Note: Intro -- Preface -- Contents -- 1: A Short Definition of Terms -- References -- 2: Studying the Human Microbiota -- 2.1 Introduction -- 2.2 Classical Microbiological Methods -- 2.2.1 Culture -- 2.2.2 Continuous Culture -- 2.2.3 Animal Models -- 2.3 Sequence-Based Approaches -- 2.3.1 Marker Gene Surveys -- 2.3.2 Whole Genome Sequencing -- 2.3.3 Metagenomics -- 2.3.4 Single-Cell Genomics -- 2.3.5 Metatranscriptomics -- 2.4 Common Pitfalls of Sequence Based Approaches -- 2.5 Other Community Profiling Approaches -- 2.5.1 Community Fingerprinting Techniques -- 2.5.2 Microarrays -- 2.6 Quantitative Approaches -- 2.6.1 Quantitative PCR -- 2.6.2 Fluorescent in situ Hybridisation (FISH) -- 2.7 Functional Analyses -- 2.7.1 Functional Metagenomics -- 2.7.2 Metaproteomics -- 2.7.3 Metabolomics -- 2.7.4 Stable Isotope Probing -- 2.8 Conclusions -- References -- 3: The Gut Microbiota and their Metabolites: Potential Implications for the Host Epigenome -- 3.1 Introduction -- 3.2 Epigenetics - the Mediator Between the Genome and Physiology -- 3.3 Interaction of Bacterial Metabolites and the Host's Metabolic Regulation -- 3.4 Putative Targets of Bacterial Metabolites - in Time and Space -- 3.5 Health Implications - Sooner or Later -- References -- 4: The Oral Microbiota -- 4.1 Variety -- 4.2 Locations of the Oral Microbiota -- 4.3 Intra-oral Dislodging: Mutual Transfer -- 4.4 Inter-oral Transmission of Bacteria and Age-Related Microbiological Changes -- 4.5 Succession of the Oral Microbiota: Biofilm Formation -- 4.6 Phases of Biofilm Development -- 4.7 Dental Plaque: A Typical Biofilm -- 4.8 "Health-Disease-­Relationship" and Significance of Oral Flora for Systemic Health -- 4.9 Prospects -- 4.10 Summary -- References -- 5: The Microbiota of the Human Skin -- 5.1 Introduction. , 5.2 The Human Skin as a Habitat for Microorganisms -- 5.3 Structure and Variability of the Healthy Skin Microbiota -- 5.3.1 The "normal" Skin Microbiota of Healthy Adults -- 5.3.1.1 Bacteria -- 5.3.1.2 Fungi, Archaea and Viruses -- 5.3.2 Factors Shaping the Composition of the Skin Microbiota -- 5.4 Functional Aspects of the Human Skin Microbiota -- 5.4.1 Protective Functions of the Human Skin Microbiota -- 5.4.2 Role in Skin Disorders and Skin Diseases -- 5.5 Manipulation of the Human Skin Microbiota -- 5.6 Outlook: Trends and Challenges -- References -- 6: Vaginal Microbiota -- 6.1 A Historic Perpective -- 6.2 Normal Vaginal Microbiota -- 6.2.1 The Normal Vaginal Microbiota: A Mixture of Many Bacteria in a Balance -- 6.2.2 Gene Polymorphisms and Vaginal Immunity -- 6.3 Abnormal Vaginal Flora -- 6.3.1 Bacterial Vaginosis (BV) -- 6.3.2 Polymicrobial Bacterial Biofilms in BV and Sexual Transmission -- 6.3.3 Aerobic Vaginitis (AV) -- 6.4 Prophylaxis and Therapy with Probiotics -- 6.5 Summary and Conclusion -- References -- 7: The Human Gut Microbiota -- 7.1 Introduction -- 7.2 The Normal Microbiota -- 7.3 Gut Microbiota Development: The Young Microbiota -- 7.4 The Role of Gut Microbiota in Disease -- 7.4.1 IBD -- 7.5 Abberant Gut Microbiota Development and Type 1 Diabetes -- 7.6 Obesity and Metabolic Diseases -- 7.7 Concluding Remarks -- References -- 8: Manipulation of the Microbiota Using Probiotics -- 8.1 Introduction -- 8.2 Irritable Bowel Syndrome -- 8.3 Inflammatory Bowel Disease (IBD) -- 8.4 Atopy/Allergy -- 8.5 Necrotizing Enterocolitis -- 8.6 Diarrhoeal Diseases -- References -- 9: How to Manipulate the Microbiota: Prebiotics -- 9.1 Introduction -- 9.2 What Is a Prebiotic? -- 9.2.1 Are Gut Bacteria Either Beneficial or Detrimental for Health? -- 9.2.2 How Selective Are Prebiotics?. , 9.2.3 Should Prebiotic Effects Be Limited to Specific Species or Genera Within the Microbiota? -- 9.2.4 Might the Beneficial Effects of a Prebiotic Be Due to Microbiota Changes Other than Stimulation of Lactic Acid Bacteria? -- 9.2.5 Does Variation in Microbiota Responses Between Individuals Need to Be Considered? -- 9.2.6 Is Microbiota Diversity Itself an Indicator for Gut Health? -- 9.3 Mechanisms of Action of Microbiota Modulation by Prebiotics (Fig. 9.3) -- 9.4 Ingredients with Confirmed Prebiotic Action and Candidate Prebiotics -- 9.4.1 Fructans -- 9.4.2 Galactooligosaccharides -- 9.4.3 Resistant Starch, Starch- and Glucose-Derived Oligosaccharides -- 9.4.4 Other Oligosaccharides -- 9.4.5 Non-carbohydrate Compounds -- 9.5 Health Effects of Prebiotics on the Host -- 9.5.1 Physiological Effects and Underlying Mechanisms -- 9.5.1.1 Improvement of Intestinal Functions (Stool Bulking, Stool Regularity, Stool Consistency) -- 9.5.1.2 Stimulation of Mineral Absorption and Improvement of Bone Density -- 9.5.1.3 Regulation of Appetite and Stimulation of Gut Peptide Secretion -- 9.5.1.4 Improvement of Intestinal Barrier Integrity -- 9.5.1.5 Regulation of Lipid and Glucose Metabolism -- 9.5.1.6 Modulation of Immune Functions -- 9.5.2 Current Evidence for Disease Prevention or Treatment -- 9.6 Conclusions -- References -- 10: How to Manipulate the Microbiota: Fecal Microbiota Transplantation -- 10.1 Microbiota Transplantation: Concept and History -- 10.2 Applications -- 10.2.1 Clostridium difficile Infection -- 10.2.2 Inflammatory Bowel Disease -- 10.2.3 Other Applications -- 10.3 Methodology and Donor Selection -- 10.4 Synthetic Communities -- 10.5 Regulations and Safety -- 10.6 Microbiota Transplantation: The future -- References -- Index.