Description
List of contributors, xviiPreface, xxi Section 1 An introduction to the human tissue microbiome, 11 The human microbiota: an historical perspective, 3Mike Wilson1.1 Introduction: the discovery of the human microbiota: why do we care?, 31.2 The importance of the indigenous microbiota in health and disease, 31.2.1 The indigenous microbiota and human disease, 41.2.2 The indigenous microbiota and human health, 41.3 The development of technologies for characterising the indigenous microbiota, 81.3.1 Light microscopy, 91.3.2 Electron microscopy, 111.3.3 Culture?]based approaches to microbial community analysis, 121.4 Culture?]independent approaches to microbial community analysis, 291.5 Determination of microbial community functions, 311.6 Closing remarks, 32Take?]home message, 32References, 332 An introduction to microbial dysbiosis, 37Mike Curtis2.1 Definition of dysbiosis, 372.2 The ‘normal’ microbiota, 382.3 Main features of dysbiosis, 452.4 Conclusions, 49Take?]home message, 53Acknowledgment, 53References, 533 The gut microbiota: an integrated interactive system, 55Hervé M. Blottière and Joël Doré3.1 Introduction, 553.2 Who is there, how is it composed?, 563.3 A system in interaction with food, 583.4 A system highly impacted by the host, 613.5 A system in interaction with human cells, 623.6 Conclusion: an intriguing integrated interactive system deserving further study, 63Take?]home message, 63References, 634 The oral microbiota, 67W. G. Wade4.1 Introduction, 674.2 Composition of the oral microbiome, 684.2.1 Archaea, 684.2.2 Fungi, 684.2.3 Protozoa, 684.2.4 Viruses, 694.2.5 Bacteria, 694.3 The oral microbiota in health, 714.3.1 Evolution of the oral microbiota, 714.3.2 Role of oral bacteria in health, 724.4 Role of oral microbiome in disease, 734.4.1 Dental caries, 734.4.2 Gingivitis, 744.4.3 Oral bacteria and non?]oral disease, 744.5 Future outlook, 75Take?]home message, 75References, 765 The skin microbiota, 81P.L.J.M. Zeeuwen and J. Schalkwijk5.1 Normal skin, 815.2 Skin diseases, 835.2.1 Atopic dermatitis, 835.2.2 Psoriasis, 845.2.3 Acne, 855.2.4 Rosacea, 855.2.5 Seborrheic dermatitis and dandruff, 865.2.6 Primary immunodeficiencies, 865.3 Experimental studies, 875.4 Dynamics of the skin microbiome, 875.5 Axillary skin microbiome transplantation, 895.6 Mouse skin microbiome studies, 895.7 Concluding remarks, 90Take?]home message, 90References, 906 Metagenomic analysis of the human microbiome, 95
