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Skin Microbiome Handbook
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Preface xvii Part 1: Healthy Skin Microbiome and Oral-Skin Interactions 1 1 The Microbiome of Healthy Skin 3 Samantha Samaras and Michael Hoptroff 1.1 Introduction 3 1.1.1 Retrospective 3 1.1.2 Next Generation Sequencing 6 1.2 The Skin Microbiome in Health 7 1.2.1 Composition 7 1.2.2 Diversity 10 1.2.3 Uniqueness 13 1.3 Healthy Skin is the Foundation of a Balanced Skin Microbiome 14 1.3.1 Physical Aspects of Skin Impacting the Microbiome 14 1.3.2 Biochemical and Defensive Aspects of Skin Impacting the Microbiome 16 1.3.2.1 The Acid Mantle 16 1.3.2.2 Antimicrobial Lipids (AMLs) 16 1.3.2.3 Antimicrobial Peptides (AMPs) 17 1.3.3 Nutritional and Microenvironmental Aspects of Skin Impacting the Microbiome 18 1.3.3.1 Amino Acids 18 1.3.3.2 Sebaceous Lipids 19 1.3.3.3 Organic Acids and Other Materials 19 1.4 A Balanced Skin Microbiome Supports the Normal Functioning of Healthy Skin 20 1.4.1 Pathogen Exclusion 20 1.4.2 Contribution to Skin pH 20 1.4.3 Microbial Contribution to Skin Barrier Integrity 21 1.5 Conclusion 22 Acknowledgments 23 References 23 2 The Gut Microbiome-Skin Axis: Impact on Skin and Systemic Health 33 David Drake 2.1 Introduction 34 2.2 The Gut-Skin Microbiome Axis 35 2.3 The Gut-Skin Microbiome Axis: Principle Pathways 35 2.4 Dysbiosis of the Gut Microbiome and Skin Dyshomeostasis 37 2.4.1 Acne Vulgaris 38 2.4.2 Atopic Dermatitis 39 2.5 Summary and Future Directions 39 References 40 3 The Skin and Oral Microbiome: An Examination of Overlap and Potential Interactions between Microbiome Communities 45 Sandra Buerger 3.1 Introduction 45 3.1.1 Focus of the Chapter 45 3.1.2 Definition of Skin Microbiome 47 3.1.3 Definition of Oral Microbiome 48 3.2 Characterization of the Microbiome 48 3.2.1 Variability and Stability of Skin and Oral Microbiome 48 3.2.2 Microbial Community 49 3.2.2.1 Permeant Mutualistic or Commensal Microbes 49 3.2.2.2 Non-Pathogenic Transient Microbes 50 3.2.2.3 Pathogenic Microbes 50 3.3 The Core Skin and Oral Microbiomes 51 3.3.1 Taxonomic Methodology 51 3.3.2 Subgroups of the Microbiome 52 3.3.2.1 Bacteriome 52 3.3.2.2 Mycobiome (and Other Eukaryotic Microbial Members) 52 3.3.2.3 Virome 53 3.4 Interactions Between Skin and Oral Microbiomes 54 3.4.1 Potential for Interactions 54 3.4.2 Quorum Sensing 54 3.4.3 Immune System Development 54 3.4.4 Future Directions 55 3.5 Conclusion 55 Acknowledgments 56 References 56 Part 2: Skin Microbiome Observational Research 59 4 Skin Microbiome Alterations in Skin Diseases 61 Travis Whitfill, Gilles R. Dube and Julia Oh 4.1 Introduction and Background 61 4.2 Interactions Between Microbes and Host 62 4.3 Summary of Known Associations Between Skin Dysbioses and Skin Diseases 64 4.3.1 The Role of S. Aureus in Skin Disease 64 4.3.2 Atopic Dermatitis 64 4.3.3 Acne Vulgaris 66 4.3.4 Psoriasis 67 4.4 Skin Dysbioses in Skin Health 68 4.5 Other Skin Conditions 68 4.6 Therapeutic Approaches to Dysbiosis-Associated Skin Diseases 69 4.6.1 Traditional Methods of Treating Dysbiosis-Associated Skin Diseases 69 4.6.1.1 Atopic Dermatitis 69 4.6.1.2 Acne Vulgaris 69 4.6.2 Emerging Therapeutic Approaches to Treating Dysbiosis-Associated Skin Diseases 70 4.7 Conclusion and Future Directions 