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Microbiology For Dummies
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Table of Contents

Introduction 1 About This Book 1 Foolish Assumptions 2 Icons Used in This Book 2 Beyond the Book 3 Where to Go from Here 3 Part 1: Getting Started With Microbiology 5 Chapter 1: Microbiology and You 7 Why Microbiology? 7 Introducing the Microorganisms 8 Deconstructing Microbiology 10 Chapter 2: Microbiology: The Young Science 11 Before Microbiology: Misconceptions and Superstitions 12 Discovering Microorganisms 12 Debunking the myth of spontaneous generation 13 Improving medicine, from surgery to antibiotics and more 14 Looking at microbiology outside the human body 16 The Future of Microbiology 16 Exciting frontiers 17 Remaining challenges 18 Chapter 3: Microbes: They're Everywhere and They Can Do Everything 21 Habitat Diversity 23 Metabolic Diversity 24 Getting energy 25 Capturing carbon 25 Making enzymes 26 Secondary metabolism 26 The Intersection of Microbes and Everyone Else 27 Part 2: Balancing the Dynamics Of Microbial Life 29 Chapter 4: Understanding Cell Structure and Function 31 Seeing the Shapes of Cells 31 Life on a Minute Scale: Considering the Size of Prokaryotes 33 The Cell: An Overview 34 Scaling the Outer Membrane and Cell Walls 35 Examining the outer membrane 35 Exploring the cell wall 37 Other Important Cell Structures 41 Divining Cell Division 43 Tackling Transport Systems 44 Coasting with the current: Passive transport 45 Upstream paddle: Active transport 46 Keeping things clean with efflux pumps 46 Getting Around with Locomotion 47 Chapter 5: Making Sense of Metabolism 49 Converting with Enzymes 49 In Charge of Energy: Oxidation and Reduction 51 Donating and accepting electrons 52 Bargaining with energy-rich compounds 54 Storing energy for later 55 Breaking Down Catabolism 56 Digesting glycolysis 56 Stepping along with respiration and electron carriers 57 Moving with the proton motive force 59 Turning the citric acid cycle 60 Stacking Up with Anabolism 61 Creating amino acids and nucleic acids 62 Making sugars and polysaccharides 63 Putting together fatty acids and lipids 65 Chapter 6: Getting the Gist of Microbial Genetics 67 Organizing Genetic Material 68 DNA: The recipe for life 68 Perfect plasmids 70 Doubling down with DNA replication 71 Assembling the Cellular Machinery 75 Making messenger RNA 75 Remembering other types of RNA 77 Synthesizing protein 78 Making the Right Amount: Regulation 80 Turning the tap on and off: DNA regulation 81 Regulating protein function 83 Changing the Genetic Code 83 Slight adjustments 83 Major rearrangements 85 Chapter 7: Measuring Microbial Growth 89 Getting Growth Requirements Right 89 Physical requirements 90 Chemical requirements 91 Culturing microbes in the lab 92 Observing Microbes 94 Counting small things 95 Seeing morphology 97 Calculating Cell Division and Population Growth 98 Dividing cells 99 Following growth phases 100 Inhibiting Microbial Growth 101 Physical methods 101 Disinfectants 102 Part 3: Sorting Out Microbial Diversity 103 Chapter 8: Appreciating Microbial Ancestry 105 Where Did Microbes Come From? 105 Tracing the origins of life 106 Diversifying early prokaryotes 107 The impact of prokaryotes on the early earth 107 Hitching a ride: Endosymbiosis 108 Understanding Evolution 111 Studying Evolution 113 Choosing marker genes 113 Seeing the direction of gene transfer in prokaryotes 114 Classifying and Naming Microbes 115 Climbing the Tree of Life 117 Chapter 9: Harnessing Energy, Fixing Carbon 119 Forging Ahead with Autotrophic Processes 120 Fixing carbon 120 Using the Energy in Light 124 Harvesting light: Chlorophylls and bacteriochlorophylls 125 Helping photosynthesis out: Carotenoids and phycobilins 127 Generating oxygen (or not): Oxygenic and anoxygenic photosynthesis 128 Getting Energy from the Elements: Chemolithotrophy 133 Harnessing hydrogen 134 Securing electrons from sulfur 134 Pumping iron 135 Oxidizing nitrate and ammonia 136 Chapter 10: Comparing Respiration and Fermentation 139 Lifestyles of the Rich and Facultative 139 Seeing the Big Picture 141 Digging into Respiration 144 Spinning the citric acid cycle 144 Stepping down the electron transport chain 146 Respiring anaerobically 147 Figuring Out Fermentation 150 Chapter 11: Uncovering a Variety of Habitats 155 Defining a Habitat 156 Understanding Nutrient Cycles 157 Carbon cycling 157 Nitrogen cycling 160 Sulfur cycling 162 Phosphorous cycles in the ocean 162 Microbes Socializing in Communities 163 Using quorum sensing to communicate 163 Living in biofilms 163 Exploring microbial mats 165 Discovering Microbes in Aquatic and Terrestrial Habitats 165 Thriving in water 166 Swarming soils 167 Getting Along with Plants and Animals 168 Living with plants 169 Living with animals 171 Living with insects 172 Living with ocean creatures 172 Tolerating Extreme Locations 173 Detecting Microbes in Unexpected Places 174 Part 4: Meeting the Microbes 175 Chapter 12: Meet the Prokaryotes 177 Getting to Know the Bacteria 178 The Gram-negative bacteria: Proteobacteria 178 More Gram-negative bacteria 182 The Gram-positive bacteria 186 Acquainting Yourself with the Archaea 188 Some like it scalding: Extreme thermophiles 190 Going beyond acidic: Extreme acidophiles 