Microbiology: A Systems Approach ISE

Cover
Title
Copyright
Brief Contents
About the Authors
Preface
Note from the Authors
Capturing Students' Attention and Learning
Changes to the Seventh Edition
Table of Contents
CHAPTER 1 The Main Themes of Microbiology
1.1 The Scope of Microbiology
1.2 The Impact of Microbes on Earth: Small Organisms with a Giant Effect
Microbial Involvement in Shaping Our Planet
1.3 Human Use of Microorganisms
1.4 Infectious Diseases and the Human Condition
1.5 The General Characteristics of Microorganisms
Cellular Organization
1.6 The Historical Foundations of Microbiology
The Development of the Microscope: "Seeing Is Believing"
Insight 1.1 MICROBIOME: What Is a Microbiome?
The Establishment of the Scientific Method
Deductive and Inductive Reasoning
The Development of Medical Microbiology
1.7 Naming, Classifying, and Identifying Microorganisms
Nomenclature: Assigning Specific Names
Classification: Constructing Taxonomy
The Origin and Evolution of Microorganisms
A Universal Tree of Life
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CHAPTER 2 The Chemistry of Biology
2.1 Atoms, Bonds, and Molecules: Fundamental Building Blocks
Different Types of Atoms: Elements and Their Properties
The Major Elements of Life and Their Primary Characteristics
Bonds and Molecules
Insight 2.1 MICROBIOME: Thanks to the Sponge, and Its Microbiome, for Letting Us Breathe
The Chemistry of Carbon and Organic Compounds
2.2 Macromolecules: Superstructures of Life
Carbohydrates: Sugars and Polysaccharides
Lipids: Fats, Phospholipids, and Waxes
Proteins: Shapers of Life
The Nucleic Acids: A Cell Computer and Its Programs
2.3 Cells: Where Chemicals Come to Life
Fundamental Characteristics of Cells
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CHAPTER 3 Tools of the Laboratory Methods for the Culturing and Microscopy of Microorganisms
3.1 Methods of Culturing Microorganisms: The Five I's
Inoculation: Producing a Culture
Incubation
Media: Providing Nutrients in the Laboratory
Isolation: Separating One Species from Another
Rounding Out the Five I's: Inspection and Identification
3.2 The Microscope: Window on an Invisible Realm
Microbial Dimensions: How Small Is Small?
Magnification and Microscope Design
Principles of Light Microscopy
Preparing Specimens for Optical Microscopes
Insight 3.1 MICROBIOME: The Microbiome of Leonardo da Vinci's Drawings
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CHAPTER 4 Bacteria and Archaea
4.1 The Bacteria 79
The Structure of a Generalized Bacterial Cell
Bacterial Arrangements and Sizes
Biofilms
4.2 External Structures
Appendages: Cell Extensions
Surface Coatings: The S Layer and the Glycocalyx
4.3 The Cell Envelope: The Boundary Layer of Bacteria
Differences in Cell Envelope Structure
Structure of the Cell Wall
Cytoplasmic Membrane Structure
The Gram-Negative Outer Membrane
The Gram Stain
Practical Considerations of Differences in Cell Envelope Structure
4.4 Bacterial Internal Structure
Contents of the Cell Cytoplasm
Bacterial Endospores: An Extremely Resistant Stage
4.5 The Archaea
4.6 Classification Systems for Bacteria and Archaea
Insight 4.1 MICROBIOME: Archaea in the Human Microbiome
Taxonomic Scheme
Diagnostic Scheme
Species and Subspecies in Bacteria and Archaea
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CHAPTER 5 Eukaryotic Cells and Microorganisms
5.1 Overview of the Eukaryotes
Becoming Eukaryotic
5.2 Form and Function of the Eukaryotic Cell: External and Boundary Structures
Appendages for Movement: Cilia and Flagella
The Glycocalyx
Boundary Structures
5.3 Form and Function of the Eukaryotic Cell: Internal Structures
The Nucleus: The Control Center
Endoplasmic Reticulum: A Passageway in the Cell
Golgi Apparatus: A Packaging Machine
Nucleus, Endoplasmic Reticulum, and Golgi Apparatus: Nature's Assembly Line
Mitochondria: Energy Generators of the Cell
Chloroplasts: Photosynthesis Machines
Ribosomes: Protein Synthesizers
The Cytoskeleton: A Support Network
Survey of Eukaryotic Microorganisms
5.4 The Fungi
Fungal Nutrition
Organization of Microscopic Fungi
Reproductive Strategies and Spore Formation
Fungal Identification and Cultivation
The Effects of Fungi on Humans and the Environment
Insight 5.1 MICROBIOME: Are Eukaryotic Microorganisms Part of Our Microbiome?