71 Acknowledgements 71 References 71 5 The Axillary Microbiome and its Relationship with Underarm Odor 79 Alexander Gordon James 5.1 Introduction 80 5.2 Composition of the Axillary Microbiome 86 5.3 16-Androstene Steroids and Axillary Malodour 95 5.4 The Axillary Microbiome, VFAs and Malodour 96 5.5 The Axillary Microbiome, Thioalcohols and Malodour 100 5.6 Perturbation of the Axillary Microbiome 108 5.7 Human Genetics - Influence on Malodour and the Axillary Microbiome 112 5.8 Conclusions and Future Perspectives 115 Acknowledgements 122 References 122 6 Infant Skin Microbiome 131 Georgios N. Stamatas 6.1 Introduction 131 6.2 Infant Skin Maturation 132 6.3 Infant Immune System Maturation 133 6.4 Infant Skin Microbiome Dynamics 134 6.5 Mother-Infant Microbial Transmission 137 6.6 Conclusion 138 References 139 Part 3: Skin Microbiome in Disequilibrium and Disease 143 7 Microbiome of Compromised Skin 145 Sara Farahmand 7.1 Atopic Dermatitis 146 7.2 Psoriasis 148 7.2.1 Diversity 149 7.2.2 Microbiome Composition 151 7.3 Acne 152 7.4 Rosacea 153 7.5 Seborrheic Dermatitis and Dandruff 155 7.6 Exposome, Skin Barrier, and Skin Microbiome 157 7.6.1 Skin Irritation and Microbiome 157 7.6.2 Diaper Dermatitis 157 7.6.3 Occupational Hand Dermatitis 158 7.6.4 Allergic Contact Dermatitis (ACD) and Skin Microbiome 159 7.7 Conclusion 160 References 163 8 Human Cutaneous Ectoparasites: A Brief Overview and Potential Therapeutic Role for Demodex 171 Stephen L. Strobel 8.1 Introduction 171 8.2 Chiggers (Trombiculidae) 172 8.3 Bedbugs (Cimex lectularius and Hemipterus) 173 8.4 Lice 173 8.5 Scabies (Sarcoptes scabiei) 174 8.6 Demodex 175 8.7 The Association Between Demodex, Rosacea and Blepharitis 176 8.8 Hypothesis 177 8.9 Demodex Folliculorum as a Drug Delivery Agent for Early Skin Cancer 177 8.10 Limitations 179 8.11 Conclusion 180 8.12 Future Considerations 181 References 182 9 Dysbiosis of the Skin Microbiome in Atopic Dermatitis 185 Joyce Cheng and Tissa Hata 9.1 Introduction 185 9.2 The Healthy Skin Microbiome 186 9.3 The Skin Microbiome in Atopic Dermatitis 187 9.4 Microbiome-Targeted Treatment Strategies 195 9.5 Conclusion 196 References 196 10 The Skin Microbiome of Inverse Psoriasis 203 Jennifer Chung, Bruce E. Strober and George M. Weinstock 10.1 Introduction 204 10.2 Methods 205 10.2.1 Subject Population 205 10.2.2 Patient Diagnosis and Characteristics of Populations 206 10.2.3 Specimen Collection 206 10.2.4 Sample DNA Extraction and Sequencing 207 10.2.5 Downstream Sequence Processing and Analysis 207 10.3 Results 208 10.3.1 Cohort Metadata 208 10.3.2 Sequencing Information 208 10.3.3 The Skin Microbiome of Intertriginous Lesion and Non-Lesional Sites on Inverse Psoriasis Subjects 208 10.3.3.1 Psoriasis Lesional Status is Associated with Relative Abundance and Presence of Specific Species 208 10.3.3.2 Psoriatic Lesions Trend to Decrease Taxonomic Diversity 210 10.3.3.3 Psoriatic Lesions are Characterized by Greater Intragroup Variability 212 10.3.4 Inverse Psoriasis vs. Plaque Psoriasis vs. Healthy (All Non-Lesion Sites) 212 10.4 Conclusions & Future Plans 212 Acknowledgements 213 References 214 Part 4: Skin's Innate Immunity 217 11 Effects of Endogenous Lipids on the Skin Microbiome 219 Carol L. Fischer and Philip W. Wertz 11.1 Introduction 219 11.2 Sebaceous Lipids -- Source