Chapter
1.3 The development of technologies for characterising the indigenous microbiota
1.3.2 Electron microscopy
1.3.3 Culture-based approaches to microbial community analysis
1.4 Culture-independent approaches to microbial community analysis
1.5 Determination of microbial community functions
Chapter 2 An introduction to microbial dysbiosis
2.1 Definition of dysbiosis
2.2 The ‘normal’ microbiota
2.3 Main features of dysbiosis
Chapter 3 The gut microbiota: an integrated interactive system
3.2 Who is there, how is it composed?
3.3 A system in interaction with food
3.4 A system highly impacted by the host
3.5 A system in interaction with human cells
3.6 Conclusion: an intriguing integrated interactive system deserving further study
Chapter 4 The oral microbiota
4.2 Composition of the oral microbiome
4.3 The oral microbiota in health
4.3.1 Evolution of the oral microbiota
4.3.2 Role of oral bacteria in health
4.4 Role of oral microbiome in disease
4.4.3 Oral bacteria and non‐oral disease
Chapter 5 The skin microbiota
5.2.5 Seborrheic dermatitis and dandruff
5.2.6 Primary immunodeficiencies
5.4 Dynamics of the skin microbiome
5.5 Axillary skin microbiome transplantation
5.6 Mouse skin microbiome studies
Chapter 6 Metagenomic analysis of the human microbiome
6.3 Changes in microbiota composition during host life cycles
6.4 The human microbiome and the environment
6.5 Disease and health implications of microbiome
6.5.1 The skin microbiota
6.5.2 The airway microbiome
6.5.4 Gut microbiota and disease
6.5.5 Metabolic disorders (obesity/diabetes)
SECTION 2 Microbiota-microbiota and microbiota-host interactions in health and disease
Chapter 7 Systems biology of bacteria‐host interactions
7.2 Computational analysis of host‐microbe interactions
7.2.1 Analysis of metagenomic data
7.2.2 Metabolic reconstruction through comparative genomics
7.3 Network-based modeling
7.3.1 Topological network modeling
7.3.2 Constraint-based modeling
7.3.3 Metabolic reconstructions of human metabolism
7.3.4 Constraint-based modeling of host-microbe interactions
7.4 Other computational modeling approaches
7.4.1 Ordinary differential equation (ODE) models
Chapter 8 Bacterial biofilm formation and immune evasion mechanisms
8.2 Biofilms in human disease
8.4 Immune responses to biofilms
8.4.1 Innate immune responses
8.4.2 Adaptive immune responses
8.4.3 Fibroblasts, epithelial cells and other immune responses
8.5 Biofilm immune evasion strategies
8.6 Vaccines and biofilm therapeutics
Chapter 9 Co-evolution of microbes and immunity and its consequences for modern-day life
9.2 Symbiosis in eukaryotic evolution
9.3 Evolution of the (innate and adaptive) immune system
9.3.2 Evolution of adaptive immunity
9.3.3 Two separate adaptive immune systems evolved
9.5 What drives the composition of the microbiota?
9.6 The pace of evolution
Chapter 10 How viruses and bacteria have shaped the human genome: the implications for disease
10.2 Mitochondria: symbiogenesis in the human
Chapter 11 The microbiota as an epigenetic control mechanism
11.2 Background on epigenetics and epigenomic programming/reprograming
11.3 Epigenomics and link with energy metabolism
11.4 The microbiota as a potential epigenetic modifier
11.5 Epigenetic control of the host genes by pathogenic and opportunistic microorganisms
11.6 Epigenetic control of the host genes by indigenous (probiotic) microorganisms
11.7 Concluding remarks and future directions
Chapter 12 The emerging role of propionibacteria in human health and disease
12.2 Microbiological features of propionibacteria
12.3 Population structure of P. acnes
12.4 Propionibacteria as indigenous probiotics of the skin
12.5 Propionibacteria as opportunistic pathogens
12.6 Host interacting traits and factors of propionibacteria
12.7 Host responses to P. acnes
12.7.1 Innate immune responses
12.7.2 Adaptive immune responses
12.7.3 Host cell tropism of P. acnes
12.8 Propionibacterium-specific bacteriophages
SECTION 3 Dysbioses and bacterial diseases: Metchnikoff’s legacy
Chapter 13 The periodontal diseases: microbial diseases or diseases of the host response?
13.1 The tooth: a potential breach in the mucosal barrier
13.2 The periodontium from health to disease
13.3 Periodontitis: one of the most common human diseases
13.4 Periodontal treatment: a non‐specific biofilm disruption
13.6 The host response in periodontitis
Chapter 14 The polymicrobial synergy and dysbiosis model of periodontal disease pathogenesis
14.2 A (very) polymicrobial etiology of periodontitis
14.3 Synergism among periodontal bacteria
14.4 Interactions between bacterial communities and epithelial cells
14.5 Manipulation of host immunity
Chapter 15 New paradigm in the relationship between periodontal disease and systemic diseases: effects of oral bacteria on the gut microbiota and metabolism
15.2 Association between periodontal and systemic diseases
15.2.1 Periodontal disease and diabetes
15.2.2 Periodontal disease and atherosclerotic vascular diseases
15.2.3 Periodontal disease and rheumatoid arthritis
15.2.4 Periodontal disease and non‐alcoholic fatty liver disease
15.2.5 Periodontal disease and pre‐term birth
15.2.6 Periodontal disease and obesity
15.2.7 Periodontal disease and cancer
15.2.8 Periodontal disease and inflammatory bowel disease
15.3 Issues in causal mechanisms of periodontal disease for systemic disease
15.3.1 Endotoxemia (bacteremia)
15.3.2 Inflammatory mediators
15.3.3 Autoimmune response from molecular mimicry
15.4 New insights into the mechanisms linking periodontal disease and systemic disease
15.5 Effect of oral administration of P. gingivalis on metabolic change and gut microbiota
Chapter 16 The vaginal microbiota in health and disease
16.1 What makes a healthy microbiota
16.1.1 How does the vaginal microbiota mediate healthiness?
16.1.2 Establishment of the vaginal microbiota
16.1.3 The role of host genetic variation on vaginal health
16.1.4 Impact of age, menstrual cycle and environmental factors on vaginal health
16.2 The vaginal microbiota in disease
16.2.1 Bacterial vaginosis
16.2.2 Clinical consequences of altered vaginal microbiota (see Figure 1)
16.2.3 Vaginal microbiota and transmission and susceptibility to HIV infection
SECTION 4 Dysbioses and chronic diseases: is there a connection?
