ISE Microbiology: A Systems Approach

Cover
Title
Copyright
Brief Contents
About the Authors
Preface
Acknowledgments
Table of Contents
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
INSIGHT 1.1: CLINICAL: Infections of the Heroin Epidemic
1.5 The General Characteristics of Microorganisms
Cellular Organization
1.6 The Historical Foundations of Microbiology
The Development of the Microscope: " Seeing Is Believing"
The Establishment of the Scientific Method
Deductive and Inductive Reasoning
INSIGHT 1.2: MICROBIOME: What Is
a Microbiome?
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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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
INSIGHT 2.2: CLINICAL: Acidic Blood in Diabetes
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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3 Tools of the Laboratory Methods for the Culturing and Microscopic Analysis 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
INSIGHT 3.1: CLINICAL: A New Human Organ?
Preparing Specimens for Optical Microscopes
INSIGHT 3.2: MICROBIOME: Diabetic Wounds and Their Microbiome as Seen by Microscopy
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4 Bacteria and Archaea
4.1 The Bacteria
The Structure of a Generalized Bacterial Cell
Bacterial Arrangements and Sizes
INSIGHT 4.1: CLINICAL: Biofilms Complicate Infections
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 4.2: MICROBIOME: Archaea in the Human Microbiome
Taxonomic Scheme
Diagnostic Scheme
Species and Subspecies in Bacteria and Archaea
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5 Eukaryotic Cells and Microorganisms
5.1 Overview of the Eukaryotes
Becoming Eukaryotic
5.2 Form and Function of the Eukaryotic Cell: External Structures 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
INSIGHT 5.2: CLINICAL: Eukaryotic Pathogens: Neglected Parasitic Infections
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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6 Viruses and Prions
6.1 The Search for the Elusive Viruses
6.2 The Position of Viruses in the Biological Spectrum
6.3 The General Structure of Viruses Size Range
Viral Components: Capsids, Envelopes, and Nucleic Acids
INSIGHT 6.1: MICROBIOME: Are Viruses Part of the Microbiome?
6.4 How Viruses Are Classified and Named
6.5 Modes of Viral Multiplication
Multiplication Cycles in Animal Viruses
Viruses That Infect Bacteria
INSIGHT 6.2: CLINICAL: Phage Therapy in Cystic Fibrosis
6.6 Techniques in Cultivating and Identifying Animal Viruses
Using Live Animal Inoculation
Using Bird Embryos
Using Cell ( Tissue) Culture Techniques
6.7 Viruses and Human Health
6.8 Prions and Other Noncellular Infectious Agents
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7 Microbial Nutrition and Growth
7.1 Microbial Nutrition
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
The Movement of Water: Osmosis
Active Transport: Bringing in Molecules Against a Gradient
7.2 Environmental Factors That Influence Microbes
Temperature
INSIGHT 7.1: CLINICAL: Inducing Fever to Treat Infections
Gases
pH
Osmotic Pressure
Radiation and Hydrostatic Pressure and Moisture
INSIGHT 7.2: MICROBIOME: The Great Oxidation Event and Earth’s Microbiome
Other Organisms
7.3 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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8 Microbial Metabolism
8.1 The Metabolism of Microbes
Enzymes: Catalyzing the Chemical Reactions of Life
Regulation of Enzymatic Activity and Metabolic Pathways
8.2 The Pursuit and Utilization of Energy
Energy in Cells
A Closer Look at Oxidation and Reduction
Adenosine Triphosphate: Metabolic Money
8.3 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
INSIGHT 8.1: CLINICAL: NADH Treats a Variety of Diseases
Anaerobic Respiration
Fermentation
Catabolism of Noncarbohydrate Compounds
8.4 Biosynthesis and the Crossing Pathways of Metabolism
The Efficiency of the Cell
Anabolism: Formation of Macromolecules
Assembly of the Cell
8.5 Photosynthesis: It All Starts with Light
INSIGHT 8.2: MICROBIOME: Electricity Eaters
Light-Dependent
Reactions
Light-Dependent
Reactions
Other Mechanisms of Photosynthesis
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9 Microbial Genetics
9.1 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
DNA Replication: Preserving the Code and Passing It On
9.2 Applications of the DNA Code: Transcription and Translation
The Gene-Protein
Connection
The Major Participants in Transcription and Translation
INSIGHT 9.1: CLINICAL: Micro RNA: Tiny but Mighty
Transcription: The First Stage of Gene Expression
Translation: The Second Stage of Gene Expression
Eukaryotic Transcription and Translation: Similar Yet Different
The Genetics of Animal Viruses
9.3 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
9.4 DNA Recombination Events
Horizontal Gene Transfer in Bacteria
Pathogenicity Islands: Special " Gifts" of Horizontal Gene Transfer?