of Fatty Acids 221 11.3 Stratum Corneum Lipids - Source of Long-Chain Bases 223 11.4 Antimicrobial Activity of Fatty Acids 226 11.5 Antimicrobial Activity of Long-Chain Bases 230 11.6 Conclusion 231 References 231 12 Innate Immunity in Epidermis 237 Miroslav Blumenberg 12.1 Introduction 237 12.2 Skin Acts as an Anatomical Physical and Chemical Barrier to Infectious Agents 238 12.3 Epidermal Cells Recognize Conserved Features of Pathogens, as well as the Indicators of Tissue Damage 239 12.4 Defensive Antimicrobial Proteins AMPs 240 12.5 Cytokines, Specific Signals that Activate Inflammation and Further Cellular Protective Mechanisms 242 12.6 Specialized White Blood Cells Identify and Remove Pathogens 243 12.7 Complement System 246 12.8 Innate Immune System Activates the Adaptive Immune System 246 12.9 Antiviral Defenses 247 12.10 Innate Immunity Memory? 247 12.11 Cutaneous Microbiome: A Newly Surfaced Contributor to Innate Immunity 248 12.12 Conclusion 251 12.13 Future Perspectives 252 References 254 Part 5: Testing and Study Design 261 13 Next Generation Sequencing Reveals the Skin Microbiome 263 Niamh B O'Hara 13.1 Introduction 263 13.2 Current Approaches to Test the Microbiome 265 13.3 The Genomics Revolution and Metagenomics 266 13.4 Metagenomics and the Skin Microbiome 267 13.5 Our Work at Biotia 268 13.6 Challenges and Solutions in Metagenomics 269 13.7 The Microbial World is our Oyster 272 13.8 The Future of Metagenomics 273 Acknowledgements 273 References 274 14 Three-Dimensional Human Skin Models to Investigate Skin Innate and Immune-Mediated Responses to Microorganisms 277 Marisa Meloni and Silvia Balzaretti 14.1 State-of-the-Art and Limits of Skin Microbiota Research 277 14.2 Mechanism-Based Approach to Study Host Response to Associated Microbiome: 3D Skin Models 279 14.3 Understanding S. epidermidis and S. aureus Behavior and Role on Reconstructed Human Epidermis (RHE) 281 14.4 Immuno-Competent Atopic Dermatitis Model 284 14.5 Conclusion and Future Perspectives 286 References 286 15 Cutibacterium acnes (formerly Propionibacterium acnes) In-Vivo Reduction Assay: A Pre-Clinical Pharmacodynamic Assay for Evaluating Antimicrobial/Antibiotic Agents in Development for Acne Treatment 289 Stuart R. Lessin and James J. Leyden 15.1 Acne Pathogenesis and the Role of Cutibacterium acnes (formerly Propionibacterium acnes) 290 15.1.1 Introduction 290 15.1.2 Pathogenesis 290 15.1.3 The Role of C. acnes and its Microbiome 290 15.2 Current Therapies and Regulatory Approval 293 15.3 In-Vivo C. acnes Reduction Assay 294 15.4 Correlations of C. acnes Reduction and Clinical Efficacy 297 15.5 Conclusion 300 References 300 Part 6: Regulatory and Legal Aspects for Skin Microbiome Related Products 303 16 Intellectual Property Tools for Protecting, Developing and Growing a Skin Microbiome Brand 305 Jeffrey K. Mills 16.1 Introduction 305 16.2 The Tools of Intellectual Property 306 16.2.1 Patents 306 16.2.2 Trademarks 307 16.2.3 Copyrights 308 16.2.4 Trade Secrets/Know-How 309 16.3 Building an Intellectual Property Portfolio for a Skin Microbiome Brand 310 16.3.1 Patents to Define "The Fence" 310 16.3.1.1 Patents "As Sticks" - Enforcement of Infringement 313 16.3.1.2 Patents "As Financial Boosts" - Licensing and Other Agreements 314 16.3.2 Trademarks to Establish Brand Recognition 