter: Appendix B: Agenda