Table of Contents

Chapter 1. Scope and History of Microbiology. Why Study Microbiology? Scope of Microbiology. The Microbes. The Microbiologists. Historical Roots. The Germ Theory of Disease. Early Studies. Pasteur's Further Contributions. Koch's Contributions. Work Toward Controlling Infections. Emergence of Special Fields of Microbiology. Immunology. Virology. Chemotherapy. Genetics and Molecular Biology. Tomorrow's History. Genomics. Retracing Our Steps. /Terminology Check. / Clinical Case Study. / Critical Thinking Questions. / Self-Quiz. / Explorations on the Web. Chapter 2. Fundamentals of Chemistry. Why Study Chemistry? Chemical Building Blocks and Chemical Bonds. Chemical Building Blocks. The Structure of Atoms. Chemical Bonds. Chemical Reactions. Water and Solutions. Water. Solutions and Colloids. Acids, Bases, and pH. Complex Organic Molecules. Carbohydrates. Lipids. Proteins. Nucleotides and Nucleic Acids. Retracing Our Steps /Terminology Check. / Clinical Case Study. / Critical Thinking Questions. / Self-Quiz. / Explorations on the Web. ANIMATIONS: Chemical Bonding,Acids and Bases,Polarity and Solubility,Types of Reactions and Equilibrium. Chapter 3. Microscopy and Staining. Historical Microscopy. Principles of Microscopy. Metric Units. Properties of Light:Wavelength and Resolution. Properties of Light: Light and Objects. Light Microscopy. The Compound Light Microscope. Dark-Field Microscopy. Phase-Contrast Microscopy. Nomarski (Differential Interface Contrast). Microscopy. Fluorescence Microscopy. Confocal Microscopy. Digital Microscopy. Electron Microscopy. Transmission Electron Microscopy. Scanning Electron Microscopy. Scanning Tunneling Microscopy. Techniques of Light Microscopy. Preparation of Specimens for the Light Microscope. Principles of Staining. Retracing Our Steps /Terminology Check / Clinical Case Study / Critical Thinking Questions / Self-Quiz / Explorations on the Web. ANIMATIONS: Staining Bacteria:The Gram Stain. Chapter 4. Characteristics of Prokaryotic. Basic Cell Types. Prokaryotic Cells. Size, Shape, and Arrangement. An Overview of Structure. The Cell Wall. The Cell Membrane. Internal Structure. External Structure. Eukaryotic Cells. An Overview of Structure. The Plasma Membrane. Internal Structure. External Structure. Evolution by Endosymbiosis. The Movement by Substances Across Membranes. Simple Diffusion. Facilitated Diffusion. Osmosis. Active Transport. Endocytosis and Exocytosis. Retracing Our Steps /Terminology Check / Clinical Case Study / Critical Thinking Questions / Self-Quiz / Explorations on the Web. ANIMATIONS: Prokaryotic Cell Structure and Function, Eukaryotic Cell Structure and Function, Simple Diffusion, Mitorsis and Meiosis Compared, Osmosis, Endocytosis and Exocytosis. Chapter 5. Essential Concepts of Metabolism. Metabolism:An Overview. Enzymes. Properties of Enzymes. Properties of Coenzymes and Cofactors. Enzyme Inhibition. Factors That Affect Enzyme Reactions. Anaerobic Metabolism: Glycolysis and Fermentation. Glycolysis. Alternatives to Glycolysis. Fermentation. Aerobic Metabolism: Respiration. The Krebs Cycle. Electron Transport and Oxidative Phosphorylation. The Significance of Energy Capture. The Metabolism of Fats and Proteins. Fat Metabolism. Protein Metabolism. Other Metabolic Processes. Photoautotrophy. Photoheterotrophy. Chemoautotrophy. The Uses of Energy. Biosynthetic Activities. Membrane Transport and Movement. Bioluminescence. Retracing Our Steps /Terminology Check / Clinical Case Study / Critical Thinking Questions / Self-Quiz / Explorations on the Web. ANIMATIONS: Functions of Enzymes and Uses of ATP, Competitive and Noncompetitive Inhibition of Enzymes, Metabolism - The Sum of