Microbiology: An Introduction, Global Edition

Cover
Brief Contents
Title Page
Copyright Page
About the Authors
Digital Authors
Preface
Acknowledgments
Contents
Features
ASM Recommended Curriculum Guidelinesfor Undergraduate Microbiology
PART ONE Fundamentals of Microbiology
	1 The Microbial World and You
		Microbes in Our Lives
			The Microbiome
		Naming and Classifying Microorganisms
			Nomenclature
			Types of Microorganisms
			Classification of Microorganisms
		A Brief History of Microbiology
			The First Observations
			The Debate over Spontaneous Generation
			The First Golden Age of Microbiology
			The Second Golden Age of Microbiology
			The Third Golden Age of Microbiology
		Microbes and Human Welfare
			Recycling Vital Elements
			Sewage Treatment: Using Microbes to Recycle Water
			Bioremediation: Using Microbes to Clean Up Pollutants
			Insect Pest Control by Microorganisms
			Biotechnology and Recombinant DNA Technology
		Microbes and Human Disease
			Biofilms
			Infectious Diseases
			Emerging Infectious Diseases
		Study Outline
		Study Questions
	2 Chemical Principles
		The Structure of Atoms
			Chemical Elements
			Electronic Configurations
		How Atoms Form Molecules: Chemical Bonds
			Ionic Bonds
			Covalent Bonds
			Hydrogen Bonds
			Molecular Mass and Moles
		Chemical Reactions
			Energy in Chemical Reactions
			Synthesis Reactions
			Decomposition Reactions
			Exchange Reactions
			The Reversibility of Chemical Reactions
		IMPORTANT BIOLOGICAL MOLECULES
		Inorganic Compounds
			Water
			Acids, Bases, and Salts
			Acid–Base Balance: The Concept of pH
		Organic Compounds
			Structure and Chemistry
			Carbohydrates
			Lipids
			Proteins
			Nucleic Acids
			Adenosine Triphosphate (ATP)
		Study Outline
		Study Questions
	3 Observing Microorganisms Through a Microscope
		Units of Measurement
		Microscopy: The Instruments
			Light Microscopy
			Two-Photon Microscopy
			Super-Resolution Light Microscopy
			Scanning Acoustic Microscopy
			Electron Microscopy
			Scanned-Probe Microscopy
		Preparation of Specimens for Light Microscopy
			Preparing Smears for Staining
			Simple Stains
			Differential Stains
			Special Stains
		Study Outline
		Study Questions
	4 Functional Anatomy of Prokaryotic and Eukaryotic Cells
		Comparing Prokaryotic and Eukaryotic Cells: An Overview
		THE PROKARYOTIC CELL
		The Size, Shape, and Arrangement of Bacterial Cells
		Structures External to the Cell Wall
			Glycocalyx
			Flagella and Archaella
			Axial Filaments
			Fimbriae and Pili
		The Cell Wall
			Composition and Characteristics
			Cell Walls and the Gram Stain Mechanism
			Atypical Cell Walls
			Damage to the Cell Wall
		Structures Internal to the Cell Wall
			The Plasma (Cytoplasmic) Membrane
			The Movement of Materials across Membranes
			Cytoplasm
			The Nucleoid
			Ribosomes
			Inclusions
			Endospores
		THE EUKARYOTIC CELL
		Flagella and Cilia
		The Cell Wall and Glycocalyx
		The Plasma (Cytoplasmic) Membrane
		Cytoplasm
		Ribosomes
		Organelles
			The Nucleus
			Endoplasmic Reticulum
			Golgi Complex
			Lysosomes
			Vacuoles
			Mitochondria
			Chloroplasts
			Peroxisomes
			Centrosome
		The Evolution of Eukaryotes
		Study Outline
		Study Questions
	5 Microbial Metabolism
		Catabolic and Anabolic Reactions
		Enzymes
			Collision Theory
			Enzymes and Chemical Reactions
			Enzyme Specificity and Efficiency
			Naming Enzymes
			Enzyme Components
			Factors Influencing Enzymatic Activity
			Feedback Inhibition
			Ribozymes
		Energy Production
			Oxidation-Reduction Reactions
			The Generation of ATP
			Metabolic Pathways of Energy Production