9.5 Mutations: Changes in the Genetic Code
Causes of Mutations
Categories of Mutations
INSIGHT 9.2: MICROBIOME: Customizing the Microbiome
Repair of Mutations
The Ames Test
Positive and Negative Effects of Mutations
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10 Genetic Analysis and Genetic Engineering
10.1 Tools and Techniques of Genetic Engineering
DNA: The Raw Material
Systems for Dicing, Splicing, and Reversing Nucleic Acids
Analysis of DNA
INSIGHT 10.1: MICROBIOME: Host Genetics and the Microbiome
Methods in Recombinant DNA Technology: How to Imitate Nature
10.2 Products of Recombinant DNA Technology
Genetically Modified Organisms
10.3 Genetic Treatments: Introducing DNA into the Body
Gene Therapy
Small RNAs as Medicine
CRISPR
INSIGHT 10.2: CLINICAL: Gene Therapy Restoring Sight
10.4 DNA Analysis: Maps and Profiles
Genome Sequencing
Profiling
Measuring Gene Expression: Microarrays
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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
INSIGHT 11.1: CLINICAL: Hospitals Using New Tools Against Bacteria
Decontamination by Filtration: Techniques for Removing Microbes
Osmotic Pressure
11.3 Chemical Agents in Microbial Control
Selecting a Microbicidal Chemical
Factors Affecting the Microbicidal Activity of Chemicals
Germicidal Categories According to Chemical Group
INSIGHT 11.2: MICROBIOME: Hand Hygiene
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12 Antimicrobial Treatment
12.1 Principles of Antimicrobial Therapy
The Origins of Antimicrobial Drugs
Starting Treatment
Identifying the Agent
Testing for the Drug Susceptibility of Microorganisms
The Art and Science of Choosing an Antimicrobial Drug
12.2 Interactions Between Drug and Microbe
Mechanisms of Drug Action
12.3 Survey of Major Antimicrobial Drug Groups
Antibacterial Drugs Targeting the Cell Wall
Antibacterial Drugs Targeting Protein Synthesis
Antibacterial Drugs Targeting Folic Acid Synthesis
Antibacterial Drugs Targeting DNA or RNA
Antibacterial Drugs Targeting Cell Membranes
Antibiotics and Biofilms
Agents to Treat Fungal Infections
Antiprotozoal and Antihelminthic Treatment
Antiviral Agents
12.4 Antimicrobial Resistance
Interactions Between Microbes and Drugs: The Acquisition of Drug Resistance
The Human Role in Antimicrobial Resistance
An Urgent Problem
INSIGHT 12.1: CLINICAL: Using Viruses as Antibiotics
New Approaches to Antimicrobial Therapy
12.5 Interactions Between Drug and Host
Toxicity to Organs
Allergic Responses to Drugs
Suppression and Alteration of the Microbiota by Antimicrobials
INSIGHT 12.2: MICROBIOME: Do Antibiotics Make Us Fat?
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13 Microbe–Human Interactions
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
13.3 Epidemiology: The Study of Disease in Populations
Reservoirs: Where Pathogens Persist
The Acquisition and Transmission of Infectious Agents
Healthcare- Associated Infections: The Hospital as a Source of Disease
Which Agent Is the Cause? Using Koch's Postulates to Determine Etiology
INSIGHT 13.2: CLINICAL: Cell Phones in Hospitals
Tracking Disease in a Population
Global Issues in Epidemiology
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14 Host Defenses I Overview and Nonspecific Defenses
14.1 Defense Mechanisms of the Host: An Overview
Tissues, Organs, and Cells Participating in Immunity
14.2 The First Line of Defense
Physical or Anatomical Barriers at the Body's Surface
Nonspecific Chemical Defenses
14.3 The Second Line of Defense
Phagocytosis: Cornerstone of Inflammation and Specific Immunity
Inflammation: A Complex Concert of Reactions to Injury
INSIGHT 14.1: MICROBIOME: Are We Treating Autoimmune Diseases Correctly?
