Atlas of Oral Microbiology: From Healthy Microflora to Disease

Preface
Contents
Editors and Contributors
Chapter 1: Basic Biology of Oral Microbes
	1.1 Cytological Basis of Microorganisms
	1.2 Microbial Morphology
		1.2.1 Microbial Size
		1.2.2 Microbial Morphology
	1.3 Microbial Cell Structure
		1.3.1 Basic Bacterial Structures
			1.3.1.1 Cell Wall
			1.3.1.2 Cell Wall-Deficient Bacteria (Bacterial L Form)
			1.3.1.3 Cell Membrane
			1.3.1.4 Cytoplasm
			1.3.1.5 Nuclear Material
		1.3.2 Special Bacterial Structures
			1.3.2.1 Capsule
			1.3.2.2 Flagellum
			1.3.2.3 Pilus
			1.3.2.4 Spore
		1.3.3 Basic Virus Structure
	1.4 Microbial Physiology
		1.4.1 Binary Fission Reproduction
		1.4.2 Bacterial Growth
	1.5 Microbial Genetics
		1.5.1 Heredity
		1.5.2 Variation
		1.5.3 Genetic Material of Bacteria
		1.5.4 Mechanism of Microbial Variation
		1.5.5 Gene Transfer and Recombination
			1.5.5.1 Transformation
			1.5.5.2 Conjugation
			1.5.5.3 Transduction
	References
Chapter 2: Techniques for Oral Microbiology
	2.1 Smear and Stain Techniques
		2.1.1 Kopeloff´s Modification of Gram Stain
			2.1.1.1 Mechanism
			2.1.1.2 Preparation of Gram Stain Reagents (Commercially Available)
			2.1.1.3 Staining Procedure
			2.1.1.4 Reporting Results
			2.1.1.5 Precautions
		2.1.2 Staining Bacterial Spores
			2.1.2.1 Gram Stain
			2.1.2.2 Fuchsin-Methylene Blue Stain
		2.1.3 Staining the Bacterial Capsule
			2.1.3.1 Murs Stain
			2.1.3.2 Wright´s Stain
		2.1.4 Flagellar Stain
			2.1.4.1 Preparation of Staining Solutions
			2.1.4.2 Smear Preparation
			2.1.4.3 Staining Protocol
		2.1.5 Staining Procedure for Special Fungal Structures
			2.1.5.1 Crystal Violet Stain
			2.1.5.2 Lactophenol Cotton Blue Stain
		2.1.6 Giemsa Stain for Mycoplasma
		2.1.7 Negative Congo Red Staining of Plaque Bacteria
		2.1.8 Protozoan Smears
			2.1.8.1 Wet Smear for Fresh Samples
			2.1.8.2 Giemsa Staining
	2.2 Isolation, Incubation, and Identification Techniques
		2.2.1 Collection and Transportation of Samples
			2.2.1.1 Sample Collection
			2.2.1.2 Sample Transportation
		2.2.2 Suspension and Dilution of Samples
			2.2.2.1 Sample Suspension in Solution
			2.2.2.2 Sample Dilution
		2.2.3 Inoculation and Incubation of Samples
			2.2.3.1 Choice of Medium
			2.2.3.2 Sample Inoculation
			2.2.3.3 Sample Incubation
		2.2.4 Growth Characteristics and Identification
			2.2.4.1 Growth Characteristics
			2.2.4.2 Biochemical Tests
		2.2.5 Instruments for Microbiological Identification
			2.2.5.1 Spiral Plater
			2.2.5.2 Microbiology Analyzer
			2.2.5.3 Microbial Identification System
	2.3 Microscopy Techniques
		2.3.1 Stereomicroscopy
		2.3.2 Scanning Electron Microscopy
			2.3.2.1 Mechanism
			2.3.2.2 Operating Procedure
			2.3.2.3 Sample Observation
		2.3.3 Transmission Electron Microscopy
			2.3.3.1 Preparation of Bacterial Samples
			2.3.3.2 Section
			2.3.3.3 Uranium Staining and Observation
		2.3.4 Confocal Laser Scanning Microscopy
			2.3.4.1 Principles of CLSM
			2.3.4.2 Application in Dental Plaque Research
	2.4 Oral Microecology Techniques
		2.4.1 Methods for Measuring Microbial Growth Curves
			2.4.1.1 Protocol
			2.4.1.2 Methods
		2.4.2 Methods for Measuring Colony Forming Units
			2.4.2.1 Protocol
			2.4.2.2 Methods
		2.4.3 Measurement of Adhesion Strength and Rate of Adhesion Inhibition
