Cover -- Title page -- Copyright page -- Contents -- Preface -- Contributors -- 1: The NIH Human Microbiome Project -- 1.1. Introduction -- 1.2. Genesis of Human Microbiome Research and the Human Microbiome Project (HMP) -- 1.3. Guiding Principles, Structure, and Initiatives of the HMP Program -- 1.3.1. HMP Guiding Principles and Creation of a Community Resource Project -- 1.3.2. HMP Large-Scale Sequencing Centers -- 1.3.3. Data Coordination and Analysis -- 1.3.4. Reference Strain Microbial Genome Sequences -- 1.3.5. Healthy Adult Cohort Study of Multiple Microbiomes -- 1.3.4. Demonstration Projects of Microbiome-Disease Associations -- 1.3.7. Technology Development -- 1.3.8. Computational Tools -- 1.3.9. Ethical, Legal, and Societal Implications of Microbiome Research -- 1.4. Products from the Human Microbiome Project -- 1.4.1. Derivative Datasets from the Healthy Adult Cohort Study -- 1.4.2. Computational Tools for Human Microbiome Research -- 1.4.3. Publications from the HMP -- 1.5. Other NIH-Supported Human Microbiome Research Activities -- 1.6. Future Directions for Human Microbiome Research -- Acknowledgments -- References -- 2: Methods for Characterizing Microbial Communities Associated with the Human Body -- 2.1. Introduction -- 2.2. Cultivation-Independent Techniques -- 2.2.1. Community Structure and Composition Using Phylogenetic Markers -- 2.2.2. Diversity of Genetic Potential -- 2.2.3. Beyond Metabolic Potential: Transcriptomics, Proteomics, Metabolomics -- 2.3. Cultivation -- 2.4. Choosing an approach -- Acknowledgments -- References -- 3: Phyloarrays -- 3.1. Introduction -- 3.2. Phylogenetic Microarray Design -- 3.3. Sample Preparation for Phylogenetic Microarray Profiling -- 3.4. The Utility of Phylogenetic Microarrays -- Acknowledgments -- References.

4: Mathematical Approaches for Describing Microbial Populations: Practice and Theory for Extrapolation of Rich Environments -- 4.1. Introduction: Practice for Extrapolation of Environments -- 4.2. Theory for Extrapolation of Environments -- 4.2.1. Urn Model -- 4.2.2. Paradigm Shift -- 4.2.3. Expected Coverage of a Sample -- 4.3. Average Analysis of Sample Coverage -- 4.4. Conditional Analysis of Sample Coverage -- 4.4.1. Thinning Property of Poisson Point Processes -- 4.4.2. Embedding Algorithm -- 4.5. Conclusions -- References -- 5: Tension at the Border: How Host Genetics and the Enteric Microbiota Conspire to Promote Crohn's Disease -- 5.1. Introduction and Overview -- 5.2. Human Inflammatory Bowel Diseases -- 5.3. The Enteric Microbiota and IBD -- 5.4. Human Genetic Loci Associated with IBD -- 5.5. How Host Genetics Shapes Enteric Microbiota -- 5.6. Modeling Dysbiosis and Crohn's Disease -- Acknowledgments -- References -- 6: The Human Airway Microbiome -- 6.1. Introduction -- 6.2. Lung-Characteristics and Conditions -- 6.2.1. Normal Lung -- 6.2.2. Cystic Fibrosis -- 6.2.3. Ventilator-Associated Pneumonia -- 6.2.4. Bronchopulmonary Dysplasia -- 6.2.5. Asthma -- 6.2.6. Chronic Obstructive Pulmonary Disease (COPD) -- 6.3. Outlook for Respiratory Tract Microbiome Studies -- References -- 7: Microbiota of the Mouth: A BLESSING OR A CURSE? -- 7.1. Introduction -- 7.1.1. Anatomy -- 7.1.2. Saliva -- 7.2. From Colonization to Communities -- 7.2.1. Initial Attachment -- 7.2.2. Physical Interbacterial Interactions -- 7.2.3. Metabolic Interbacterial Interactions -- 7.2.4. Antagonistic Interbacterial Interactions -- 7.2.5. Interbacterial Signaling -- 7.2.6. Biofilm Matrix -- 7.3. Communities in Health and Disease -- 7.3.1. Health -- 7.3.2. Disease -- 7.4. Oral Communities and Systemic Disease -- 7.4.1. Bacteremia -- 7.4.2. Infective Endocarditis.