		Carbohydrate Catabolism
			Glycolysis
			Additional Pathways to Glycolysis
			Cellular Respiration
			Fermentation
		Lipid and Protein Catabolism
		Biochemical Tests and Bacterial Identification
		Photosynthesis
			The Light-Dependent Reactions: Photophosphorylation
			The Light-Independent Reactions: The Calvin-Benson Cycle
		A Summary of Energy Production Mechanisms
		Metabolic Diversity among Organisms
			Photoautotrophs
			Photoheterotrophs
			Chemoautotrophs
			Chemoheterotrophs
		Metabolic Pathways of Energy Use
			Polysaccharide Biosynthesis
			Lipid Biosynthesis
			Amino Acid and Protein Biosynthesis
			Purine and Pyrimidine Biosynthesis
		The Integration of Metabolism
		Study Outline
		Study Questions
	6 Microbial Growth
		The Requirements for Growth
			Physical Requirements
			Chemical Requirements
		Biofilms
		Culture Media
			Chemically Defined Media
			Complex Media
			Anaerobic Growth Media and Methods
			Special Culture Techniques
			Selective and Differential Media
			Enrichment Culture
		Obtaining Pure Cultures
		Preserving Bacterial Cultures
		The Growth of Bacterial Cultures
			Bacterial Division
			Generation Time
			Logarithmic Representation of Bacterial Populations
			Phases of Growth
			Direct Measurement of Microbial Growth
			Estimating Bacterial Numbers by Indirect Methods
		Study Outline
		Study Questions
	7 The Control of Microbial Growth
		The Terminology of Microbial Control
		The Rate of Microbial Death
		Actions of Microbial Control Agents
			Alteration of Membrane Permeability
			Damage to Proteins and Nucleic Acids
		Physical Methods of Microbial Control
			Heat
			Filtration
			Low Temperatures
			High Pressure
			Desiccation
			Osmotic Pressure
			Radiation
		Chemical Methods of Microbial Control
			Principles of Effective Disinfection
			Evaluating a Disinfectant
			Types of Disinfectants
		Microbial Characteristics and Microbial Control
		Study Outline
		Study Questions
	8 Microbial Genetics
		Structure and Function of the Genetic Material
			Genotype and Phenotype
			DNA and Chromosomes
			The Flow of Genetic Information
			DNA Replication
			RNA and Protein Synthesis
		The Regulation of Bacterial Gene Expression
			Pre-transcriptional Control
			Post-transcriptional Control
		Changes in Genetic Material
			Mutation
			Types of Mutations
			Mutagens
			The Frequency of Mutation
			Identifying Mutants
			Identifying Chemical Carcinogens
		Genetic Transfer and Recombination
			Plasmids and Transposons
			Transformation in Bacteria
			Conjugation in Bacteria
			Transduction in Bacteria
		Genes and Evolution
		Study Outline
		Study Questions
	9 Biotechnology and DNA Technology
		Introduction to Biotechnology
			Recombinant DNA Technology
			An Overview of Recombinant DNA Procedures
		Tools of Biotechnology
			Selection
			Mutation
			Restriction Enzymes
			Vectors
			Polymerase Chain Reaction
		Techniques of Genetic Modification
			Inserting Foreign DNA into Cells
			Obtaining DNA
			Selecting a Clone
			Making a Gene Product
		Applications of DNA Technology
			Therapeutic Applications
			Genome Projects
			Scientific Applications
			Agricultural Applications
		Safety Issues and the Ethics of Using DNA Technology
		Study Outline
		Study Questions
PART TWO A Survey of the Microbial World
	10 Classification of Microorganisms
		The Study of Phylogenetic Relationships
			The Three Domains
			A Phylogenetic Tree
		Classification of Organisms
			Scientific Nomenclature
			The Taxonomic Hierarchy
			Classification of Prokaryotes
			Classification of Eukaryotes
			Classification of Viruses