Chapter 17 Reactive arthritis: the hidden bacterial connection
17.3 Pathophysiology of ReA
Chapter 18 Rheumatoid arthritis: the bacterial connection
18.1 Preclinical rheumatoid arthritis
18.2 Predisposition to RA
18.3 MCH-HLA and genetic predisposition to RA
18.4 Molecular mimicry in RA
18.5 Innate immune system and RA
18.6 Bystander activation and pattern recognition receptors
18.7 Antibodies and neoepitopes
18.10 Bacterial DNA and peptidoglycans
18.11 Heat-shock proteins
18.12 Toll-like and bacterial infections
18.14 Porphyromonas gingivalis and RA
18.15 Gastrointestinal flora and RA
18.16 Smoking, lung infection and RA
18.17 Where to go from here?
Chapter 19 Inflammatory bowel disease and the gut microbiota
19.1 The microbiota in inflammatory bowel disease
19.2 Dysbiosis and IBD pathogenesis
19.3 Environmental factors affecting microbiome composition
19.4 Genetics and application to the immune system and dysbiosis in IBD
19.5 An overview of gut microbiota studies in IBD
19.6 Specific bacterial changes in IBD
19.6.3 Anti‐inflammatory effects of microbiota (functional dysbiosis)
19.7 Functional composition of microbiota in IBD
Chapter 20 Ankylosing spondylitis, Klebsiella and the low‐starch diet
20.2 Clinical features of AS
20.3 Gut bacteria and total serum IgA
20.4 Molecular mimicry in AS
20.5 Pullulanase system and collagens
20.6 Specific antibodies to Klebsiella in AS patients
20.7 The low-starch diet in AS
Chapter 21 Microbiome of chronic plaque psoriasis
21.2 Microbiota in psoriasis
21.3 Variation of microbiota with site
21.4 Swabs versus biopsies
21.6 Microbiome and immunity
21.7 Evidence that the skin microbiome may be involved in the pathogenesis of psoriasis
21.7.1 Psoriasis and crohn’s disease
21.8 New hypothesis on the pathogenesis of psoriasis
Chapter 22 Liver disease: interactions with the intestinal microbiota
22.2 Non-alcoholic fatty liver disease
22.3 Qualitative and quantitative changes in the intestinal microbiota
22.7 Alcoholic liver disease
22.7.1 Qualitative and quantitative changes in the intestinal microbiome
22.7.2 Contribution of dysbiosis to alcoholic liver disease
Chapter 23 The gut microbiota: a predisposing factor in obesity, diabetes and atherosclerosis