Catabolism and Anabolism, Cell Respiration, Catabolism of Fats and Proteins,Nonspecific Disease-Resistance Mechanisms. Chapter 6. Growth and Culturing of Bacteria. Growth and Cell Division. Microbial Growth Defined. Cell Division. Phases of Growth. Measuring Bacterial Growth. Factors Affecting Bacterial Growth. Physical Factors. Nutritional Factors. Sporulation. Other Sporelike Bacterial Structures. Culturing Bacteria. Methods of Obtaining Pure Cultures. Culture Media. Methods of Perfoming Multiple Diagnostic Tests. Living, But Nonculturable, Organisms. Retracing Our Steps /Terminology Check / Clinical Case Study / Critical Thinking Questions / Self-Quiz / Explorations on the Web. ANIMATIONS: Binary Fission, Endospore Formation, Budding, and Streak Plate Method. Chapter 7. Microbial Genetics. An Overview of Genetic Processes. The Basis of Heredity. Nucleic Acids in Information Storage and Transfer. DNA Replication. Protein Synthesis. Transcription. Kinds of RNA. Translation. The Regulation of Metabolism. The Significance of Regulatory Mechanisms. Categories of Regulatory Mechanisms. Feedback Inhibition. Enzyme Induction. Enzyme Repression. Mutations. Types of Mutations and Their Effects. Phenotypic Variation. Spontaneous and Induced Mutations. Chemical Mutagens. Radiation as a Mutagen. The Repair of DNA Damage. The Study of Mutations. The Ames Test. Retracing Our Steps /Terminology Check / Clinical Case Study / Critical Thinking Questions / Self-Quiz / Explorations on the Web. ANIMATIONS: Eukaryotic Genes Contain Introns, Polymerase Chain Reaction,DNA Replication in a Prokaryote, Protein Synthesis, End Product Inhibition,Enzyme Induction - the lac Operon, Mutations,Thymine Dimer Repair. Chapter 8. Gene Transfer and Genetic Engineering. The Types and Significance of Gene Transfer. Transformation. The Discovery of Transformation. The Mechanism of Transformation. The Significance of Transfomation. Transduction. The Discovery of Transduction. The Mechanisms of Transduction. The Significance of Transduction. Conjugation. The Discovery of Conjugation. The Mechanisms of Conjugation. The Significance of Conjugation. Gene Transfer Mechanisms Compared. Plasmids. Characteristics of Plasmids. Resistance Plasmids. Transposons. Bacteriocinogens. Genetic Engineering. Genetic Fusion. Protoplast Fusion. Gene Amplification. Recombinant DNA Technology. Hybridomas. Weighing the Risks and Benefits of Recombinant DNA. Retracing Our Steps /Terminology Check / Clinical Case Study / Critical Thinking Questions / Self-Quiz / Explorations on the Web. ANIMATIONS: Gene Transfer - Transformation, Transduction, and Conjugation, Recombinant DNA. Chapter 9. An Introduction to Taxonomy: The Bacteria. Taxonomy:The Science of Classification. Linnaeus, the Father of Taxonomy. Using a Taxonomic Key. Problems in Taxonomy. Developments Since Linnaeus's Time. The Five-Kingdom Classification System. Kingdom Monera. Kingdom Protista. Kingdom Fungi. Kingdom Plantae. Kingdom Animalia. The Three-Domain Classification System. The Evolution of Prokaryotic Organisms. The Tree of Life is Replaced by a Shrub. The Archaea. Classification of Viruses. The Search for Evolutionary Relationships. Special Methods Needed for Prokaryotes. Numerical Taxonomy. Genetic Homology. Other Techniques. The Significance of Findings. Bacterial Taxonomy and Nomenclature. Criteria for Classifying Bacteria. The History and Significance of Bergey's Manual. Problems Associated with Bacterial Taxonomy. Bacterial Nomenclature. Bacteria by Section of Bergey's Manual,First Edition . Bacterial Taxonomy and You. Retracing Our Steps /Terminology Check / Clinical Case Study / Critical Thinking Questions / Self-Quiz / Explorations on