		Methods of Classifying and Identifying Microorganisms
			Morphological Characteristics
			Differential Staining
			Biochemical Tests
			Serology
			Phage Typing
			Fatty Acid Profiles
			Flow Cytometry
			DNA Sequencing
			DNA Fingerprinting
			Nucleic Acid Hybridization
			Putting Classification Methods Together
		Study Outline
		Study Questions
	11 The Prokaryotes: Domains Bacteria and Archaea
		The Prokaryotic Groups
		DOMAIN BACTERIA
		Gram-Negative Bacteria
			Proteobacteria
			The Nonproteobacteria Gram-Negative Bacteria
		The Gram-Positive Bacteria
			Firmicutes (Low G + C Gram-Positive Bacteria)
			Tenericutes
			Actinobacteria (High G + C Gram-Positive Bacteria)
		DOMAIN ARCHAEA
		Diversity within the Archaea
		MICROBIAL DIVERSITY
		Discoveries Illustrating the Range of Diversity
		Study Outline
		Study Questions
	12 The Eukaryotes: Fungi, Algae, Protozoa, and Helminths
		Fungi
			Characteristics of Fungi
			Medically Important Fungi
			Fungal Diseases
			Economic Effects of Fungi
		Lichens
		Algae
			Characteristics of Algae
			Selected Phyla of Algae
			Roles of Algae in Nature
		Protozoa
			Characteristics of Protozoa
			Medically Important Protozoa
		Slime Molds
		Helminths
			Characteristics of Helminths
			Platyhelminths
			Nematodes
		Arthropods as Vectors
		Study Outline
		Study Questions
	13 Viruses, Viroids, and Prions
		General Characteristics of Viruses
			Host Range
			Viral Size
		Viral Structure
			Nucleic Acid
			Capsid and Envelope
			General Morphology
		Taxonomy of Viruses
		Isolation, Cultivation, and Identification of Viruses
			Growing Bacteriophages in the Laboratory
			Growing Animal Viruses in the Laboratory
			Viral Identification
		Viral Multiplication
			Multiplication of Bacteriophages
			Multiplication of Animal Viruses
		Viruses and Cancer
			The Transformation of Normal Cells into Tumor Cells
			DNA Oncogenic Viruses
			RNA Oncogenic Viruses
			Viruses to Treat Cancer
		Latent Viral Infections
		Persistent Viral Infections
		Plant Viruses and Viroids
		Prions
		Study Outline
		Study Questions
PART THREE Interaction between Microbe and Host
	14 Principles of Disease and Epidemiology
		Pathology, Infection, and Disease
		Human Microbiome
			Relationships between the Normal Microbiota and the Host
			Opportunistic Microorganisms
			Cooperation among Microorganisms
		The Etiology of Infectious Diseases
			Koch’s Postulates
			Exceptions to Koch's Postulates
		Classifying Infectious Diseases
			Occurrence of a Disease
			Severity or Duration of a Disease
			Extent of Host Involvement
		Patterns of Disease
			Predisposing Factors
			Development of Disease
		The Spread of Infection
			Reservoirs of Infection
			Transmission of Disease
		Healthcare-Associated Infections (HAIs)
			Microorganisms in the Hospital
			Compromised Host
			Chain of Transmission
			Control of Healthcare-Associated Infections
		Emerging Infectious Diseases
		Epidemiology
			Descriptive Epidemiology
			Analytical Epidemiology
			Experimental Epidemiology
			Case Reporting
			The Centers for Disease Control and Prevention (CDC)
		Study Outline
		Study Questions
	15 Microbial Mechanisms of Pathogenicity
		How Microorganisms Enter a Host
			Portals of Entry
			The Preferred Portal of Entry
			Numbers of Invading Microbes
			Adherence
		How Bacterial Pathogens Penetrate Host Defenses
			Capsules
			Cell Wall Components
			Enzymes
			Antigenic Variation
			Penetration into the Host
			Biofilms
		How Bacterial Pathogens Damage Host Cells
			Using the Host’s Nutrients: Siderophores
			Direct Damage
			Production of Toxins
			Plasmids, Lysogeny, and Pathogenicity