23.2 The “obesogenic” microbiota: evidence from animal models
23.3 The “obesogenic” microbiota in humans
23.4 A leaky gut contributing to inflammation and adiposity
23.5 Obesity-proneness: mediated by the gut microbiota?
23.6 Bacterial metabolites provide a link between bacteria and host metabolism
23.7 Fecal microbiota transplants: can we change our gut bacterial profiles?
23.8 What happens with the gut microbiota during weight loss?
23.9 The “diabetic” microbiota
23.9.1 Type I diabetes and the gut microbiota
23.10 The “atherosclerotic” microbiota
Chapter 24 The microbiota and susceptibility to asthma
24.2 The microenvironment of the lower airways
24.3 Development of the airway microbiota in the neonate
24.3.1 Intrauterine microbial exposure and airway microbiota
24.3.2 Perinatal events and airway microbiota
24.3.3 Breast milk as a source of airway microbiota
24.3.4 Airborne microbiota and airway microbiota
24.4 Upper airway microbiota
24.5 What constitutes a healthy airway microbiota
24.6 Microbiota and asthma
24.7 Dietary metabolites and asthma
24.8 Conclusion, future perspectives and clinical implications
Chapter 25 Microbiome and cancer
25.2 Microbiome and cancer: where is the link?
25.3 Microbiome and barrier disruption
25.4 Microbiome and different types of cancer
25.4.5 Local microbes affecting distant cancers
25.5 Microbiota and metabolism: the good and the bad sides
25.6 Chemotherapy, the microbiome and the immune system
25.7.1 Modulation of bacterial enzyme activity
25.7.3 Pre- and probiotics
25.7.4 Fecal transplantation
25.8 Unresolved questions and future work
Chapter 26 Colorectal cancer and the microbiota
26.2 Colon carcinogenesis and epidemiological data
26.2.1 Human carcinogenesis model
26.2.2 Age-related risk in the general population
26.2.3 Gene- and familial-related risks
26.2.4 Environment-related risk
26.4 Bacteria and CRCs links
26.4.3 Experimental data and mechanisms involved
26.5 Hypotheses and perspectives
Chapter 27 The gut microbiota and the CNS: an old story with a new beginning
27.2 The microbiota-gut-brain axis: a historical framework
27.3 The microbiota-gut-brain axis: an evolutionary perspective
27.4 The gut microbiota influence on brain and behavior
27.5 Microbes and the hardwired gut brain axis
27.5.2 The enteric nervous system
27.6 Hormonal pathways to the brain
27.7 Microbes and immune pathways to the brain
27.8 Metabolites of the microbiota: short‐chain fatty acids
27.9 Clinical implications of the microbiota‐gut‐brain axis
Chapter 28 Genetic dysbiosis: how host genetic variants may affect microbial biofilms
28.1 The holobiont: humans as supra‐organisms
28.2 Genetic variants in the host response to microbes
28.2.1 Bacterial recognition pathway
28.2.2 Bacterial proliferation
28.3.1 Genetic dysbiosis of oral biofilm
28.3.2 Genetic dysbiosis of gut biofilm
28.3.3 Genetic dysbiosis of skin biofilm
28.3.4 Genetic dysbiosis of vaginal biofilm
28.4 Summary and conclusions
SECTION 5 Mirroring the future: dysbiosis therapy
Chapter 29 Diet and dysbiosis
29.2 Coevolution of the host‐microbiota super‐organism
29.3 Gut microbiota in personalized diets
29.4 The evolution of diet
29.5 Plasticity of the microbiota and diet
29.6 Interaction among gut microbiota, host and food
29.7 Consequences of diet‐induced dysbiosis on host health
29.8 The role of gut microbes on the digestion of macronutrients
29.9 Diet induces dysbiosis in the host
29.10 The effect of maternal diet on offspring microbiota
29.11 The effects of post‐natal diet on the developing microbiota of neonates
Chapter 30 Probiotics and prebiotics: what are they and what can they do for us?
30.1 The gut microbiota, a partnership with the host
30.2.1 Probiotics, a story that began a long time ago
30.2.2 What are probiotics?
30.2.3 How do probiotics work?
30.2.4 Safety of probiotics
30.3.1 What are prebiotics?
30.3.2 How do prebiotics work?
30.5 Pro-, pre-, and synbiotics in human medicine today
30.5.1 Pro- and prebiotics and infectious diarrhea
30.5.2 Pro- and prebiotics and inflammatory bowel diseases
30.5.3 Pro- and prebiotics and irritable bowel syndrome
30.5.4 Pro- and prebiotics and allergy
30.5.5 Pro- and prebiotics and obesity and diabetes
30.5.7 Pre- and probiotics in pediatrics
Chapter 31 The microbiota as target for therapeutic intervention in pediatric intestinal diseases
31.2 Use of probiotics in pediatric intestinal diseases
31.2.2 Inflammatory bowel diseases
31.2.3 Irritable bowel syndrome
31.2.5 Necrotizing enterocolitis
31.3 Fecal microbiota transplantation for treatment of intestinal diseases
31.3.1 Preparation and administration
31.3.2 Advantages and barriers
31.3.3 The use of FMT in specific intestinal diseases
Chapter 32 Microbial therapy for cystic fibrosis
32.1 Introduction: pathophysiology of cystic fibrosis
32.2 Intestinal inflammation in CF
32.4 Microbial therapy in CF
The Human Microbiota and Chronic Disease
：Dysbiosis as a Cause of Human Pathology
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