the Web. ANIMATIONS: Endosymbiosis,Five-Kingdom System, Shrub of Life, Lateral Gene Transfer, and DNA Hybridization. Chapter 10. Viruses. General Characteristics of Viruses. What Are Viruses? Components of Viruses. Sizes and Shapes. Host Range and Specificity of Viruses. Origins of Viruses. Classification of Viruses. RNA Viruses. DNA Viruses. Emerging Viruses. Viral Replication. General Characteristics of Replication. Replication of Bacteriophages. Lysogeny. Replication of Animal Viruses. Latent Viral Infections. Culturing of Animal Viruses. Development of Culturing Methods. Types of Cell Cultures. Viruses and Teratogenesis. Viruslike Agents: Satellites,Viroids and Prions. Satellites. Delta Hepatitis. Viroids. Prions. Viruses and Cancer. Human Cancer Viruses. How Cancer Viruses Cause Cancer. Oncogenes. Retracing Our Steps/Terminology Check/ Clinical Case Study / Critical Thinking Questions / Self-Quiz / Explorations on the Web. ANIMATIONS: Viruses. Chapter 11. Eukaryotic Microorganisms and Parasites. Principles of Parasitology. The Significance of Parasitism. Parasites in Relation to Their Hosts. Protists. Characteristics of Protists. The Importance of Protists. Classification of Protists. Fungi. Characterictics of Fungi. The Importance of Fungi. Classification of Fungi. Helminths. Characteristics of Helminths. Parasitic Helminths. Arthropods. Characteristics of Arthropods. Classification of Arthropods. Retracing Our Steps /Terminology Check / Clinical Case Study / Critical Thinking Questions / Self-Quiz / Explorations on the Web. Chapter 12. Sterilization and Disinfection. Principles of Sterilization and Disinfection. The Control of Microbial Growth. Chemical Antimicrobial Agents. The Potency of Chemical Agents. Evaluating the Effectiveness of Chemical Agents. Disinfectant Selection. Mechanisms of Action of Chemical Agents. Specific Chemical Antimicrobial Agents. Physical Antimicrobial Agents. Principles and Applications of Heat Killing. Dry Heat, Moist Heat, and Pasteurization. Refrigeration,Freezing, Drying, and Freeze-Drying. Radiation. Sonic and Ultrasonic Waves. Filtration. Osmotic Pressure. Retracing Our Steps /Terminology Check / Clinical Case Study / Critical Thinking Questions / Self-Quiz / Explorations on the Web. Chapter 13. Antimicrobial Therapy. Antimicrobial Chemotherapy. The History of Chemotherapy. General Properties of Antimicrobial Agents. Selective Toxicity. The Spectrum of Activity. Modes of Action. Kinds of Side Effects. The Resistance of Microorganisms. Determining Microbial Sensitivities to Antimicrobial Agents. The Disk Diffusion Method. The Dilution Method. Serum Killing Power. Automated Methods. Attributes of an Ideal Antimicrobial Agent. Antibacterial Agents. Inhibitors of Cell Wall Synthesis. Disrupters of Cell Membranes. Inhibitors of Protein Synthesis. Inhibitors of Nucleic Acid Synthesis. Antimetabolites and Other Antibacterial Agents. Antifungal Agents. Antiviral Agents. Antiprotozoan Agents. Antihelminthic Agents. Special Problems with Drug-Resistant Hospital Infections. Retracing Our Steps Terminology Check / Clinical Case Study / Critical Thinking Questions / Self-Quiz / Explorations on the Web. ANIMATIONS: Effects of Premature Termination of Antibiotic Treatment. Chapter 14. Host-Microbe Relationships and Disease Processes. Host-Microbe Relationships. Symbiosis. Contamination, Infection, and Disease. Pathogens, Pathogenicity, and Virulence. Normal (Indigenous) Microflora. Koch's Postulates. Kinds of Diseases. Infectious and Noninfectious Diseases. Classification of Diseases. Communicable and Noncommunicable Diseases. The Disease Process. How Microbes Cause Disease. Signs, Symptoms, and Syndromes. Types of