		Pathogenic Properties of Viruses
			Viral Mechanisms for Evading Host Defenses
			Cytopathic Effects of Viruses
		Pathogenic Properties of Fungi, Protozoa, Helminths, and Algae
			Fungi
			Protozoa
			Helminths
			Algae
		Portals of Exit
		Study Outline
		Study Questions
	16 Innate Immunity: Nonspecific Defenses of the Host
		The Concept of Immunity
		FIRST LINE OF DEFENSE: SKIN AND MUCOUS MEMBRANES
		Physical Factors
		Chemical Factors
		Normal Microbiota and Innate Immunity
		SECOND LINE OF DEFENSE
		Formed Elements in Blood
		The Lymphatic System
		Phagocytes
			Actions of Phagocytic Cells
			The Mechanism of Phagocytosis
		Inflammation
			Vasodilation and Increased Permeability of Blood Vessels
			Phagocyte Migration and Phagocytosis
			Tissue Repair
		Fever
		Antimicrobial Substances
			The Complement System
			Interferons
			Iron-Binding Proteins
			Antimicrobial Peptides
			Other Factors
		Study Outline
		Study Questions
	17 Adaptive Immunity: Specific Defenses of the Host
		The Adaptive Immune System
		Dual Nature of the Adaptive Immune System
			Overview of Humoral Immunity
			Overview of Cellular Immunity
		Cytokines: Chemical Messengers of Immune Cells
		Antigens and Antibodies
			Antigens
			Humoral Immunity: Antibodies
		Humoral Immunity Response Process
			Activation and Clonal Expansion of Antibody-Producing Cells
			The Diversity of Antibodies
		Results of the Antigen–Antibody Interaction
		Cellular Immunity Response Process
			Antigen-Presenting Cells (APCs)
			Classes of T Cells
		Nonspecific Cells and Extracellular Killing by the Adaptive Immune System
		Immunological Memory
		Types of Adaptive Immunity
		Study Outline
		Study Questions
	18 Practical Applications of Immunology
		Vaccines
			Principles and Effects of Vaccination
			Types of Vaccines and Their Characteristics
			Vaccine Production, Delivery Methods, and Formulations
		Diagnostic Immunology
			Use of Monoclonal Antibodies
			Precipitation Reactions
			Agglutination Reactions
			Neutralization Reactions
			Complement-Fixation Reactions
			Fluorescent-Antibody Techniques
			Enzyme-Linked Immunosorbent Assay (ELISA)
			Western Blotting (Immunoblotting)
			The Future of Diagnostic and Therapeutic Immunology
		Study Outline
		Study Questions
	19 Disorders Associated with the Immune System
		Hypersensitivity
			Allergies and the Microbiome
			Type I (Anaphylactic) Reactions
			Type II (Cytotoxic) Reactions
			Type III (Immune Complex) Reactions
			Type IV (Delayed Cell-Mediated) Reactions
		Autoimmune Diseases
			Cytotoxic Autoimmune Reactions
			Immune Complex Autoimmune Reactions
			Cell-Mediated Autoimmune Reactions
		Reactions to Transplantation
			Immunosuppression to Prevent Transplant Rejection
		The Immune System and Cancer
			Immunotherapy for Cancer
		Immunodeficiencies
			Congenital Immunodeficiencies
			Acquired Immunodeficiencies
		Acquired Immunodeficiency Syndrome (AIDS)
			The Origin of AIDS
			HIV Infection
			Diagnostic Methods
			HIV Transmission
			AIDS Worldwide
			Preventing and Treating AIDS
		Study Outline
		Study Questions
	20 Antimicrobial Drugs
		The History of Chemotherapy
			Antibiotic Use and Discovery Today
		Spectrum of Antimicrobial Activity
		The Action of Antimicrobial Drugs
			Inhibiting Cell Wall Synthesis
			Inhibiting Protein Synthesis
			Injuring the Plasma Membrane
			Inhibiting Nucleic Acid Synthesis
			Inhibiting the Synthesis of Essential Metabolites
		Common Antimicrobial Drugs
			Antibacterial Antibiotics: Inhibitors of Cell Wall Synthesis
			Inhibitors of Protein Synthesis
			Injury to Membranes
			Nucleic Acid Synthesis Inhibitors