The Stages of Inflammation
Fever: An Adjunct to Inflammation
INSIGHT 14.2: CLINICAL: Fever: To Treat or Not to Treat?
Antimicrobial Products
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15 Host Defenses II Specific Immunity and Immunization
15.1 Specific 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
15.2 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
15.3 Step II: Presentation of Antigens
Characteristics of Antigens
Encounters with Antigens
The Role of Antigen Processing and Presentation
15.4 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
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
INSIGHT 15.1: MICROBIOME: Cancer and the Microbiome
Gamma- Delta T Cells
Additional Cells with Orders to Kill
15.6 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
15.7 Specific Immunity and Vaccination
Artificial Passive Immunization: Immunotherapy
Artificial Active Immunity: Vaccination
Development of New Vaccines
Route of Administration and Side Effects of Vaccines
Vaccinating: Who and When?
INSIGHT 15.2: CLINICAL: The Coalition for Epidemic Preparedness Innovations
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16 Disorders in Immunity
16.1 The Immune Response: A Two- Sided Coin
Hypersensitivity: Four Types
16.2 Type I Allergic Reactions: Atopy and Anaphylaxis
INSIGHT 16.1: MICROBIOME: Asthma and the Airway—and Gut—Microbiome
Who Is Affected, and How?
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
Anaphylaxis: An Overpowering Systemic Reaction
Diagnosis of Allergy
Treatment of Allergy
INSIGHT 16.2: CLINICAL: Take Two Hookworms and Call Me in the Morning
16.3 Type II Hypersensitivities: Reactions That Lyse Foreign 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
16.4 Type III Hypersensitivities: Immune Complex Reactions
Mechanisms of Immune Complex Disease
Types of Immune Complex Disease
16.5 Type IV Hypersensitivities: Cell-Mediated (Delayed) Reactions
Delayed Hypersensitivity to Microbes
Contact Dermatitis
T Cells and Their Role in Organ Transplantation
16.6 An Inappropriate Response Against Self: Autoimmunity
Possible Causes of Autoimmune Disease
The Origins of Autoimmune Disease
Examples of Autoimmune Disease
16.7 Immunodeficiency Diseases: Hyposensitivity of the Immune System
Primary Immunodeficiency Diseases
Secondary Immunodeficiency Diseases
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17 Diagnosing Infections
17.1 Preparation for the Survey of Microbial Diseases
Phenotypic Methods
Immunologic Methods
Genotypic Methods
17.2 First Steps: Specimen Collection
INSIGHT 17.1: MICROBIOME: The Human Microbiome Project and Diagnosis of Infection
Overview of Laboratory Techniques
17.3 Phenotypic Methods
Immediate Direct Examination of Specimen
Methods Requiring Growth
Determining Clinical Significance of Cultures
17.4 Immunologic Methods
Different Kinds of Antigen- Antibody Interactions
In Vivo Testing
General Features of Immune Testing
17.5 Genotypic Methods
Polymerase Chain Reaction ( PCR): The Backbone of New Diagnostics
Hybridization: Probing for Identity
Whole- Genome Sequencing
Pulsed- Field Gel Electrophoresis: Microbial Fingerprints
17.6 Additional Diagnostic Technologies
Lab on a Chip
Mass Spectrometry
INSIGHT 17.2: CLINICAL: Quick Test for Zika
Imaging
Entirely New Diagnostic Strategies
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18 Infectious Diseases Affecting the Skin and Eyes
18.1 The Skin and Its Defenses
18.2 Normal Biota of the Skin
INSIGHT 18.1: MICROBIOME: C-Section Babies vs. Vaginally Delivered Babies
18.3 Skin Diseases Caused by Microorganisms
INSIGHT 18.2: CLINICAL: Skin, Staph, and Strep
18.4 The Surface of the Eye and Its Defenses
18.5 Normal Biota of the Eye
18.6 Eye Diseases Caused by Microorganisms
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19 Infectious Diseases Affecting the Nervous System
19.1 The Nervous System and Its Defenses
