Oral Microbiology and Immunology

Cover
Table of Contents
Contributors
Preface
About the Editors
SECTION I. GENERAL PRINCIPLES OF ORAL MICROBIOLOGY AND IMMUNOLOGY
	1. General Microbiology
		Introduction
		Biological Classification Scheme
		Bacterial Classification
		Bacterial Architecture
			Membranes
			Cell Wall Peptidoglycan
			Lipopolysaccharides
			Lipoteichoic Acids
		Other Important Components Produced by Bacteria
			Capsule
			Fimbriae and Pili
			Fibrillar Layers
			Flagella
			Vesicles
			Surface Layers
			Endospores
		Genetic Organization in Bacteria
			The Bacterial Chromosome
			Chromosome Replication in Bacteria
			Gene Transfer in Bacteria
		Bacterial Growth and Nutrition
			Growth
			Nutrient Acquisition
			Environmental Sensing
			Secretion
		Introduction to Fundamental Concepts in Oral Microbial Ecology
			Microbial Biofilms
			Microbial Cooperativity
			Microbial Antagonism
			Polymicrobial Communities
			Ecology of the Oral Microbiota and Development of Oral Diseases
		KEY POINTS
	2. The Immune System and Its Functions
		Introduction—What Is Immunity?
		Innate and Adaptive Immunity
		BOX: Cells of the Immune System
		Immune Recognition Mechanisms
			Innate Immune Recognition: Pattern Recognition Receptors
			Adaptive Immune Recognition: Antigen Receptors
		Induction and Stages of the Immune Response
		Tailored Immunity Requires Specialized Subsets of Immune Cells
		Hallmark Properties of Immunity
			Properties of Adaptive Immunity
			Properties of Innate Immunity
		KEY POINTS
		FURTHER READING
	3. The Oral Environment
		Introduction
		Oral Diseases
		General Features of the Oral Environment
			Teeth
			The Oral Soft Tissues (Periodontium, Oral Mucosa, and Tongue)
		Physical and Host Parameters Affecting Oral Microbial Colonization
			Temperature
			pH
			Oxygen
			Mechanical Abrasive Forces
			Fluid Flow
			Host Age
		The Oral Microbiota
			Tooth (Dental) Plaque: Early Determinants of Plaque Formation
			Calculus
			The Mucosal Microbiota
		Recent Concepts of Dental Biofilm Formation
		Saliva and the Salivary Proteome
		Saliva-Microbe Interactions
		Clearance of Bacteria from the Oral Cavity: Agglutinins
		Pellicle Adhesion Receptors
		Antimicrobial Components in Saliva
		Antiviral Components in Saliva
		Saliva as a Source of Bacterial Nutrition
		Gingival Crevicular Fluid
		KEY POINTS
		FURTHER READING
	4. Isolation, Classification, and Identification of Oral Bacteria
		Introduction
		Diversity of the Oral Microbiota
		The Ribosomal 16S rRNA Gene and Bacterial Identification and Classification
			16S rRNA Genes and Phylogeny
		Sampling Oral Bacteria and Recovery of Bacterial DNA from Samples
		Identifying Oral Bacteria Using Molecular Techniques
			PCR Detection
			Quantitative PCR
			DNA Hybridization Assays
			Ribosomal 16S rRNA Gene Cloning and Sequence Analysis
			Next-Generation Sequencing of 16S rRNA Genes
		Metagenomic Sequence Analysis
		Species and Strains of Oral Bacteria
		Naming of Bacteria and Molecular Analysis
		Direct Observation of Oral Bacteria
		Cultivation of Oral Bacteria
			Oxygen Requirements
			Culture Media
			Innovations in Bacterial Cultivation
		Single-Cell Genomics
		Classification of Cultured Bacteria
		Antibiotic Susceptibility
		Other Oral Microorganisms
		KEY POINTS
		FURTHER READING
	5. Oral Microbial Ecology
		Introduction
		Acquisition of Oral Bacteria
		Colonization by Oral Bacteria
			Surface Structures and Molecules Involved in Adhesion
			Mechanisms of Adhesion
			Host Surface-Specific Constraints on Bacterial Adhesion
			Adhesion and Metabolism
		Bacterial Communication
			Quorum Sensing
			Competence
			Contact-Dependent Interactions
			Antagonism
			Multicomponent Interactions
			Communication with Host Cells
		Gene Regulation
		KEY POINTS
		FURTHER READING
	6. Oral Microbial Physiology
		Introduction
		Survey of Metabolic Activities Important to the Oral Bacterial Community
			Carbohydrate Fermentation