5.5 The Protists
The Algae: Photosynthetic Protists
Biology of the Protozoa
Classification of Selected Important Protozoa
Protozoan Identification and Cultivation
Important Protozoan Pathogens
5.6 The Helminths
General Worm Morphology
Life Cycles and Reproduction
A Helminth Cycle: The Pinworm
Helminth Classification and Identification
Distribution and Importance of Parasitic Worms
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CHAPTER 6 Microbial Genetics
6.1 Introduction to Genetics and Genes: Unlocking the Secrets of Heredity
The Nature of the Genetic Material
The DNA Code: A Simple Yet Profound Message
The Significance of DNA Structure
Insight 6.1 MICROBIOME: Customizing the Microbiome
DNA Replication: Preserving the Code and Passing It On
6.2 Transcription and Translation
The Gene–Protein Connection
The Major Participants in Transcription and Translation
Transcription: The First Stage of Gene Expression
Translation: The Second Stage of Gene Expression
Eukaryotic Transcription and Translation: Similar Yet Different
6.3 Genetic Regulation of Protein Synthesis
The Lactose Operon: A Model for Inducible Gene Regulation in Bacteria
A Repressible Operon
Phase Variation
Antibiotics That Affect Transcription and Translation
6.4 DNA Recombination Events
Horizontal Gene Transfer in Bacteria
Pathogenicity Islands: Special "Gifts" of Horizontal Gene Transfer?
6.5 Mutations: Changes in the Genetic Code
Causes of Mutations
Categories of Mutations
Repair of Mutations
The Ames Test
Positive and Negative Effects of Mutations
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CHAPTER 7 Viruses and Prions
7.1 Introduction to Viruses
Insight 7.1 MICROBIOME: Are Viruses Part of the Microbiome?
7.2 The General Structure of Viruses
Size Range
Viral Components: Capsids, Envelopes, and Nucleic Acids
7.3 How Viruses Are Classified and Named
7.4 How Viruses Multiply
Multiplication Cycles in Animal Viruses
Viruses That Infect Bacteria
7.5 Techniques in Cultivating and Identifying Animal Viruses
Using Live Animal Inoculation
Using Bird Embryos
Using Cell (Tissue) Culture Techniques
7.6 Viruses and Human Health
7.7 Prions and Other Noncellular Infectious Agents
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CHAPTER 8 Genetic Analysis and Recombinant DNA Technology
8.1 Tools and Techniques of Recombinant DNA Technology
DNA: The Raw Material
Systems for Cutting, Splicing, Amplifying, and Moving DNA
Recombinant DNA Technology and Gene Cloning
8.2 DNA Analysis
Visualizing DNA
Insight 8.1 MICROBIOME: Host Genetics and the Microbiome
DNA Profiling
Measuring Gene Expression: Microarrays
8.3 Genetic Approaches to Healing Disease
Using the Genome Sequence to Tailor Treatments
Products of Recombinant DNA Technology
Genetically Modified Organisms
Gene Therapy
Small RNAs as Medicine
CAR-T Cell Treatment of Cancer
CRISPR
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CHAPTER 9 Microbial Nutrition and Growth
9.1 Microbial Nutrition
A Chemical Analysis of Microbial Cytoplasm
Sources of Essential Nutrients
How Microbes Feed: Nutritional Types
How Microbes Feed: Nutrient Absorption
The Movement of Molecules: Diffusion and Transport
9.2 Environmental Factors That Influence Microbes
Temperature
Gases
pH
Osmotic Pressure
Radiation, Hydrostatic Pressure, and Moisture
Insight 9.1 MICROBIOME: The Great Oxidation Event and Earth's Microbiome
Other Organisms
9.3 The Study of Microbial Growth
The Basis of Population Growth: Binary Fission
The Rate of Population Growth
The Population Growth Curve
Other Methods of Analyzing Population Growth
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CHAPTER 10 Microbial Metabolism
10.1 The Metabolism of Microbes
Enzymes: Catalyzing the Chemical Reactions of Life
Regulation of Enzymatic Activity and Metabolic Pathways
10.2 Finding and Making Use of Energy
Energy in Cells
A Closer Look at Oxidation and Reduction
Adenosine Triphosphate: Metabolic Money
10.3 Catabolism: Getting Materials and Energy
Overview of Catabolism
Aerobic Respiration
Pyruvic Acid: A Central Metabolite
The Krebs Cycle: A Carbon and Energy Wheel
The Respiratory Chain: Electron Transport and Oxidative Phosphorylation
Summary of Aerobic Respiration
Anaerobic Respiration
Fermentation
Catabolism of Noncarbohydrate Compounds
10.4 Biosynthesis and the Crossing Pathways of Metabolism
The Efficiency of the Cell
Anabolism: Formation of Macromolecules
Assembly of the Cell
10.5 Photosynthesis: It Starts with Light
Insight 10.1 MICROBIOME: Electricity Eaters
Light-Dependent Reaction
Light-Independent Reactions
Other Mechanisms of Photosynthesis
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CHAPTER 11 Physical and Chemical Control of Microbes
11.1 Controlling Microorganisms
General Considerations in Microbial Control
Relative Resistance of Microbial Forms
Methods of Microbial Control
What Is Microbial Death?