7.4.3. Atherosclerosis -- 7.4.4. Diabetes -- 7.4.5. Obesity -- 7.4.6. Adverse Pregnancy Outcomes -- 7.5. Summary -- References -- 8: Microbiota of the Genitourinary Tract -- 8.1. Introduction -- 8.2. Microbial Ecosystems of the Female Reproductive Tract: A Biogeographic Perspective of Their Impact on Reproduction -- 8.3. Scientific Controversy Regarding Bacterial Vaginosis -- 8.4. Perspectives on the Vaginal Microbiome in the Age of High-Throughput Sequencing -- 8.5. Vaginal Health In 2025: How Understanding the Microbiome Will Shape the Future of Women's Healthcare -- 8.6. The Male Microbiota: Two Sides of the Same Coin or a Different Currency? -- 8.7. Conclusion -- References -- 9: Functional Structure of Intestinal Microbiota in Health and Disease -- 9.1. Introduction -- 9.2. Intestinal Microbiota -- 9.2.1. Bacteria in the Upper Gastrointestinal Tract -- 9.2.2. Small Intestine -- 9.2.3. Bacteria in the Large Intestine -- 9.2.4. The Role of Microbiota in Colonic Function -- 9.2.5. Mucus Barrier -- 9.2.6. Fecal Microbiota -- 9.3. Changes of the Colonic Microbiota in Disease -- 9.3.1. Break of the Mucus Barrier in Inflammatory Bowel Disease -- 9.3.2. Factors Potentially Constitute the Mucus Barrier -- 9.3.3. The Role of Facultative Pathogens -- 9.3.4. Substances Reducing the Viscosity of the Mucus Barrier -- 9.4. Possible Ways to Remodel the Mucus Barrier -- 9.5. Biostructure of Fecal Microbiota in Health, Inflammatory Bowel Disease, and Other GI Diseases -- 9.6. Site-Dependent Changes of Colonic Microbial Biostructure -- 9.6.1. The Mucus Layer -- 9.6.2. The Working (Luminal) Area of the Colonic Biofermenter -- 9.6.3. The Germinal Zone of the Colonic Biofermenter -- 9.7. Conclusions -- References -- 10: From Fly to Human: Understanding How Commensal Microorganisms Influence Host Immunity and Health -- 10.1. Introduction.

10.2. Microbial Diversity in Humans and Animal Models -- 10.3. Comparative Immunity: Immune System Development in Animals -- 10.4. Maintaining Intestinal Homeostasis -- 10.5. The Role of Commensal Bacteria in Host Health -- 10.5.1. Inflammatory Bowel Disease -- 10.5.2. Multiple Sclerosis -- 10.5.3. Diabetes -- 10.6. Finding the Right Mix of Bacteria: Harnessing Our Understanding of Commensal Host Relationships for Therapeutic Benefit -- References -- 11: Insights into the Human Microbiome from Animal Models -- 11.1. Introduction -- 11.2. Animal Model Systems -- 11.2.1. Squid -- 11.2.2. Nematode -- 11.2.3. Hydra -- 11.2.4. Leech -- 11.2.5. Gypsy Moth -- 11.2.6. Fruit Fly -- 11.2.7. Termite -- 11.2.8. Mouse -- 11.2.9. Zebrafish -- 11.3. Establishment of Host-Associated Microbial Communities -- 11.3.1. Visualizing Colonization and Identifying Symbiosis-Defective Bacterial Mutants -- 11.3.2. Identifying Host Genetic Determinants of Microbiota Composition -- 11.4. The Function of Resident Microbial Communities in Host Biology -- 11.4.1. Microbial Influences on Epithelial Tissues -- 11.4.2. Microbial Influences on the Immune System -- 11.5. Concluding Remarks -- References -- 12: To Grow or Not to Grow: Isolation and Cultivation Procedures in the Genomic Age -- 12.1. Introduction -- 12.2. Isolation, Growth, And Cultivation -- 12.2.1. Isolation -- 12.2.2. Growth -- 12.2.3. Cultivation -- 12.3. Changes in a Changing World -- References -- 13: New Approaches to Cultivation of Human Microbiota -- 13.1. Introduction -- 13.2. Microbiota Cultivation Methodology -- 13.3. Application to Human Microbiota -- 13.4. Looking Ahead -- Acknowledgments -- References -- 14: Manipulating the Indigenous Microbiota in Humans: Prebiotics, Probiotics, and Synbiotics -- 14.1. Introduction -- 14.2. Probiotics -- 14.2.1. Health Benefits Associated With Probiotics -- 14.2.2. Aging.

14.2.3. Other Uses of Probiotics -- 14.3. Prebiotics -- 14.3.1. Health Benefits Associated with Prebiotics -- 14.4. Synbiotics -- 14.4.1. Inflammatory Bowel Disease -- 14.4.2. Other Uses of Synbiotics -- 14.5. Conclusion -- References -- Index.