Overview of Gut Immunology -- The Commensal Microbiology of the Gastrointestinal Tract -- Overview of the Gastrointestinal Microbiota -- Effects of Microbiota on GI Health: Gnotobiotic Research -- Positive Interactions with the Microbiota: Probiotics -- Negative Interactions with the Microbiota: IBD -- Diet, Immunity and Functional Foods -- Host-Microbe Communication within the GI Tract -- Host-Microbe Symbiosis: The Squid-Vibrio Association—A Naturally Occurring, Experimental Model of Animal/Bacterial Partnerships -- The “Microflora Hypothesis” of Allergic Disease -- The Damage-Response Framework of Microbial Pathogenesis and Infectious Diseases.