How Antimicrobial Agents Work: Their Modes of Action
11.2 Methods of Physical Control
Heat as an Agent of Microbial Control
The Effects of Cold and Desiccation
Radiation as a Microbial Control Agent
Decontamination by Filtration: Techniques for Removing Microbes
Osmotic Pressure
11.3 Methods of Chemical Control
Selecting a Microbicidal Chemical
Factors Affecting the Microbicidal Activity of Chemicals
Germicidal Categories According to Chemical Group
Insight 11.1 MICROBIOME: Hand Hygiene
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CHAPTER 12 Antimicrobial Treatment
12.1 Principles of Antimicrobial Therapy
The Origins of Antimicrobial Drugs
Starting Treatment
Identifying the Infection
Testing to See Which Drug Will Work
Affecting Microbes, Affecting Humans
Mechanisms of Drug Action on Microbes
The Effects of Antimicrobials on Humans
Toxicity to Human Organs
Human Allergic Responses to Drugs
Suppression and Alteration of the Human Microbiota by Antimicrobials
Insight 12.1 MICROBIOME: Do Antibiotics Make Us Fat?
12.2 Survey of Major Antimicrobial Drug Groups
Antibacterial Drugs Targeting the Cell Wall
Antibacterial Drugs Targeting Protein Synthesis (Ribosomes)
Antibacterial Drugs Targeting Folic Acid Synthesis
Antibacterial Drugs Targeting DNA or RNA
Antibacterial Drugs Targeting Cell Membranes
Antibacterial Drugs and Biofilms
Agents to Treat Fungal Infections
Antiprotozoal and Antihelminthic Treatment
Antiviral Agents
12.3 Antimicrobial Resistance
Interactions Between Microbes and Drugs: The Acquisition of Drug Resistance
The Human Role in Antimicrobial Resistance
An Urgent Problem
New Approaches to Antimicrobial Therapy
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CHAPTER 13 Microbe–Human Interactions Health and Disease
13.1 The Human Host and Its Microbiome
Colonization, Infection, Disease—A Continuum
The Human Microbiome Project
Insight 13.1 MICROBIOME: Breast Cancer and the Breast Microbiome
13.2 When Colonization Leads to Disease
Becoming Established: Step One— Portals of Entry
Becoming Established: Step Two—Attaching to the Host and Interacting with the Microbiome
Becoming Established: Step Three—Surviving Host Defenses
Step Four—Causing Disease
Step Five—Vacating the Host: Portals of Exit
Long-Term Infections and Long-Term Effects
The Course of an Infection
Reservoirs: Where Pathogens Persist
The Acquisition and Transmission of Infectious Agents
Which Agent Is the Cause? Using Koch's Postulates to Determine Etiology
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CHAPTER 14 Epidemiology of Infectious Diseases
14.1 Epidemiology Basics and History
Who, What, Where, When, and Why
Public Health and Epidemiology
History of Epidemiology
U.S. Epidemiology in the Last 75 Years
14.2 Units of Measure
Patterns
The Natural History of Diseases
Causality
Insight 14.1 MICROBIOME: Why Does Increased Weight Lead to Cognitive Impairment?