			2.4.3.1 Measurement of Adhesion Strength
			2.4.3.2 Measuring the Rate of Adhesion Inhibition
		2.4.4 Techniques for the Detection of Plaque Biofilm
			2.4.4.1 Biofilm Formation Assay
			2.4.4.2 Biofilm Detection and Analysis
	2.5 Oral Microbiome Techniques
		2.5.1 Denaturing Gradient Gel Electrophoresis and Temperature Gradient Gel Electrophoresis
		2.5.2 Sanger Sequencing
		2.5.3 Next-Generation Sequencing
			2.5.3.1 Pyrosequencing
			2.5.3.2 Illumina Sequencing
	References
Chapter 3: Supragingival Microbes
	3.1 Gram-Positive Bacteria
		3.1.1 Actinomyces
			3.1.1.1 Actinomyces israelii
			3.1.1.2 Actinomyces naeslundii
			3.1.1.3 Actinomyces odontolyticus
			3.1.1.4 Actinomyces viscosus
		3.1.2 Bifidobacterium
			3.1.2.1 Bifidobacterium dentium
			3.1.2.2 Bifidobacterium breve
		3.1.3 Lactobacillus
			3.1.3.1 Lactobacillus acidophilus
			3.1.3.2 Lactobacillus casei
			3.1.3.3 Lactobacillus fermentum
		3.1.4 Rothia
		3.1.5 Staphylococcus
		3.1.6 Streptococcus
			3.1.6.1 Streptococcus salivarius
			3.1.6.2 Streptococcus sanguinis
			3.1.6.3 Streptococcus gordonii
			3.1.6.4 Streptococcus mutans
			3.1.6.5 Streptococcus sobrinus
			3.1.6.6 Streptococcus oralis
			3.1.6.7 α-Hemolytic Streptococcus
			3.1.6.8 β-Hemolytic Streptococcus
	3.2 Gram-Negative Bacteria
		3.2.1 Leptotrichia
		3.2.2 Veillonella
			3.2.2.1 Veillonella parvula subsp. parvula
	References
Chapter 4: Subgingival Microbes
	4.1 Gram-Positive Bacteria
		4.1.1 Enterococcus
		4.1.2 Eubacterium
		4.1.3 Peptostreptococcus
		4.1.4 Propionibacterium
	4.2 Gram-Negative Bacteria
		4.2.1 Bacteroides
			4.2.1.1 Bacteroides fragilis
			4.2.1.2 Bacteroides thetaiotaomicron
		4.2.2 Capnocytophaga
			4.2.2.1 Capnocytophaga gingivalis
			4.2.2.2 Capnocytophaga sputigena
		4.2.3 Eikenella
		4.2.4 Fusobacterium
			4.2.4.1 Fusobacterium nucleatum
			4.2.4.2 Fusobacterium necrophorum
			4.2.4.3 Fusobacterium varium
		4.2.5 Helicobacter
		4.2.6 Aggregatibacter
		4.2.7 Prevotella
			4.2.7.1 Prevotella intermedia
			4.2.7.2 Prevotella nigrescens
			4.2.7.3 Prevotella melaninogenica
			4.2.7.4 Prevotella corporis
			4.2.7.5 Prevotella loescheii
		4.2.8 Porphyromonas
			4.2.8.1 Porphyromonas gingivalis
			4.2.8.2 Porphyromonas endodontalis
		4.2.9 Treponema
	References
Chapter 5: Oral Mucosal Microbes
	5.1 Gram-Positive Bacteria
		5.1.1 Staphylococcus
		5.1.2 Streptococcus
			5.1.2.1 Streptococcus mitis
			5.1.2.2 Streptococcus pyogenes
			5.1.2.3 Streptococcus pneumoniae
			5.1.2.4 Streptococcus vestibularis
	5.2 Gram-Negative Bacteria
		5.2.1 Escherichia
		5.2.2 Haemophilus
		5.2.3 Moraxella
		5.2.4 Neisseria
	5.3 Mycoplasma
	5.4 Fungi
		5.4.1 Saccharomyces
			5.4.1.1 Candida albicans
	5.5 Virus
	References
Chapter 6: New Oral Microbial Isolations
	6.1 Gram-Positive Bacteria
		6.1.1 Leuconostoc lactis
		6.1.2 Corynebacterium argentoratense
	6.2 Gram-Negative Bacteria
		6.2.1 Stenotrophomonas maltophilia
		6.2.2 Chryseobacterium indologenes
		6.2.3 Elizabethkingia anophelis
		6.2.4 Klebsiella pneumoniae
		6.2.5 Escherichia coli
		6.2.6 Campylobacter jejuni
		6.2.7 Veillonella atypica
	6.3 Fungi
		6.3.1 Candida tropicalis
		6.3.2 Candida glabrata
		6.3.3 Candida parapsilosis
		6.3.4 Candida krusei
		6.3.5 Aspergillus fumigatus
	References
