Individually and collectively, resident microbes play important roles in host health and survival. Shaping and shaped by their host environments, these microorganisms form intricate communities that are in a state of dynamic equilibrium. This ecologic and dynamic view of host-microbe interactions is rapidly redefining our view of health and disease. It is now accepted that the vast majority of microbes are, for the most part, not intrinsically harmful, but rather become established as persistent, co-adapted colonists in equilibrium with their environment, providing useful goods and services to their hosts while deriving benefits from these host associations. Disruption of such alliances may have consequences for host health, and investigations in a wide variety of organisms have begun to illuminate the complex and dynamic network of interaction - across the spectrum of hosts, microbes, and environmental niches - that influence the formation, function, and stability of host-associated microbial communities. Microbial Ecology in States of Health and Disease is the summary of a workshop convened by the Institute of Medicine's Forum on Microbial Threats in March 2013 to explore the scientific and therapeutic implications of microbial ecology in states of health and disease. Participants explored host-microbe interactions in humans, animals, and plants; emerging insights into how microbes may influence the development and maintenance of states of health and disease; the effects of environmental change(s) on the formation, function, and stability of microbial communities; and research challenges and opportunities for this emerging field of inquiry. Table of ContentsFront MatterWorkshop OverviewA1 Effector and memory T cell responses to commensalbacteria--Yasmine Belkaid, Nicolas Bouladoux, and Timothy W. HandA2 What are the consequences of the disappearing humanmicrobiota?--Martin J. Blaser and Stanley FalkowA3 Pathways in microbe-induced obesity--Laura M. Cox and Martin J. BlaserA4 Microbial exposure during early life has persistent effects onnatural killer T Cell function--Torsten Olszak, Dingding An,Sebastian Zeissig, Miguel Penilla Vera, Julia Richter, AndreFranke, Jonathan N. Glickman, Reiner Siebert, Rebecca M. Barron,Dennis L. Kasper, and Richard S. BlumbergA5 The application of ecological theory toward an understanding ofthe human microbiome--Elizabeth K. Costello, Keaton Stagaman, LesDethlefsen, Brendan J. M. Bohannan, and David A. RelmanA6 Seasonal restructuring of the ground squirrel gutmicrobiota overthe annual hibernation cycle--Hannah V. Carey, William A. Walters,and Rob KnightA7 Lessons from studying insect symbioses--Angela E. DouglasA8 A new vision of immunity: homeostasis of thesuperorganism--Grard EberlA9 Host defense and immunomodulation of mucosal candidiasis--PaulL. Fidel, Jr., and Mairi C. NoverrA10 Microbiota-targeted therapies: An ecologicalperspective--Katherine P. Lemon, Gary C. Armitage, David A. Relman,and Michael FischbachA11 Community ecology and the vaginal microbiome--Larry J. Forneyand Jacques RavelA12 Investigating bacterial-animal symbioses with light sheetmicroscopy--Michael J. Taormina, Matthew Jemielita, W. ZacStephens, Adam R. Burns, Joshua V. Troll, Raghuveer Parthasarathy,and Karen GuilleminA13 Clinical application of fecal microbiota transplantation inClostridium difficile infection and beyond--Josbert J. Keller andEls van NoodA14 Consumption of human milk glycoconjugates by infant-associatedbifidobacteria: Mechanisms and implications--Daniel Garrido, DavidC. Dallas, and David A. MillsA15 Bacteriophage adhering to mucus providea nonhost-derivedimmunity--Jeremy J. Barr, Rita Auro, Mike Furlan, Katrine L. Whiteson, Marcella L. Erb, Joe Pogliano, Aleksandr Stotland, RolandWolkowicz, Andrew S. Cutting, Kelly S. Doran, Peter Salamon, MerryYoule, and Forest RohwerA16 Topographic diversity of fungal and bacterial communities inhuman skin--Keisha Findley, Julia Oh, Joy Yang, Sean Conlan,Clayton Deming, Jennifer A. Meyer, Deborah Schoenfeld, EffieNomicos, Morgan Park, NIH Intramural Sequencing Center ComparativeSequencing Program, Heidi H. Kong, and Julia A. SegreA17 Distinct microbial communities within the endosphere andrhizosphere of Populus deltoides roots across contrasting soiltypes--Neil R. Gottel, Hector F. Castro, Marilyn Kerley, ZaminYang, Dale A. Pelletier, Mircea Podar, Tatiana Karpinets, EdUberbacher, Gerald A. Tuskan, Rytas Vilgalys, Mitchel J. Doktycz,and Christopher W. SchadtA18 Interactions between commensal fungi and the C-type lectinreceptor 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, DermotP. B. McGovern, Gordon D. Brown, and David M. UnderhillA19 Metagenomics and personalized medicine--Herbert W. Virgin andJohn A. ToddA20 From genetics of inflammatory bowel disease towards mechanisticinsights--Daniel B. Graham and Ramnik J. XavierA21 Antimicrobial peptides and the microbiome--Michael ZasloffAppendix B: AgendaAppendix C: AcronymsAppendix D: GlossaryAppendix E: Speaker Biographies