			Metabolism of Organic Acids
			Energy Generation Using Lactate
			Metabolism of Amino Acids
			The Role of Proteases in Energy Generation
			Amino Acid Metabolism by the Stickland Reaction
			Amino Acid Fermentation by Fusobacterium nucleatum
			Arginine Metabolism by the Arginine Deiminase System
			Cross Feeding and Cross Respiration
		Acid-Base Physiology of Oral Microorganisms
			Acid-Base Cycling in the Mouth
			The Range of Acid Tolerance among Oral Bacteria Related to Oral Ecology
			Acid Tolerance Related to Specific Functions
			Constitutive and Adaptive Acid Tolerance
			Alkali Production and Tolerance
			Acid-Base Physiology, Virulence, and Disease
		Oxygen Metabolism, Oxidative Stress, and Adaptation
			Sources of Oxygen for Oral Bacteria
			Oxygen Levels and Oxidation-Reduction Potentials in Dental Plaque
			Oxygen Metabolism in Oral Bacteria, Reactive Oxygen Species, and Oxidative Damage
			Repair Systems
		Physiology of Oral Biofilms
			Physicochemical Gradients in Oral Biofilms and Concentrative Capacities of Biofilms for Fluoride and Other Antimicrobials
			Plaque Nutrition Related to Biofilm Physiology
		KEY POINTS
		FURTHER READING
	7. Genetics and Molecular Biology of Oral Microorganisms
		Introduction
			Fundamental Terms in Bacterial Genetics
		Bacterial DNA Inheritance
			Vertical Gene Transfer
			Horizontal Gene Transfer
			Defense from Foreign DNA
		Genetic Manipulation and Analysis
			Cloning and Vectors
			Mutagenesis
			Complementation
			Transposon Mutagenesis
			Screening
		Conclusions
		KEY POINTS
		FURTHER READING
	8. Applied Molecular Biology and the Oral Microbes
		Introduction
		Genomics
			Gene Organization and Regulation
			Transcriptional Initiation
			Measurement of Gene Expression
		Genomic Structure
			Small Noncoding RNAs
			CRISPR
			Tn-Seq
		Transcriptomics
		Proteomics
			Methods for Protein Identification
			Posttranslational Modifications
			Protein Expression Levels
		Metabolomics and Metabonomics
			Metabolic Fingerprint
			Metabonomics
		Multi-Omics
		KEY POINTS
		FURTHER READING
	9. Population Genetics of Oral Bacteria
		Introduction
		Bacterial Species Show Different Patterns of Evolution
		Localized Sex in Bacteria
		Differences in Pathogenicity of Strains
		Specific Host Adaptation of Bacterial Clones
		Population Sizes of Pathogenic and Commensal Bacteria
		Oral Bacteria Show Varying Degrees of Genetic Diversity
		The Oral Microbiome Is a Dynamic Population Undergoing Constant Changes
		Virulence Differences within Species of Oral Bacteria?
		Methods of Strain Differentiation and Search for Virulent Clones
		Population Genetics Structure of Oral Bacteria
		KEY POINTS
		FURTHER READING
	10. Immunology of the Oral Cavity
		Introduction
		Oral Secretory Immunity
			Overview of Innate Host Defense Factors in Saliva
			Cationic Antimicrobial Peptides
			Proteins with Bacterial Agglutination Properties
			Metal Ion Chelators
			Protease Inhibitors
			Enzymes Acting against Bacterial Cell Walls
			The Peroxidase System
			Overview of Specific Host Defense Factors in Saliva
			The Mucosal Immune System and Induction of S-IgA Antibodies in Saliva
			Biological Activities of S-IgA Antibodies
		Subgingival Immunity
			Innate and Adaptive Immune Players below the Gum Line
			Features of the Subgingival Environment and Their Impact on Host Response
			Toll-Like Receptors and Coreceptors
			Neutrophils
			Complement
			Gingival Crevicular Epithelium
			Adaptive Immunity in the Periodontium
		KEY POINTS
		FURTHER READING
SECTION II. INFECTION-DRIVEN ORAL DISEASES
	11. Dental Caries: Etiology and Pathogenesis
		Introduction
		Tooth Structure and Development
		Sites of Carious Lesions
			Coronal Caries
			Root Surface Caries
		Diet and Dental Caries
			Cariogenic Effect of the Diet
			Anticariogenic Properties of Food
		Cariogenic Dental Biofilm Formation
		Biochemical Composition of the Cariogenic Biofilm