19.2 Normal Biota of the Nervous System
19.3 Nervous System Diseases Caused by Microorganisms
INSIGHT 19.1: CLINICAL: Mysterious Polio-Like Disease
INSIGHT 19.2: MICROBIOME: This Is Your Brain on Toxo
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20 Infectious Diseases Affecting the Cardiovascular and Lymphatic Systems
20.1 The Cardiovascular and Lymphatic Systems and Their Defenses
The Cardiovascular System
The Lymphatic System
Defenses of the Cardiovascular and Lymphatic Systems
20.2 Normal Biota of the Cardiovascular and Lymphatic Systems
20.3 Cardiovascular and Lymphatic System Diseases Caused by Microorganisms
INSIGHT 20.1: CLINICAL: Ebola
INSIGHT 20.2: MICROBIOME: Gut Microbiome and High Blood Pressure
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21 Infectious Diseases Affecting the Respiratory System
21.1 The Respiratory Tract and Its Defenses
21.2 Normal Biota of the Respiratory Tract
INSIGHT 21.1: MICROBIOME: The Lungs Are Not Sterile
21.3 Upper Respiratory Tract Diseases Caused by Microorganisms
21.4 Diseases Caused by Microorganisms Affecting Both the Upper and Lower Respiratory Tracts
INSIGHT 21.2: CLINICAL: Influenza: A Time Line
21.5 Lower Respiratory Tract Diseases Caused by Microorganisms
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22 Infectious Diseases Affecting the Gastrointestinal Tract
22.1 The Gastrointestinal Tract and Its Defenses
22.2 Normal Biota of the Gastrointestinal Tract
INSIGHT 22.1: MICROBIOME: Crohn’s Disease and the Gut Microbiome
22.3 Gastrointestinal Tract Diseases Caused by Microorganisms ( Nonhelminthic)
22.4 Gastrointestinal Tract Diseases Caused by Helminths
General Clinical Considerations
INSIGHT 22.2: CLINICAL: Right Here at Home: Neglected Parasitic Infections
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23 Infectious Diseases Affecting the Genitourinary System
23.1 The Genitourinary Tract and Its Defenses
23.2 Normal Biota of the Genitourinary Tract
Normal Biota of the Male Genital Tract
Normal Biota of the Female Genital Tract
INSIGHT 23.1: MICROBIOME: Save the World with the Vaginal Microbiome
23.3 Urinary Tract Diseases Caused by Microorganisms
23.4 Reproductive Tract Diseases Caused by Microorganisms
INSIGHT 23.2: CLINICAL: Pelvic Inflammatory Disease: Infertility Before You Are
Ready to Conceive
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24 Microbes and the Environment
24.1 Ecology: The Interconnecting Web of Life
The Organization of Ecosystems
Energy and Nutritional Flow in Ecosystems
INSIGHT 24.1: CLINICAL: Microbiome of Decomposing Bodies Can Catch a Murderer
24.2 The Natural Recycling of Bioelements
Atmospheric Cycles
Sedimentary Cycles
Other Forms of Cycling
24.3 Microbes on Land and in Water
Environmental Sampling in the Genomic Era
Soil Microbiology
Deep Subsurface Microbiology
Aquatic Microbiology
INSIGHT 24.2: MICROBIOME: Novel Hot Spring Viruses Migrate on Water Droplets
24.4 The Concept of "One Health"
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25 Applied Microbiology and Food and Water Safety
25.1 Applied Microbiology and Biotechnology
INSIGHT 25.1: MICROBIOME: Bioremediation
25.2 Microorganisms in Water and Wastewater Treatment
INSIGHT 25.2: CLINICAL: Preventing Diarrhea by Cleaning Up Muddy Water
Water Monitoring to Prevent Disease
25.3 Microorganisms Making Food and Spoiling Food
Microbial Fermentations in Food Products from Plants
Microbes in Milk and Other Dairy Products
Microorganisms as Food
Microbial Involvement in Foodborne Diseases
Prevention Measures for Food Poisoning and Spoilage
25.4 Using Microorganisms to Make Things We Need
From Microbial Factories to Industrial Factories
Substance Production
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APPENDIX A: Answers to Multiple-Choice Questions inSmartGrid
APPENDIX B: Exponents
APPENDIX C: An Introduction to Concept Mapping
Glossary
Index