14.3 Infectious Disease Epidemiology
Surveillance and Notifiable Disease
Healthcare-Associated Infections: The Hospital as a Source of Disease
Reproducibility Rate and Case Fatality Rate
Vaccinology
Global Issues in Epidemiology
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CHAPTER 15 Host Defenses I Overview and Innate Immunity
15.1 Defense Mechanisms of the Host: An Overview
Tissues, Organs, and Cells Participating in Immunity
Insight 15.1 MICROBIOME: The Gut Microbiome and Colorectal Cancer
15.2 The First Line of Defense
Physical or Anatomical Barriers at the Body's Surface
Innate Chemical Defenses
15.3 The Second Line of Defense
Phagocytosis: Cornerstone of Inflammation and Adaptive Immunity
Inflammation: A Complex Concert of Reactions to Injury
The Stages of Inflammation
Fever: An Adjunct to Inflammation
Antimicrobial Products
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CHAPTER 16 Host Defenses II Adaptive Immunity and Immunization
16.1 Adaptive Immunity: The Third Line of Defense
A Brief Overview of the Major Immune System Components
Entrance and Presentation of Antigens
Antigen Challenge and Clonal Selection
16.2 Step I: The Development of Lymphocyte Diversity
Specific Events in T-Cell Development
Specific Events in B-Cell Development
Building Immunologic Diversity
Clonal Deletion and Selection
16.3 Step II: Presentation of Antigens
Characteristics of Antigens
Encounters with Antigens
The Role of Antigen Processing and Presentation
16.4 Step III: Antigenic Challenge of T Cells and B Cells
The Activation of T Cells and Their Differentiation into Subsets
The Activation of B Cells: Clonal Expansion and Antibody Production
16.5 Step IV (1): The T-Cell Response
T Helper (TH) Cells
Regulatory T (TR) Cells: Cells That Maintain the Happy Medium
Cytotoxic T (TC) Cells: Cells That Kill Other Cells
Gamma-Delta T Cells
Insight 16.1 MICROBIOME: Cancer and the Microbiome
Additional Cells with Orders to Kill
16.6 Step IV ( 2): The B-Cell Response
The Structure of Immunoglobulins
Antibody-Antigen Interactions and the Function of the Fab
Functions of the Fc Fragment
Accessory Molecules on Immunoglobulins
The Classes of Immunoglobulins
Monitoring Antibody Production over Time: Primary and Secondary Responses to Antigens
16.7 Adaptive Immunity and Vaccination
Artificial Passive Immunization: Immunotherapy
Artificial Active Immunity: Vaccination
COVID-19 Vaccines
Vaccine Technologies in the Pipeline
Route of Administration and Side Effects of Vaccines
Vaccinating: Who and When?
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CHAPTER 17 Disorders in Immunity
17.1 The Immune Response: A Two-Sided Coin
Hypersensitivity: Four Types
17.2 Type I Allergic Reactions: Atopy and Anaphylaxis
Who Is Affected, and How?
Insight 17.1 MICROBIOME: Asthma and the Airway—and Gut—Microbiome
The Nature of Allergens and Their Portals of Entry
Mechanisms of Type I Allergy: Sensitization and Provocation
Cytokines, Target Organs, and Allergic Symptoms
IgE- and Mast-Cell-Mediated Allergic Conditions
Diagnosis of Allergy
Treatment of Allergy
17.3 Type II Hypersensitivities: Reactions That Lyse Cells
The Basis of Human ABO Antigens and Blood Types
Antibodies Against A and B Antigens
The Rh Factor and Its Clinical Importance
Other RBC Antigens
17.4 Type III Hypersensitivities: Immune Complex Reactions
Mechanisms of Immune Complex Disease
Types of Immune Complex Disease
17.5 Type IV Hypersensitivities: Cell-Mediated (Delayed) Reactions
Delayed Hypersensitivity to Microbes
Contact Dermatitis
T Cells and Their Role in Organ Transplantation
17.6 An Inappropriate Response Against Self: Autoimmunity
Possible Causes of Autoimmune Disease
The Origins of Autoimmune Disease
Examples of Autoimmune Disease
17.7 Immunodeficiency Diseases: Hyposensitivities
Primary Immunodeficiency Diseases
Secondary Immunodeficiency Diseases
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CHAPTER 18 Diagnosing Infections
18.1 Preparation for the Survey of Microbial Diseases
Phenotypic Methods
Immunologic Methods
Genotypic Methods
Special Case: Bloodstream Infections
18.2 First Steps: Specimen Collection