315 16.3.3 Copyrights to Maintain Information 317 16.3.4 Trade Secrets/Know-How to Keep A Competitive Edge 318 16.4 Conclusion 320 17 Regulatory Aspects of Probiotics and Other Microbial Products Intended for Skin Care: The European Approach 321 Atte von Wright 17.1 Introduction 322 17.2 The Governing Bodies and Decision-Making in the EU 322 17.2.1 The Legal Instruments of the EU 323 17.3 Probiotic Foods and the European Regulations 324 17.3.1 The Safety Assessment of Microorganisms by EFSA, The QPS Concept 324 17.3.1.1 The Safety Assessment of Non-QPS Microorganisms 327 17.3.2 The Case of GMMs 328 17.3.3 Microorganisms as Novel Foods 329 17.3.4 Human Probiotics and Functional Claims 329 17.4 Probiotic Skin Care Products as Pharmaceuticals 330 17.4.1 The Authorization Procedure for Medicines 331 17.4.1.1 The Centralized Procedure 332 17.4.1.2 National Authorizations and Authorizations by Mutual Recognition or Decentralized Procedures 333 17.4.2 Bacteria as Medical Devices 334 17.5 Probiotics in Cosmetics 335 17.5.1 Safety Aspects 336 17.5.1.1 Microorganisms on Skin - Problems of Safety Evaluation 337 17.5.2 The Permissible Cosmetic Claims in the EU 338 17.6 Conclusions 338 References 340 Legal Acts and Guidance Documents 340 18 Regulation of Probiotic and Other Live Biologic Products: The United States Approach 343 Ronie M. Schmelz 18.1 Introduction 343 18.1.1 U.S. Legislative Landscape 344 18.1.2 Foods 345 18.1.2.1 Permissible Food Claims 350 18.1.2.2 Additional Regulatory Considerations 354 18.1.3 Dietary Supplements 355 18.1.3.1 Permissible Dietary Supplement Claims 357 18.1.3.2 Additional Regulatory Considerations 359 18.1.4 Drugs 360 18.1.4.1 Drug Approval Process 361 18.1.4.2 Additional Regulatory Considerations 364 18.1.5 Cosmetics 364 18.2 Summary of Product Categorization and Regulatory Requirements 365 18.3 Resources 369 18.4 Endnotes 369 19 A Future Research Perspective Is There a Connection Between Sun Exposure, Microbiome and Skin Cancer? 377 Nava Dayan 19.1 Introduction 378 19.2 Ultraviolet Light (UV) - The Skin Microbiome and Cancer 378 19.3 Conclusion 386 Acknowledgment 386 References 387 Glossary 389 Index 399

About the Author

Nava Dayan Ph.D. Pharm D. is a research scientist who has specialized in skin product development for nearly 3 decades. She is the owner of Dr. Nava Dayan L.L.C, a skin science and research consultancy serving the pharmaceutical, cosmetic, and personal care industries; dermal and transdermal. The uniqueness of Dr. Dayan's approach is in its comprehensiveness since she covers biology, physics, efficacy, toxicology, formulations product development, and bio-availability. With her many years of experience in the skin care sector, she has produced more than 150 publication credits in numerous industry-respected journals and in four books. Her research focus is on feasibility in skin care, composition of R&D plans covering efficacy and toxicology; planning, execution and data interpretation into claims, formulations, delivery for improved efficacy and attenuated toxicity, drug-skin interaction, bio-markers, skin/age related sensitivities, inflammatory skin disorders, innate immunity and skin microbiome. This is her fifth book and her 2nd with the Wiley-Scrivener imprint.

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