Gut Microbiota in Health and Disease

I. Preface 860 II. Overview of the Mammalian Gut Microbiota 860 A. Humans as microbial depots 860 B. Who are they? 860 C. Where are they? 861 D. Where do they come from? 861 E. How are they selected? 862 III. Microbiota in Health: Combine and Conquer 862 A. Immunomodulation 863 B. Protection 866 C. Structure and function of the GIT 867 D. Outside of the GIT 868 E. Nutrition and metabolism 868 F. Concluding remarks 870 IV. Microbiota in Disease: Mechanisms of Fine Balance 870 A. Imbalance leads to chaos 870 B. Microbial intruders of the GIT 871 C. Disorders of the GIT 872 D. Disorders of the GIT accessory organs 876 E. Complex multifactorial disorders and diseases of remote organ systems 877 F. Bacterial translocation and disease 880 G. Concluding remarks 881 V. Signaling in the Mammalian Gut 881 A. Signaling between the microbiota and the host 881 B. Signaling between the microbiota and pathogens 884 C. Signaling between members of the microbiota 884 D. Signaling between the host and pathogens 885 VI. Models to Study Microbiota 885 A. Germ-free animals 885 B. Mono-associated and bi-associated animals 887 C. Poly-associated animals 887 D. Human flora-associated animals 888 VII. Techniques to Study Microbiota Diversity 889 A. Culture-based analysis 889 B. Culture-independent techniques 889 C. Sequencing methods 889 D. “Fingerprinting” Methods 892 E. DNA microarrays 893 F. FISH and qPCR 893 G. The “meta” family of function-focused analyses 893 VIII. Future Perspectives: Have We Got the Guts for It? 895