Insight 18.1 MICROBIOME: The Human Microbiome Project and Diagnosis of Infection
Overview of Laboratory Techniques
18.3 Phenotypic Methods
Immediate Direct Examination of Specimen
Methods Requiring Growth
Determining Clinical Significance of Cultures
18.4 Immunologic Methods
Different Kinds of Antigen-Antibody Interactions
Complement Fixation Test
In Vivo Testing
General Features of Immune Testing
18.5 Genotypic Methods
Polymerase Chain Reaction (PCR): The Backbone of New Diagnostics
Hybridization: Probing for Identity
Whole-Genome Sequencing
Special Case: Bloodstream Infections
18.6 Additional Diagnostic Technologies
Microarrays
Lab on a Chip
Mass Spectrometry
Imaging
Special Case: Bloodstream Infections
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CHAPTER 19 Infectious Diseases Manifesting on the Skin and Eyes
19.1 The Skin and Its Defenses
Normal Biota of the Skin
Insight 19.1 MICROBIOME: C-Section Babies vs. Vaginally Delivered Babies
19.2 Infectious Diseases Manifesting on the Skin
19.3 The Surface of the Eye, Its Defenses, and Normal Biota
Normal Biota of the Eye
19.4 Infectious Diseases Manifesting in the Eye
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CHAPTER 20 Infectious Diseases Manifesting in the Nervous System
20.1 The Nervous System, Its Defenses, and Normal Biota
20.2 Infectious Diseases Manifesting in the Nervous System
Insight 20.1 MICROBIOME: Mysterious Polio-Like Disease
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CHAPTER 21 Infectious Diseases Manifesting in the Cardiovascular and Lymphatic Systems
21.1 The Cardiovascular and Lymphatic Systems, Their Defenses, and Normal Biota
The Cardiovascular System
The Lymphatic System
Defenses of the Cardiovascular and Lymphatic Systems
Normal Biota of the Cardiovascular and Lymphatic Systems
21.2 Infectious Diseases Manifesting in the Cardiovascular and Lymphatic Systems
Insight 21.1 MICROBIOME: Gut Microbiome and High Blood Pressure
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CHAPTER 22 Infectious Diseases Manifesting in the Respiratory System
22.1 The Respiratory Tract, Its Defenses, and Normal Biota
Insight 22.1 MICROBIOME: The Lungs Are Not Sterile
22.2 Infectious Diseases Manifesting in the Upper Respiratory Tracts
22.3 Infectious Diseases Manifesting in Both the Upper and Lower Respiratory Tracts
22.4 Infectious Diseases Manifesting in the Lower Respiratory Tract
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CHAPTER 23 Infectious Diseases Manifesting in the Gastrointestinal Tract
23.1 The Gastrointestinal Tract, Its Defenses, and Normal Biota
Insight 23.1 MICROBIOME: Crohn's Disease and the Gut Microbiome
23.2 Infectious Diseases Manifesting in the Gastrointestinal Tract ( Nonhelminthic)
23.3 Helminthic Diseases Manifesting in the Gastrointestinal Tract
General Clinical Considerations
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CHAPTER 24 Infectious Diseases Manifesting in the Genitourinary System
24.1 The Genitourinary Tract, Its Defenses, and Normal Biota
Normal Biota of the Genitourinary Tract
Insight 24.1 MICROBIOME: Save the World with the Vaginal Microbiome
24.2 Infectious Diseases Manifesting in the Urinary Tract
24.3 Infectious Diseases Manifesting in the Reproductive Tract
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CHAPTER 25 Microbes in Our Environment and the Concept of One Health
25.1 Microbial Ecology and Element Cycling
Carbon and Nitrogen Cycling
The Carbon Cycle
The Nitrogen Cycle
25.2 Microbes on Land and in Water
Environmental Sampling in the Genomic Era
Soil Microbiology
Deep Subsurface Microbiology
Aquatic Microbiology
25.3 Applied Microbiology and Biotechnology
Microorganisms in Water and Wastewater Treatment
Insight 25.1 MICROBIOME: Bioremediation
Microorganisms Making Food and Drink
25.4 The Concept of "One Health"
How Infectious Diseases Move into New Populations, and New Species
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APPENDIX A: Answers to Multiple-Choice Questions in SmartGrid
APPENDIX B: Exponents
APPENDIX C: An Introduction to Concept Mapping
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