Infectious Disease. Stages of an Infectious Disease. Infectious Diseases-Past, Present, and Future. Retracing Our Steps/Terminology Check / Clinical Case Study / Critical Thinking Questions / Self-Quiz / Explorations on the Web. Chapter 15. Epidemiology and Nosocomial Infections. Epidemiology. What Is Epidemiology? Diseases in Populations. Epidemiologic Studies. Descriptive Studies. Reservoirs of Infection. Portals of Entry. Portals of Exit. Modes of Disease Transmission. Disease Cycles. Herd Immunity. Controlling Disease Transmission. Public Health Organizations. Notifiable Diseases. Nosocomial Infections. The Epidemiology of Nosocomial Infections. Preventing and Controlling Nosocomial Infections. Bioterrorism. Retracing Our Steps /Terminology Check / Clinical Case Study / Critical Thinking Questions / Self-Quiz / Explorations on the Web. Chapter 16. Innate Host Defenses. Innate and Adaptive Host Defenses. Physical Barriers. Chemical Barriers. Cellular Defenses. Defensive Cells. Phagocytes. The Process of Phagocytosis. Extracellular Killing. The Lymphatic System. Inflammation. Characteristics of Inflammation. The Acute Inflammatory Process. Repair and Regeneration. Chronic Inflammation. Fever. Molecular Defenses. Interferon. Complement. Acute Phase Response. Retracing Our Steps /Terminology Check / Clinical Case Study / Critical Thinking Questions / Self-Quiz / Explorations on the Web. ANIMATIONS: Introduction to Disease Resistance, Nonspecific Disease Resistance Mechanisms. Chapter 17. Immunology I: Basic Principles of Adaptive Immunity and Immunization. Immunology and Immunity. Types of Immunity. Acquired Immunity. Active and Passive Immunity. Characteristics of the Immune System. Antigens and Antibodies. Cells and Tissues of the Immune System. Dual Nature of the Immune System. General Properties of Immune Responses. Humoral Immunity. Properties of Antibodies (Immunoglobulins). Primary and Secondary Responses. Kinds of Antigen-Antibody Reactions. Monoclonal Antibodies. Cell-Mediated Immunity. The Cell-Mediated Immune Reaction. How Killer Cells Kill. The Role of Activated Macrophages. Superantigens. Mucosal Immune System. Factors That Modify Immune Responses. Immunization. Active Immunization. Hazards of Vaccines. Passive Immunization. Future of Immunization. Immunity to Various Kinds of Pathogens. Bacteria. Viruses. Fungi. Protozoa and Helminths. Retracing Our Steps /Terminology Check / Clinical Case Study / Critical Thinking Questions / Self-Quiz / Explorations on the Web. ANIMATIONS: Production of Monoclonal Antibodies. Chapter 18. Immunology II: Immunological Disorders and Tests. Overview of Immunological Disorders. Hypersensitivity. Immunodeficiency. Immediate (Type I) Hypersensitivity. Allergen. Mechanism of Immediate Hypersensitivity. Localized Anaphylaxis. Generalized Anaphylaxis. Genetic Factors in Allergy. Treatment of Allergies. Cytotoxic (Type II) Hypersensitivity. Mechanism of Cytotoxic Reactions. Examples of Cytotoxic Reactions. Immune Complex (Type III) Hypersensitivity. Mechanism of Immune Complex Disorders. Examples of Immune Complex Disorders. Cell-Mediated (Type IV) Hypersensitivity. Mechanism of Cell-Mediated Reactions. Examples of Cell-Mediated Disorders. Autoimmune Disorders. Autoimmunization. Examples of Autoimmune Disorders. Transplantation. Histocompatibility Antigens. Transplant Rejection. Tolerance of Fetus During Pregnancy. Immunosuppression. Drug Reactions. Immunodeficiency Diseases. Primary Immunodeficiency Diseases. Secondary (or Acquired) Immunodeficiency Diseases. Immunological Tests. The Precipitin Test. Agglutination Reactions. Tagged Antibody Tests. Retracing Our Steps /Terminology Check / Clinical Case Study / Critical