1 Scope and History of Microbiology 1

Why Study Microbiology? 2

Scope of Microbiology 4

Historical Roots 9

The Germ Theory of Disease 11

Emergence of Special Fields of Microbiology 15

Tomorrow’s History 19

2 The Microbiome 25

Introduction to the Microbiome 26

Fat or Lean 26

Diversity of Microbiomes 27

3 Fundamentals of Chemistry 31

Why Study Chemistry? 32

Chemical Building Blocks and Chemical Bonds 32

Water and Solutions 36

Complex Organic Molecules 40

4 Microscopy and Staining 53

Historical Microscopy 54

Principles of Microscopy 54

Light Microscopy 60

Electron Microscopy 64

Techniques of Light Microscopy 70

5 Characteristics of Prokaryotic and Eukaryotic Cells 77

Basic Cell Types 78

Prokaryotic Cells 78

Eukaryotic Cells 97

Evolution by Endosymbiosis 103

The Movement of Substances across Membranes 105

6 Essential Concepts of Metabolism 113

Metabolism: An Overview 114

Enzymes 116

Enzyme Inhibition 118

Anaerobic Metabolism: Glycolysis and Fermentation 122

Aerobic Metabolism: Respiration 126

The Metabolism of Fats and Proteins 132

Other Metabolic Processes 133

The Uses of Energy 136

7 Growth and Culturing of Bacteria 142

Growth and Cell Division 143

Factors Affecting Bacterial Growth 152

Sporulation 161

Culturing Bacteria 163

Living, But Nonculturable, Organisms 170

8 Microbial Genetics 173

An Overview of Genetic Processes 174

DNA Replication 178

Protein Synthesis 179

The Regulation of Metabolism 187

Mutations 191

9 Gene Transfer and Genetic Engineering 205

The Types and Significance of Gene Transfer 206

Transformation 206

Transduction 208

Conjugation 212

Gene Transfer Mechanisms Compared 216

Plasmids 216

Genetic Engineering 220

10 An Introduction to Taxonomy: the Bacteria 232

Taxonomy: the Science of Classification 233

Using A Taxonomic Key 235

The Five-Kingdom Classification System 236

The Three-Domain Classification System 240

Classification of Viruses 244

The Search for Evolutionary Relationships 246

Bacterial Taxonomy and Nomenclature 249

11 Viruses 258

General Characteristics of Viruses 260

Classification of Viruses 263

Emerging Viruses 271

Viral Replication 274

Culturing of Animal Viruses 285

Viruses and Teratogenesis 287

Viruslike Agents: Satellites, Virophages, Viroids, and Prions 288

Viruses and Cancer 292

Human Cancer Viruses 292

12 Eukaryotic Microorganisms and Parasites 297

Principles of Parasitology 298

Protists 300

Fungi 307

Helminths 315

Arthropods 323

13 Sterilization and Disinfection 329

Principles of Sterilization and Disinfection 330

Chemical Antimicrobial Agents 331

Physical Antimicrobial Agents 341

14 Antimicrobial Therapy 353

Antimicrobial Chemotherapy 354

The History of Chemotherapy 355

General Properties of Antimicrobial Agents 356

Determining Microbial Sensitivities to Antimicrobial Agents 364

Attributes of An Ideal Antimicrobial Agent 367

Antibacterial Agents 367

Antifungal Agents 373

Antiviral Agents 376

Antiprotozoan Agents 378

Antihelminthic Agents 379

Special Problems with Drug-Resistant Hospital Infections 379

15 Host-Microbe Relationships and Disease Processes 385

Host–Microbe Relationships 386

Koch’s Postulates 391

Kinds of Diseases 392

The Disease Process 393

Infectious Diseases—Past, Present, and Future 405

16 Epidemiology and Nosocomial Infections 409

Epidemiology 410

Nosocomial Infections 431

Bioterrorism 439

17 Innate Host Defenses 445

Innate and Adaptive Host Defenses 446

Physical Barriers 446

Chemical Barriers 447

Cellular Defenses 447

Inflammation 456

Fever 458

Molecular Defenses 459

Development of the Immune System: Who Has One? 465

18 Basic Principles of Adaptive Immunity and Immunization 469

Immunology and Immunity 470

Types of Immunity 470

Characteristics of the Immune System 472

Humoral Immunity 478

Monoclonal Antibodies 484

Cell-Mediated Immunity 486

Mucosal Immune System 490

Immunization 492

Immunity to Various Kinds of Pathogens 501

19 Immune Disorders 508

Overview of Immunological Disorders 509

Immediate (Type I) Hypersensitivity 510

Cytotoxic (Type II) Hypersensitivity 514

Immune Complex (Type Iii) Hypersensitivity 518

Cell-Mediated (Type IV) Hypersensitivity 521

Autoimmune Disorders 523

Transplantation 527

Drug Reactions 530

Immunodeficiency Diseases 531

Immunological Tests 540

20 Diseases of the Skin and Eyes; Wounds and Bites 551

The Skin, Mucous Membranes, and Eyes 552

Diseases of the Skin 555

Diseases of the Eyes 569

Wounds and Bites 573

21 Urogenital and Sexually Transmitted Diseases 581

Components of the Urogenital System 582

Urogenital Diseases Usually Not Transmitted Sexually 585

Sexually Transmitted Diseases 591

22 Diseases of the Respiratory System 613

Components of the Respiratory System 614

Diseases of the Upper Respiratory Tract 617

Diseases of the Lower Respiratory Tract 624

23 Oral and Gastrointestinal Diseases 650

Components of the Digestive System 651

Diseases of the Oral Cavity 653

Gastrointestinal Diseases Caused By Bacteria 658

Gastrointestinal Diseases Caused By Other Pathogens 669

24 Cardiovascular, Lymphatic, and Systemic Diseases 690

The Cardiovascular System 691

Cardiovascular and Lymphatic Diseases 692

Systemic Diseases 697

25 Diseases of the Nervous System 727

Components of the Nervous System 728

Diseases of the Brain and Meninges 728

Other Diseases of the Nervous System 737

26 Environmental Microbiology 754

Fundamentals of Ecology 755

Biogeochemical Cycles 755

Air 765

Soil 766

Water 770

Marine Environments 771

Sewage Treatment 778

Bioremediation 780

27 Applied Microbiology 785

Microorganisms Found in Food 786

Preventing Disease Transmission and Food Spoilage 793

Microorganisms as Food and in Food Production 799

Beer, Wine, and Spirits 804

Industrial and Pharmaceutical Microbiology 806

Useful Organic Products 808

Microbiological Mining 811

Microbiological Waste Disposal 812

Appendices

A Metric System Measurements, Conversions, and Math Tools A-1

B Classification of Viruses B-1

C Word Roots Commonly Encountered in Microbiology C-1

D Safety Precautions in the Handling of Clinical Specimens D-1

E Metabolic Pathways E-1

F Diseases and the Organisms That Cause Them*

G Pathogens and the Diseases They Cause*

H parasites*

Glossary G-1

Index I-1