			Competitive Inhibition of Essential Metabolites
			Antifungal Drugs
			Antiviral Drugs
			Antiprotozoan and Antihelminthic Drugs
		Tests to Guide Chemotherapy
			The Diffusion Methods
			Broth Dilution Tests
		Resistance to Antimicrobial Drugs
			Mechanisms of Resistance
			Antibiotic Misuse
			Cost and Prevention of Resistance
		Antibiotic Safety
		Effects of Combinations of Drugs
		Future of Chemotherapeutic Agents
		Study Outline
		Study Questions
PART FOUR Microorganisms and Human Disease
	21 Microbial Diseases of the Skin and Eyes
		Structure and Function of the Skin
			Mucous Membranes
		Normal Microbiota of the Skin
		Microbial Diseases of the Skin
			Bacterial Diseases of the Skin
			Viral Diseases of the Skin
			Fungal Diseases of the Skin and Nails
			Parasitic Infestation of the Skin
		Microbial Diseases of the Eye
			Inflammation of the Eye Membranes: Conjunctivitis
			Bacterial Diseases of the Eye
			Other Infectious Diseases of the Eye
		Study Outline
		Study Questions
	22 Microbial Diseases of the Nervous System
		Structure and Function of the Nervous System
		Bacterial Diseases of the Nervous System
			Bacterial Meningitis
			Tetanus
			Botulism
			Leprosy
		Viral Diseases of the Nervous System
			Poliomyelitis
			Rabies
			Arboviral Encephalitis
		Fungal Disease of the Nervous System
			Cryptococcus neoformans Meningitis (Cryptococcosis)
		Protozoan Diseases of the Nervous System
			African Trypanosomiasis
			Amebic Meningoencephalitis
		Nervous System Diseases Caused by Prions
			Bovine Spongiform Encephalopathy and Variant Creutzfeldt-Jakob Disease
		Diseases Caused by Unidentified Agents
		Study Outline
		Study Questions
	23 Microbial Diseases of the Cardiovascular and Lymphatic Systems
		Structure and Function of the Cardiovascular and Lymphatic Systems
		Bacterial Diseases of the Cardiovascular and Lymphatic Systems
			Sepsis and Septic Shock
			Bacterial Infections of the Heart
			Rheumatic Fever
			Tularemia
			Brucellosis (Undulant Fever)
			Anthrax
			Gangrene
			Systemic Diseases Caused by Bites and Scratches
			Vector-Transmitted Diseases
		Viral Diseases of the Cardiovascular and Lymphatic Systems
			Burkitt’s Lymphoma
			Infectious Mononucleosis
			Other Diseases and Epstein-Barr Virus
			Cytomegalovirus Infections
			Chikungunya
			Classic Viral Hemorrhagic Fevers
			Emerging Viral Hemorrhagic Fevers
		Protozoan Diseases of the Cardiovascular and Lymphatic Systems
			Chagas Disease (American Trypanosomiasis)
			Toxoplasmosis
			Malaria
			Leishmaniasis
			Babesiosis
		Helminthic Disease of the Cardiovascular and Lymphatic Systems
			Schistosomiasis
		Disease of Unknown Etiology
			Kawasaki Syndrome
		Study Outline
		Study Questions
	24 Microbial Diseases of the Respiratory System
		Structure and Function of the Respiratory System
		Normal Microbiota of the Respiratory System
		MICROBIAL DISEASES OF THE UPPER RESPIRATORY SYSTEM
		Bacterial Diseases of the Upper Respiratory System
			Streptococcal Pharyngitis (Strep Throat)
			Scarlet Fever
			Diphtheria
			Otitis Media
		Viral Disease of the Upper Respiratory System
			The Common Cold
		MICROBIAL DISEASES OF THE LOWER RESPIRATORY SYSTEM
		Bacterial Diseases of the Lower Respiratory System
			Pertussis (Whooping Cough)
			Tuberculosis
			Bacterial Pneumonias
			Melioidosis
		Viral Diseases of the Lower Respiratory System
			Viral Pneumonia
			Respiratory Syncytial Virus (RSV)
			Influenza (Flu)
		Fungal Diseases of the Lower Respiratory System
			Histoplasmosis
			Coccidioidomycosis
			Pneumocystis Pneumonia
			Blastomycosis (North American Blastomycosis)