Thinking Questions / Self-Quiz / Explorations on the Web. ANIMATIONS: Four Types of Hypersenstivity,Antibody Mediated Immunity,Cell Mediated Immunity. Chapter 19. Diseases of the Skin and Eyes: Wounds and Bites. The Skin, Mucous Membranes, and Eyes. The Skin. Mucous Membranes. The Eyes. Normal Microflora of the Skin. Diseases of the Skin. Bacterial Skin Diseases. Viral Skin Diseases. Fungal Skin Diseases. Other Skin Diseases. Diseases of the Eyes. Bacterial Eye Diseases. Viral Eye Diseases. Parasitic Eye Diseases. Wound and Bites. Wound Infections. Other Anaerobic Infections. Anthropod Bites and Diseases. Retracing Our Steps /Terminology Check / Clinical Case Study / Critical Thinking Questions / Self-Quiz / Explorations on the Web. Chapter 20. Urogenital and Sexually Transmitted Diseases. Components of the Urogenital System. The Urinary System. The Female Reproductive System. The Male Reproductive System. Normal Microflora of the Urogenital System. Urogenital Diseases Usually Not Transmitted Sexually. Bacterial Urogenital Diseases. Parasitic Urogenital Diseases. Sexually Transmitted Diseases. Acquired Immune Deficiency Syndrome (AIDS). Bacterial Sexually Transmitted Diseases. Viral Sexually Transmitted Diseases. Retracing Our Steps /Terminology Check / Clinical Case Study / Critical Thinking Questions / Self-Quiz / Explorations on the Web. Chapter 21. Diseases of the Respiratory System. Components of the Respiratory System. The Upper Respiratory Tract. The Lower Respiratory Tract. The Ears. Normal Microflora of the Respiratory System. Diseases of the Upper Repiratory Tract. Bacterial Upper Respiratory Diseases. Viral Upper Respiratory Diseases. Diseases of the Lower Respiratory Tract. Bacterial Lower Respiratory Diseases. Viral Lower Respiratory Diseases. Fungal Respiratory Diseases. Parasitic Respiratory Diseases. Retracing Our Steps/Terminology Check/ Clinical Case Study / Critical Thinking Questions / Self-Quiz / Explorations on the Web. Chapter 22. Oral and Gastrointestinal Diseases. Components of the Digestive System. The Mouth. The Stomach. The Small Intestine. The Large Intestine. Normal Microflora of the Mouth and Digestive System. Diseases of the Oral Cavity. Bacterial Diseases of the Oral Cavity. Viral Diseases of the Oral Cavity. Gastrointestinal Diseases Caused by Bacteria. Bacterial Food Poisoning. Bacterial Enteritis and Enteric Fevers. Bacterial Infections of the Stomach, Esophagus, and Intestines. Bacterial Infections of the Gallbladder and Biliary Tract. Gastrointestinal Diseases Caused by Other Pathogens. Viral Gastrointestinal Diseases. Protozoan Gastrointestinal Diseases. Effects of Fungal Toxins. Helminth Gastrointestinal Diseases. Retracing Our Steps /Terminology Check / Clinical Case Study / Critical Thinking Questions / Self-Quiz / Explorations on the Web. Chapter 23. Cardiovascular, Lymphatic, and Systemic Diseases. The Cardiovascular System. The Heart and Blood Vessels. The Blood. Normal Microflora of the Cardiovascular System. Cardiovascular and Lymphatic Diseases. Bacterial Septicemias and Related Diseases. Helminthic Diseases of the Blood and Lymph. Systemic Diseases. Bacterial Systemic Diseases. Rickettsial and Related Systemic Diseases. Viral Systemic Diseases. Protozoan Systemic Diseases. Retracing Our Steps /Terminology Check/ Clinical Case Study / Critical Thinking Questions / Self-Quiz / Explorations on the Web. Chapter 24. Diseases of the Nervous System. Components of the Nervous System. Normal Microflora of the Nervous System. Diseases of the Brain and Meninges. Bacterial Diseases of the Brain and Meninges. Viral Diseases of the Brain and Meninges. Other Diseases of the Nervous System. Bacterial Nerve