Chapter 7: The Oral Microbiome Bank of China
	7.1 Introduction
	7.2 Results
		7.2.1 Overview of the Online Database
			7.2.1.1 Web-Accessible Functions
	7.3 Discussion
	7.4 Materials and Methods
		7.4.1 Collection and Transport of Samples
		7.4.2 Dispersion and Dilution of Samples
		7.4.3 Inoculation and Incubation of Samples
		7.4.4 Smear and Stain
		7.4.5 Growth Characteristics and Identification
		7.4.6 Biochemical Tests
		7.4.7 Molecular Method
		7.4.8 DNA Extraction and Sequencing
		7.4.9 16S rRNA Alignment
		7.4.10 Database and Web Design
		7.4.11 Curation
		7.4.12 Service and Function
	References
Chapter 8: Invasion of Oral Microbiota into the Gut
	8.1 Introduction
	8.2 Results
		8.2.1 The Oral Microbiota of the HOMA Mouse Model
		8.2.2 Biogeography of the Host Gut-Selected Oral Microbiota
		8.2.3 Ecological Invasion by Oral Microbiota in the Gut
		8.2.4 Porphyromonas Competed for Colonization with the Small Intestinal Microbiota
	8.3 Discussion
	8.4 Materials and Methods
		8.4.1 Sample Collection from Humans
		8.4.2 Animal Husbandry
		8.4.3 Establishment of the HOMA and HMA Mouse Models
		8.4.4 Cohousing Experiment
		8.4.5 16S rRNA Gene Sequencing
		8.4.6 Bioinformatics and Statistical Analysis
	References
Chapter 9: Mycobiome Dysbiosis in Oral Lichen Planus
	9.1 Introduction
	9.2 Results
		9.2.1 Participant Demographics and Sequence Data
		9.2.2 Lower Saliva Biodiversity of the Mycobiome and Higher Biodiversity of the Bacteriome in OLP
		9.2.3 Taxonomic Differences Among Healthy Individuals and OLP Patients
		9.2.4 Inversion of Myco-Bacteriome Co-occurrence Patterns from Antagonization to Co-prosperity
		9.2.5 Distinct Network Topology Between OLP and Healthy Individuals
		9.2.6 Fungal Disturbance Promotes OLP Exacerbation
	9.3 Discussion
	9.4 Materials and Methods
		9.4.1 Subject Recruitment and Sample Collection
		9.4.2 Cytokine Assay
		9.4.3 DNA Extraction
		9.4.4 Illumina Sequencing
		9.4.5 Data Preprocessing, OTU Clustering, and Taxonomic Classification
		9.4.6 Statistical Analysis
	9.5 Data Availability
	9.6 Ethics Statement
	References
Chapter 10: Intestinal Microbiota and Osteoporosis
	10.1 Introduction
		10.1.1 The Intestinal Microbiota and Its Regulators
		10.1.2 The Intestinal Microbiota Regulates Bone Metabolism
			10.1.2.1 Involvement of the Intestinal Microbiota in Bone Metabolism
			10.1.2.2 Mechanisms by Which the Gut Microbiota Regulates Bone Metabolism
		10.1.3 Relationship Between the Intestinal Microbiota and PMO
			10.1.3.1 PMO Animal Models
			10.1.3.2 PMO Development Depends on the Intestinal Microbiota and Host Genetic Background
			10.1.3.3 Probiotics Prevent Bone Loss in PMO Murine Models
		10.1.4 Host and Microbiota Interactions in the Pathogenesis and Treatment of PMO
			10.1.4.1 Intestinal Microbial Diversity in PMO Is Regulated by Estrogen and Probiotics
			10.1.4.2 Intestinal Epithelial Barrier Function in PMO Is Regulated by Estrogen and Probiotics
			10.1.4.3 Host Immune Responses in PMO Are Regulated by Estrogen and the Intestinal Microbiota
			10.1.4.4 The Intestinal Microbiota and Estrogen Orchestrate Calcium Absorption
			10.1.4.5 The Gut Microbiota Produces Estrogen-Like Metabolites with Regulatory Effects on Bone Metabolism
		10.1.5 Conclusion
	References
Index