List of contributors xvii Preface xxi Section 1 An introduction to the human tissue microbiome 1 1 The human microbiota: an historical perspective 3 Michael Wilson 1.1 Introduction: the discovery of the human microbiota: why do we care? 3 1.2 The importance of the indigenous microbiota in health and disease 3 1.3 The development of technologies for characterising the indigenous microbiota 8 1.4 Cultureindependent approaches to microbial community analysis 29 1.5 Determination of microbial community functions 31 1.6 Closing remarks 32 Takehome message 32 References 33 2 An introduction to microbial dysbiosis 37 Mike Curtis 2.1 Definition of dysbiosis 37 2.
2 The ''normal'' microbiota 38 2.3 Main features of dysbiosis 45 2.4 Conclusions 49 Takehome message 53 Acknowledgment 53 References 53 3 The gut microbiota: an integrated interactive system 55 Hervé M. Blottière and Joël Doré 3.1 Introduction 55 3.2 Who is there how is it composed? 56 3.3 A system in interaction with food 58 3.4 A system highly impacted by the host 61 3.
5 A system in interaction with human cells 62 3.6 Conclusion: an intriguing integrated interactive system deserving further study 63 Takehome message 63 References 63 4 The oral microbiota 67 William G. Wade 4.1 Introduction 67 4.2 Composition of the oral microbiome 68 4.3 The oral microbiota in health 71 4.4 Role of oral microbiome in disease 73 4.5 Future outlook 75 Takehome message 75 References 76 5 The skin microbiota 81 Patrick L.
J.M. Zeeuwen and Joost Schalkwijk 5.1 Normal skin 81 5.2 Skin diseases 83 5.3 Experimental studies 87 5.4 Dynamics of the skin microbiome 87 5.5 Axillary skin microbiome transplantation 89 5.
6 Mouse skin microbiome studies 89 5.7 Concluding remarks 90 Takehome message 90 References 90 6 Metagenomic analysis of the human microbiome 95 Luis G. BermúdezHumarán 6.1 Introduction 95 6.2 The human microbiome 96 6.3 Changes in microbiota composition during host life cycles 97 6.4 The human microbiome and the environment 98 6.5 Disease and health implications of microbiome 99 6.
6 Conclusions 105 Takehome message 105 References 106 Section 2 Microbiota-microbiota and microbiota-host interactions in health and disease 113 7 Systems biology of bacteriahost interactions 115 Almut Heinken Dmitry A. Ravcheev and Ines Thiele 7.1 Introduction 115 7.2 Computational analysis of hostmicrobe interactions 118 7.3 Networkbased modeling 121 7.4 Other computational modeling approaches 127 7.5 Conclusion 129 Takehome message 130 Acknowledgments 130 References 131 8 Bacterial biofilm formation and immune evasion mechanisms 139 Jessica Snowden 8.1 Introduction 139 8.
2 Biofilms in human disease 139 8.3 Biofilm formation 141 8.4 Immune responses to biofilms 143 8.5 Biofilm immune evasion strategies 147 8.6 Vaccines and biofilm therapeutics 148 8.7 Conclusions 149 Takehome message 149 References 150 9 Coevolution of microbes and immunity and its consequences for modernday life 155 Markus B. Geuking 9.1 Introduction 155 9.
2 Symbiosis in eukaryotic evolution 156 9.3 Evolution of the (innate and adaptive) immune system 157 9.4 Hygiene hypothesis 159 9.5 What drives the composition of the microbiota? 160 9.6 The pace of evolution 161 Takehome message 162 References 162 10 How viruses and bacteria have shaped the human genome: the implications for disease 165 Frank Ryan 10.1 Genetic symbiosis 165 10.2 Mitochondria: symbiogenesis in the human 167 10.3 Viral symbiogenesis 169 10.
4 HERV proteins 172 Takehome message 174 References 174 11 The microbiota as an epigenetic control mechanism 179 Boris A. Shenderov 11.1 Introduction 179 11.2 Background on epigenetics and epigenomic programming/ reprograming 180 11.3 Epigenomics and link with energy metabolism 184 11.4 The microbiota as a potential epigenetic modifier 185 11.5 Epigenetic control of the host genes by pathogenic and opportunistic microorganisms 188 11.6 Epigenetic control of the host genes by indigenous (probiotic) microorganisms 189 11.