Diseases. Viral Nerve Diseases. Prion Diseases of the Nervous System. Parasitic Diseases of the Nervous System. Retracing Our Steps/Terminology Check/ Clinical Case Study/ Critical Thinking Questions / Self-Quiz / Explorations on the Web. Chapter 25. Environmental Microbiology. Fundamentals of Ecology. The Nature of Ecosystems. The Flow of Energy in Ecosystems. Biogeochemical Cycles. The Water Cycle. The Carbon Cycle. The Nitrogen Cycle and Nitrogen Bacteria. The Sulfur Cycle and Sulfur Bacteria. Other Biogeochemical Cycles. The Deep Hot Biosphere. Air. Microorganisms Found in Air. Methods for Controlling Microorganisms in Air. Soil. Components of Soil. Microorganisms in Soil. Soil Pathogens. Caves. Water. Freshwater Environments. Marine Environments. Deep Ocean Vents. Water Pollution. Water Purification. Sewage Treatment. Primary Treatment. Secondary Treatment. Tertiary Treatment. Septic Tanks. Bioremediation. Retracing Our Steps /Terminology Check / Clinical Case Study / Critical Thinking Questions / Self-Quiz / Explorations on the Web. Chapter 26. Applied Microbiology. Microorganisms Found in Food. Grains. Fruits and Vegetables. Meats and Poultry. Fish and Shellfish. Milk. Other Edible Substances. Preventing Disease Transmission and Food Spoilage. Food Preservation. Drying and Lyophilization. Pasteurization of Milk. Standards for Food and Milk Production. Microorganisms as Food and in Food Production. Algae, Fungi, and Bacteria as Food. Food Production. Beer,Wine, and Spirits. Industrial and Pharmaceutical Microbiology. Useful Metabolic Processes. Problems of Industrial Microbiology. Useful Organic Products. Simple Organic Compounds. Antibiotics. Enzymes. Amino Acids. Other Biological Products. Microbiological Mining. Microbiological Waste Disposal. Retracing Our Steps /Terminology Check/ Clinical Case Study / Critical Thinking Questions / Self-Quiz / Explorations on the Web. APPENDICES. Appendix A: Metric System Measurements, Conversions, and Math Tools. Appendix B: Classification of Bacteria and Viruses. Appendix C: Word Roots Commonly Encountered in Microbiology. Appendix D: Safety Precautions in the Handling of Clinical Specimens. Appendix E: Metabolic Pathways. Glossary. Clinical Case Study Answers. Critical Thinking Questions Answers. Self-Quiz Answers. Photo Credits. Index.

About the Author

Jacquelyn Black received her B.A., B.S., and M.S. from the University of Chicago and her Ph.D. from Catholic University of America. She has been teaching microbiology to undergraduates since 1970. She is a member of the American Society for Microbiology, and she has received grants for conducting teacher-training programs. In May of 2000, the Washington Academy of Sciences gave Jackie the Leo Schubert Award for Excellence in Teaching of Science in College. This award is given for exceptional teaching and writing in the field of microbiology, with particular emphasis on the teaching of undergraduate students. In addition to her extensive teaching experience, Dr. Black has engaged in fieldwork and studies throughout the globe. Her travels have taken her from the interior of Iceland to Belgium, Germany, Lappland, China, South America, Portugal, tot he barrier reef of Belize, and most recently to over a dozen universities in Russia. Dr. Black describes herself as an "incorrigible snoop," interested in all the various aspects and applications of microbiology. This natural curiosity, coupled with her classroom and laboratory experience, makes her uniquely qualified to author an introductory microbiology textbook. This book conveys her sense of excitement for microbiology and offers the most current information on developments and applications within this field.