191 Super salty: Extreme halophiles 192 Not terribly extreme Archaea 193 Chapter 13: Say Hello to the Eukaryotes 195 Fun with Fungi 196 Figuring out fungal physiology 196 Itemizing fungal diversity 199 Interacting with plant roots 201 Ask us about the Ascomycetes 202 Mushrooms: Basidiomycetes 203 Perusing the Protists 204 Making us sick: Apicoplexans 205 Making plants sick: Oomycetes 207 Chasing amoeba and ciliates 207 Encountering the algae 210 Chapter 14: Examining the Vastness of Viruses 215 Hijacking Cells 215 Frugal viral structure 216 Simplifying viral function 217 Making Heads or Tails of Bacteriophage 219 Lytic phage 219 Temperate phage 220 Transposable phage 222 Discussing Viruses of Eukaryotes 224 Infecting animal cells 224 Following plant viruses 227 How Host Cells Fight Back 229 Restriction enzymes 229 CRISPR 230 Interfering with RNA viruses: RNAi 232 Part 5: Seeing the Impact Of Microbes 233 Chapter 15: Understanding Microbes in Human Health and Disease 235 Clarifying the Host Immune Response 236 Putting up barriers to infection 236 Raising a red flag with inflammation 237 Holding down the fort with innate immunity 237 Sending out the troops for adaptive immunity 238 Antibodies in action 240 Relying on Antimicrobials for Treating Disease 243 Fundamental features of antibiotics 244 Targets of destruction 245 Unraveling microbial drug resistance 247 Discovering new antibiotics 249 Searching Out Superbugs 250 Staying ahead of vancomycin-resistant enterococci 251 Battling methicillin-resistant Staphylococcus aureus 251 Outcompeting Clostridium difficile 253 Pressure from extended-spectrum beta-lactamases 253 Knowing the Benefits of Prebiotics and Probiotics 254 Attacking Viruses with Antiviral Drugs 255 Chapter 16: Putting Microbes to Work: Biotechnology 257 Using Recombinant DNA Technology 258 Making the insert 258 Employing plasmids 261 Cutting with restriction enzymes 262 Getting microbes to take up DNA 264 Using promoters to drive expression 267 Making use of expression vectors 267 Properly folding proteins 268 Being mindful of metabolic load 269 Making long, multi-gene constructs 269 Providing Therapies 272 Improving antibiotics 272 Developing vaccines 272 Using Microbes Industrially 273 Protecting plants with microbial insecticides 274 Making biofuels 275 Bioleaching metals 276 Cleaning up with microbes 276 Chapter 17: Fighting Microbial Diseases 279 Protecting Public Health: Epidemiology 279 Tracking diseases 280 Investigating outbreaks 280 Identifying a Microbial Pathogen 283 Characterizing morphology 283 Using biochemical tests 284 Typing strains with phage 286 Using serology 287 Testing antibiotic susceptibility 288 Understanding Vaccines 289 Understanding how vaccines work 290 Ranking the types of vaccines 291 Part 6: New Frontiers in Microbiology 293 Chapter 18: Teasing Apart Communities 295 Studying Microbial Communities 295 Borrowing from ecology 296 Seeing what sets microbial communities apart from plants and animals 296 Observing Communities: Microbial Ecology Methods 297 Selecting something special with enrichment 297 Seeing cells through lenses 298 Measuring microbial activity 299 Identifying species using marker genes 300 Getting the Hang of Microbial Genetics and Systematics 301 Sequencing whole genomes 301 Using metagenomics to study microbial communities 302 Reading microbial transcriptomics 303 Figuring out proteomics and metabolomics 304 Looking for Microbial Dark Matter 306 Chapter 19: Synthesizing Life 307 Regulating Genes: The lac Operon 308 Using a good natural system 308 Improving a good system 310 Designing Genetic Networks 312 Switching from one state to another 313 Oscillating between states 314 Keeping signals short 315 The Synthetic Biologist's Toolbox 315 Making it modular 315 Participating in the iGEM competition 316 Part 7: The Part of Tens 319 Chapter 20: Ten (or So) Diseases Caused by Microbes 321 Ebola 322 Anthrax 322 Influenza 323 Tuberculosis 324 HIV 324 Cholera 325 Smallpox 325 Primary Amoebic Menigoencephalitis 326 The Unknown 327 Chapter 21: Ten Great Uses for Microbes 329 Making Delicious Foods 329 Growing Legumes 330 Brewing Beer, Liquor, and Wine 330 Killing Insect Pests 331 Treating Sewage 331 Contributing to Medicine 332 Setting Up Your Aquarium 332 Making and Breaking Down Biodegradable Plastics 333 Turning Over Compostable Waste 333 Maintaining a Balance 334 Chapter 22: Ten Great Uses for Microbiology 335 Medical Care: Keeping People Healthy 335 Dental Care: Keeping Those Pearly Whites Shining Bright 336 Veterinary Care: Helping Fido and Fluffy to Feel Their Best 337 Monitoring the Environment 338 Making Plants Happy 339 Keeping Fish Swimming Strong 339 Producing Food, Wine, and Beer 340 Science Hacking 341 Looking for Microbes in Clean Rooms 341 Producing Pharmaceuticals 342 Index 343

About the Author

Jennifer C. Stearns, PhD, is an Assistant Professor in the Department of Medicine at McMaster University. She studies how we get our gut microbiome in early life and how it can keep us healthy over time. Michael G. Surette, PhD, is a Professor in the Department of Medicine at McMaster University, where he pushes the boundaries of microbial research. Julienne C. Kaiser, PhD, is a doctoral career educator.

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