		Physicochemical Phenomena in Dental Biofilm
		Caries Prevention Using Fluoride
		Experimental Caries Models
			Laboratorial Methods
			Animal Models
			In Situ (Intraoral) Models
		KEY POINTS
		FURTHER READING
	12. Pathogenic Mechanisms in Dental Caries
		Introduction
		The Cariogenic Biofilm: Mutans Group Streptococci and Dietary Sugars
			Exopolysaccharides and Biofilm Matrix
			Sugar Transport and Acid Production
			Acid Stress Tolerance and Survival
			Other Stress Resistance-and Virulence-Related Mechanisms
		Polymicrobial Interactions and Cariogenicity
			Commensal-Pathogen Interactions
			Acidogenic Interactions
			Alkalinogenic Interactions
			Bacterial-Fungal interactions
			Future Directions and Perspectives
		KEY POINTS
		FURTHER READING
	13. Periodontal Diseases: General Concepts
		Introduction
		Current Classification of Periodontal Diseases
		Epidemiology of Periodontal Diseases
		Microbial Etiology of Periodontal Diseases
		Prevention and Control of Periodontal Diseases
		Periodontal Diseases and General Health Outcomes
		KEY POINTS
		FURTHER READING
	14. Virulence Factors of Periodontal Bacteria
		Introduction
		Colonization
			Localization in the Gingival Crevice
			Attachment
			Invasion
			Community Development
		Toxins
			Leukotoxin
			Cytolethal Distending Toxin
		Proteolytic Enzymes
		Acquisition of Iron
		Surface-Associated Bioactive Components
			Lipopolysaccharide
			Capsule and Exopolysaccharide
			Toxic Bacterial Components and Enzymes
			Outer Membrane Vesicles
		Secretion of Virulence Factors
		Resistance to Neutrophil Killing
		KEY POINTS
		FURTHER READING
	15. Immunopathogenic Mechanisms in Periodontal Disease
		Introduction
		Immune Players in Periodontal Disease
		Complement: Microbial Manipulation and Destructive Inflammation
		Neutrophils: More Than Just Acute Responders
		Macrophages: Little Known, More To Unearth
		Osteoimmunology: Linking Inflammation to Bone Loss
		Adaptive Immunity: More Harm Than Good?
			T Lymphocytes
			B-Lineage Cells
		Aging and the Host Response: Inflamm-Aging of the Periodontium
		KEY POINTS
		FURTHER READING
	16. Oral Virology
		Introduction
			What Is Oral Virology?
			What Is a Virus?
			How Is a Virus Transmitted?
			The Virus
			How Viruses Change: Viral Evolution
		The Viral Life Cycle
		Virus Taxonomy
			Discovery of New Viruses
		Oral Virology: The Viruses
		Viruses That Can Cause Pathologies in the Oral Cavity
			Picornaviridae
			Human Herpesviruses
			Herpes Simplex Viruses 1 and 2
			Varicella-Zoster Virus
			Cytomegalovirus and Epstein-Barr Virus
			Human Herpesviruses 6, 7, and 8
			Human Papillomaviruses
		Viruses Present in the Oral Cavity
			Hepatitis B Virus
			Hepatitis C Virus
			Human Immunodeficiency Virus
		Viral Immune Responses
			Viruses and the Innate Immune System
			Viruses and the Adaptive Immune System
			Viral Evasion Strategies
		Antiviral Vaccines and Therapies
			History of Viral Vaccines
			Antiviral Immunoglobulin Preparations and Vaccines
			Antiviral Compounds and Therapies
		KEY POINTS
		FURTHER READING
	17. Fungi and Fungal Infections of the Oral Cavity
		Introduction
		Biology
			Morphology
			Fungal Interactions
			Replication
		Pathogenesis
			Acquisition
			Virulence
		Host Defenses against Fungal Infection
			Nonspecific Defense Mechanisms
			Specific Defense Mechanisms
		Antifungal Therapy
			Growth and Identification of Fungi
			Principles of Antifungal Chemotherapy
		Clinical Conditions
			Candidiasis
			Aspergillosis
			Cryptococcosis
			Histoplasmosis
			Blastomycosis
			Paracoccidioidomycosis
			Mucormycosis
		KEY POINTS
		FURTHER READING
	18. Endodontic Infections and Therapeutic Approaches
		Introduction
		Overall Definitions and Concepts
		Pathways of Root Canal Infection
		Microbial Agents of Endodontic Infections
			Microbes Associated with Primary Apical Periodontitis
			Microbes Associated with Posttreatment Apical Periodontitis
			Extraradicular Infection
