Section I. Overview Chapters 1. Overview of Gut Immunology Katie Lynn Mason, Gary B. Huffnagle, Mairi C. Noverr and John Y. Kao Abstract Introduction: Tolerance vs. Inflammation Gastrointestinal Tract Architecture Components of the Gut Immune Response Coordination of the Gut Immune Response Importance of the Gi Microbiota Summary 2. The Commensal Microbiology of the Gastrointestinal Tract Janet M. Manson, Marcus Rauch and Michael S. Gilmore Abstract Introduction Culture-Dependent Versus Culture-Independent Techniques Bacterial Diversity Regional Colonization of the GI Tract Influences on Microbiota Future Study of GI Tract Ecology Section II. Current Techniques 3. Overview of the Gastrointestinal Microbiota Vincent B. Young and Thomas M. Schmidt Abstract Introduction Structure of the Intestinal Microbial Community Functional Aspects of the Intestinal Microbiota Methods to Study the Structure and Function of the Gut Microbiota The Microbiota in the Context of the Intestinal Ecosystem Ecologic Statistical Analysis as a Means to Reduce Data Complexity Summary 4. Effects of Microbiota on Gi Health: Gnotobiotic Research Robert Doug Wagner Abstract Introduction Immunodeficient Gnotobiotic Models Immunological Effects of GI Tract Infections in Gnotobiotic Animals Gnotobiotic Studies of Microbial Antagonism Microbiota Effects on Gut Associated Lymphoid Tissue Architecture Inflammatory Responses to the Microbiota New Directions for Gnotobiotic Studies of the Microbiota and Immunity Section III. Interaction with the Host 5. positive interactions with the microbiota: Probiotics Marko Kalliomäki, Seppo Salminen and ErikaIsolauri Abstract Introduction Definition of a probiotic Traditional selection criteria for probiotics and rationale for new ones Importance of Viability of Probiotics Probiotics augment gut barrier mechanisms Probiotics have anti-inflammatory properties in the gut Atopic disease is a target for probiotic intervention Probiotics in clinical studies with allergic diseases Probiotics May have additive positive effects with infant diet Novel molecular technologies aid in uncovering complex host-probiotic interactions and constructing probiotics with new properties Summary 6. Negative Interactions with the Microbiota: IBD Nita H. Salzman and Charles L. Bevins Abstract Introduction IBD Evidence of Bacterial Involvement in Intestinal Inflammation Primary Cause-Bacteria? Primary Cause-Host? Concluding Comments Section IV. Role of the Diet 7. Diet, Immunity and Functional Foods Lesley Hoyles and Jelena Vulevic Abstract Introduction Colonic Functional Foods Prebiotics Effects of Prebiotics on Immunity Mechanisms for the Effects of Prebiotics on the Immune System Dietary Fibers Other Functional Foods Summary Section V. Host-Microbe Signaling 8. Host-Microbe Communication within the GI Tract Christopher A. Allen and Alfredo G. Torres Abstract The Gastrointestinal Tract Maintaining Physiological and Immunological Homeostasis in the Gut Host-Bacterial Interactions in the Gut Host-Mediated Regulatory Mechanisms Bacterial-Mediated Regulatory Mechanisms The Role of Gut Flora in Immune System Development and Immunological Tolerance Commensal Bacteria, Mucosal Immunity and Development of Inflammatory Disease Novel Mechan