			Other Fungi Involved in Respiratory Disease
		Study Outline
		Study Questions
	25 Microbial Diseases of the Digestive System
		Structure and Function of the Digestive System
		Normal Microbiota of the Digestive System
		Bacterial Diseases of the Mouth
			Dental Caries (Tooth Decay)
			Periodontal Disease
		Bacterial Diseases of the Lower Digestive System
			Staphylococcal Food Poisoning (Staphylococcal Enterotoxicosis)
			Shigellosis (Bacillary Dysentery)
			Salmonellosis (Salmonella Gastroenteritis)
			Typhoid Fever
			Cholera
			Noncholera Vibrios
			Escherichia coli Gastroenteritis
			Campylobacteriosis (Campylobacter Gastroenteritis)
			Helicobacter Peptic Ulcer Disease
			Yersinia Gastroenteritis
			Clostridium perfringens Gastroenteritis
			Clostridium difficile–Associated Diarrhea
			Bacillus cereus Gastroenteritis
		Viral Diseases of the Digestive System
			Mumps
			Hepatitis
			Viral Gastroenteritis
		Fungal Diseases of the Digestive System
		Protozoan Diseases of the Digestive System
			Giardiasis
			Cryptosporidiosis
			Cyclosporiasis
			Amebic Dysentery (Amebiasis)
		Helminthic Diseases of the Digestive System
			Tapeworms
			Hydatid Disease
			Nematodes
		Study Outline
		Study Questions
	26 Microbial Diseases of the Urinary and Reproductive Systems
		Structure and Function of the Urinary System
		Structure and Function of the Reproductive Systems
		Normal Microbiota of the Urinary and Reproductive Systems
		DISEASES OF THE URINARY SYSTEM
		Bacterial Diseases of the Urinary System
			Cystitis
			Pyelonephritis
			Leptospirosis
		DISEASES OF THE REPRODUCTIVE SYSTEMS
		Bacterial Diseases of the Reproductive Systems
			Gonorrhea
			Nongonococcal Urethritis (NGU)
			Pelvic Inflammatory Disease (PID)
			Syphilis
			Lymphogranuloma Venereum (LGV)
			Chancroid (Soft Chancre)
			Bacterial Vaginosis
		Viral Diseases of the Reproductive Systems
			Genital Herpes
			Genital Warts
			AIDS
		Fungal Disease of the Reproductive Systems
			Candidiasis
		Protozoan Disease of the Reproductive Systems
			Trichomoniasis
		Study Outline
		Study Questions
PART FIVE Environmental and Applied Microbiology
	27 Environmental Microbiology
		Microbial Diversity and Habitats
			Symbiosis
		Soil Microbiology and Biogeochemical Cycles
			The Carbon Cycle
			The Nitrogen Cycle
			The Sulfur Cycle
			Life without Sunshine
			The Phosphorus Cycle
			The Degradation of Synthetic Chemicals in Soil and Water
		Aquatic Microbiology and Sewage Treatment
			Aquatic Microorganisms
			The Role of Microorganisms in Water Quality
			Water Treatment
			Sewage (Wastewater) Treatment
		Study Outline
		Study Questions
	28 Applied and Industrial Microbiology
		Food Microbiology
			Foods and Disease
			Industrial Food Canning
			Aseptic Packaging
			Radiation and Industrial Food Preservation
			High-Pressure Food Preservation
			The Role of Microorganisms in Food Production
		Industrial Microbiology and Biotechnology
			Fermentation Technology
			Industrial Products
			Alternative Energy Sources Using Microorganisms
			Biofuels
			Industrial Microbiology and the Future
		Study Outline
		Study Questions
Answers to Knowledge and Comprehension Study Questions
Appendix A Metabolic Pathways
Appendix B Exponents, Exponential Notation, Logarithms, and Generation Time
Appendix C Methods for Taking Clinical Samples
Appendix D Pronunciation Rules and Word Roots
Appendix E Classification of Prokaryotes According to Bergey’s Manual
Glossary
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Credits
Trademark Attributions
Index
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