		Biofilms and the Endodontic Microenvironment
		Root Canal Treatment: Challenges and Current Therapeutic Approaches
			Variations in Bacterial Susceptibility to Disinfection Procedures
			Chemomechanical Preparation
			Root Canal Irrigation
			Intracanal Medication
			Root Canal Obturation and Coronal Restoration
		Concluding Remarks and Perspectives
		KEY POINTS
		FURTHER READING
	19. Systemic Disease and the Oral Microbiota
		Introduction
		Routes from Oral to Systemic Compartments
			Breaches in the Oral Mucosa
			Transport and Translocation of Microbes
		The Potential of Commensal Bacteria To Behave as Pathogens
			Microbial Chameleons: Changing Gene Expression in Response to Environmental Signals
		Host Defenses
		Systemic Diseases Associated with Oral Microbes
			Bacteremia
			Infective Endocarditis
			Disseminated Intravascular Coagulation
			Atherosclerosis
			Adverse Pregnancy Outcomes
			Rheumatoid Arthritis
			Diabetes
			Obesity
			Certain Cancers
			Sequelae of Oral Viral Infections
		Immunological Aspects of Oral Microbes and Systemic Disease
			Heat Shock Proteins
			Autorecognition Induced by Oral Microorganisms
			Inflammation: A Link Between Local Dental Disease and Systemic Pathology
		Summary
		KEY POINTS
		FURTHER READING
SECTION III. CONTROL OF ORAL DISEASES
	20. Antibiotics: Mechanisms of Action, Resistance, and Clinical Use in Dentistry
		Introduction
		Antibiotics: Types and Mechanisms of Action
			Cell Wall-Active Agents
			Antiribosomal Agents
			Antifolate Agents
			Topoisomerase Inhibitors
			Miscellaneous Agents
			Antibiotic Combinations
			Antibiotic Adjuvants
			Measuring the Effects of Antibiotics
			Nonantibiotic Antimicrobial Agents and Disinfectants
		Bacterial Resistance to Antibiotics
			Resistance: Health Effects and Economic Costs
			Overview of Resistance Mechanisms
			Intrinsic and Acquired Resistance
			Biofilm-Associated Drug Tolerance
		Use of Antibiotics in Dentistry
			Treatment of Endodontic (Periapical) Infections
			Treatment of Odontogenic Infections
			Systemic Antibiotics Commonly Used To Treat Odontogenic Infections
			Empirical Antibiotics of Choice for Treating Odontogenic Infections
			Use of Systemic Antibiotics in Periodontal Therapy
			Use of Antibiotics To Prevent Infection
		KEY POINTS
		FURTHER READING
	21. Therapeutic Approaches for Biofilm Control and Host Modulation in Oral Diseases
		Introduction
		Bacterial Adhesion and Biofilm Formation
		Antibiofilm Approaches To Control Oral Diseases
			Oral Surface Modification
			Control of Bacterial Force-Sensing
			EPS Inhibition
			Probiotic Strategies
		Disruption of Biofilms
			Antimicrobial Peptides
			EPS Matrix Degradation
			Metabolic Strategies
			Atmospheric-Pressure Nonthermal Plasma (Cold Plasma)
			Antimicrobial Nanoparticles
			New Generation of Antibiofilm Nanostructures
		Host Response Modulation in Oral Diseases
			Immunization against Dental Caries
			Rationale and Scope for Host Modulation Therapies in Periodontal Disease
			Immunization against Periodontal Disease
			Strategies for Inhibition and Resolution of Periodontal Inflammation
			Approaches for Direct Inhibition of Periodontal Tissue Destruction
			Potential Safety Issues
		KEY POINTS
		FURTHER READING
	22. Infection Prevention and Control in Dentistry
		Introduction
		Introduction to Risk Control
			Quality Assurance Is the Promise of Performance
			Cross-Infection Control Is Essentially a Set of Management Strategies for Risk Control
			What Is Risk Management?
		Cross-Infection Risks in Dentistry
			Routes of Spread of Infection
			Management of Recently Identified Infection Control Risks
		Practical Application of Infection Control Measures in General Dentistry
			Definition of Terms
			Problems Posed for Prevention of Cross-Infection in General Dental Practice
			Standard Precautions
			Infection Control Checklist
			Sterilization of Instruments
		KEY POINTS
		FURTHER READING
Index