7 Concluding remarks and future directions 191 Takehome message 193 References 193 12 The emerging role of propionibacteria in human health and disease 199 Holger Brüggemann 12.1 Introduction 199 12.2 Microbiological features of propionibacteria 199 12.3 Population structure of P. acnes 201 12.4 Propionibacteria as indigenous probiotics of the skin 202 12.5 Propionibacteria as opportunistic pathogens 203 12.6 Host interacting traits and factors of propionibacteria 205 12.
7 Host responses to P. acnes 206 12.8 Propionibacteriumspecific bacteriophages 208 12.9 Concluding remarks 209 Takehome message 210 References 210 Section 3 Dysbioses and bacterial diseases: Metchnikoff''s legacy 215 13 The periodontal diseases: microbial diseases or diseases of the host response? 217 Luigi Nibali 13.1 The tooth: a potential breach in the mucosal barrier 217 13.2 The periodontium from health to disease 217 13.3 Periodontitis: one of the most common human diseases 219 13.4 Periodontal treatment: a nonspecific biofilm disruption 220 13.
5 Microbial etiology 220 13.6 The host response in periodontitis 221 13.7 Conclusions 223 Takehome message 223 References 223 14 The polymicrobial synergy and dysbiosis model of periodontal disease pathogenesis 227 George Hajishengallis and Richard J. Lamont 14.1 Introduction 227 14.2 A (very) polymicrobial etiology of periodontitis 229 14.3 Synergism among periodontal bacteria 230 14.4 Interactions between bacterial communities and epithelial cells 232 14.
5 Manipulation of host immunity 233 14.6 Conclusions 237 Takehome message 238 References 239 15 New paradigm in the relationship between periodontal disease and systemic diseases: effects of oral bacteria on the gut microbiota and metabolism 243 Kazuhisa Yamazaki 15.1 Introduction 243 15.2 Association between periodontal and systemic diseases 244 15.3 Issues in causal mechanisms of periodontal disease for systemic disease 249 15.4 New insights into the mechanisms linking periodontal disease and s ystemic disease 252 15.5 Effect of oral administration of P. gingivalis on metabolic change and gut microbiota 252 15.
6 Conclusions 254 Takehome message 255 References 255 16 The vaginal microbiota in health and disease 263 S. Tariq Sadiq and Phillip Hay 16.1 What makes a healthy microbiota 263 16.2 The vaginal microbiota in disease 265 16.3 Conclusions 269 Takehome message 269 References 270 Section 4 Dysbioses and chronic diseases: is there a connection? 273 17 Reactive arthritis: the hidden bacterial connection 275 John D. Carter 17.1 Introduction 275 17.2 Reactive arthritis 276 17.
3 Pathophysiology of ReA 277 17.4 Questions remain 279 17.5 Conclusion 280 Takehome message 280 References 280 18 Rheumatoid arthritis: the bacterial connection 283 Jacqueline Detert 18.1 Preclinical rheumatoid arthritis 283 18.2 Predisposition to RA 284 18.3 MCHHLA and genetic predisposition to RA 284 18.4 Molecular mimicry in RA 285 18.5 Innate immune system and RA 285 18.
6 Bystander activation and pattern recognition receptors 286 18.7 Antibodies and neoepitopes 287 18.8 Superantigens 287 18.9 Lps 287 18.10 Bacterial DNA and peptidoglycans 288 18.11 Heatshock proteins 288 18.12 Tolllike and bacterial infections 288 18.13 Proteus mirabilis 288 18.
14 Porphyromonas gingivalis and RA 289 18.15 Gastrointestinal flora and RA 290 18.16 Smoking lung infection and RA 291 18.17 Where to go from here? 291 Takehome message 291 References 292 19 Inflammatory bowel disease and the gut microbiota 301 Nik Ding and Ailsa Hart 19.1 The microbiota in inflammatory bowel disease 301 19.2 Dysbiosis and IBD pathogenesis 301 19.3 Environmental factors affecting microbiome composition 302 19.4 Genetics and application to the immune system and dysbiosis in IBD 303 19.
5 An overview of gut microbiota studies in IBD 305 19.6 Specific bacterial changes in IBD 306 19.7 Functional composition of microbiota in IBD 308 19.8 Challenges 310 19.9 Conclusion 310 Takehome message 310 References 310 20 Ankylosing spondylitis klebsiella and the lowstarch diet 317 Al.