Microbes : concepts and applications

717 Pages·2012·18.3 MB·English

by  Prakash S Bisen

MICROBES

MICROBES
Concepts and Applications
Prakash S. Bisen
Emeritus Scientist
Defence Research Development Establishment
Defence Research Development Organization
Ministry of Defence, Government of India
Gwalior, India
Mousumi Debnath
Associate Professor
Department of Biotechnology
Central University of Rajasthan
City Road, Kishangargh
Ajmer, India
Godavarthi B. K. S. Prasad
Professor
School of Studies in Biochemistry and Biotechnology
Jiwaji University
Gwalior, India
A JOHN WILEY & SONS, INC., PUBLICATION
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LibraryofCongressCataloging-in-PublicationData:
Bisen,PrakashS.
Microbes:conceptsandapplications/PrakashS.Bisen,MousumiDebnath,GodavarthiB.K.S.Prasad.
p.cm.
Includesbibliographicalreferencesandindex.
ISBN978-0-470-90594-4
1.Microbiology.2.Microbialdiversity.3.Microbialecology.4.Microbialbiotechnology.
5.Microorganisms.I.Debnath,Mousumi.II.Prasad,GodavarthiB.K.S.III.Title.
QR41.2.B5762012
616.9(cid:2)041–dc23
2011044258
PrintedintheUnitedStatesofAmerica
10987654321
CONTENTS
PREFACE xiii
ACKNOWLEDGMENTS xv
1
HUMANANDMICROBIALWORLD 1
1.1 Prologue 1
1.2 Innovations in Microbiology for Human Welfare 1
1.2.1 Impact of Microbes on the Human Genome Project, 2
1.2.2 Microbial Biosensors, 5
1.2.3 Molecular Diagnostics, 7
1.2.4 Nanomedicine, 13
1.2.5 Personalized Medicine, 16
1.2.6 Biowarfare, 21
1.3 The Microbial World 24
1.3.1 Classification System, 25
1.3.2 Viruses, Viroids, and Prions, 26
1.3.3 Bacteria, 32
1.3.4 Eucarya, 35
1.3.5 Algae, 39
1.3.6 Fungi, 44
1.3.7 Protozoa, 47
1.3.8 Microscopic Invertebrates, 51
1.3.9 Microbial Interrelationships, 54
1.3.10 Probiotic Microbes, 56
1.4 Future Challenges: Metagenomics 57
References 60
2
GENETECHNOLOGY:APPLICATIONSANDTECHNIQUES 65
2.1 Prologue 65
2.2 Introduction to Gene Technology 65
2.2.1 Genes and Bacteria, 67
2.2.2 Reporter Genes, 68
2.2.3 Recombinant DNA Pharmaceuticals, 69
2.2.4 Invitro DNA Selection, 73
2.3 Nucleic Acid Hybridization 75
2.3.1 Colony Blot and Southern Blot, 76
2.3.2 Dot Blot and Zoo Blot, 77
v
vi CONTENTS
2.3.3 Insitu Hybridization, 79
2.3.4 Microarray Technology, 83
2.3.5 Molecular Diagnostic Research, 87
2.4 DNA Sequencing 88
2.4.1 Dideoxychain Termination Method, 89
2.4.2 Automated DNA Sequencing, 90
2.4.3 Maxam and Gilbert Method, 92
2.4.4 Primer Walking, 96
2.4.5 Contig Sequencing, 97
2.4.6 Shotgun Sequencing, 97
2.4.7 Importance of Sequencing, 99
2.5 Polymerase Chain Reaction 99
2.6 Omics Technology and Microbes 103
2.6.1 Genomics: A Tool for Understanding Genes, 104
2.6.2 Transcriptomics: A Tool for Deciphering Gene Function, 108
2.6.3 Proteomics: A Tool to Unravel the Mysteries of Protein, 112
2.6.4 Metabolomics: A Tool to Ultimately Understand the Whole
Metabolome, 116
2.6.5 Integration of Omics, 121
2.7 Bioinformatics in Microbial Technology 124
2.8 Future Challenges: The Biochips 126
References 137
3
MEDICALMICROBIOLOGYANDMOLECULARDIAGNOSTICS 151
3.1 Prologue 151
3.2 Microbial Biology 152
3.2.1 Morphology and Nature of Microorganisms, 152
3.2.2 Use of Bergey’s Manual and Identibacter Interactus, 154
3.2.3 Bacterial Growth and Physiology, 154
3.2.4 Antimicrobial Agents, 156
3.2.5 Bacterial Genetic Variations, 158
3.2.6 Bacterial Pathogenecity, 158
3.2.7 Virus–Cell Interaction, 159
3.3 Infection and Immunity 160
3.3.1 Overview of the Immune System, 160
3.3.2 The Organs of the Immune System, 161
3.3.3 Cells of the Immune System, 162
3.3.4 Innate Immunity, 164
3.3.5 Adaptive Immunity, 165
3.3.6 Hypersensitivity, 180
3.3.7 Immunity in Viral Infections, 183
3.4 Bacterial Pathogens and Associated Diseases 185
3.4.1 Airborne Bacterial Infections, 186
3.4.2 Foodborne and Waterborne Diseases, 190
3.4.3 Soilborne Bacterial Infections, 198
CONTENTS vii
3.4.4 Arthropodborne Bacterial Infections, 200
3.4.5 Sexually Transmitted Bacterial Infections, 201
3.4.6 Other Important Bacterial Diseases, 203
3.4.7 Actinomycetes Mycetoma, 204
3.5 Viral Pathogens and Associated Diseases 209
3.5.1 Herpes Simplex Viruses, 210
3.5.2 Varicella Zoster Virus, 210
3.5.3 Cytomegalovirus, 210
3.5.4 Epstein–Barr Virus, 211
3.5.5 Human Herpes Virus, 211
3.5.6 Hepatitis, 211
3.5.7 Respiratory Syncytial Virus, 213
3.5.8 Influenza Viruses, 214
3.5.9 Parainfluenza Viruses, 215
3.5.10 Adenoviruses, 215
3.5.11 Rhinoviruses, 215
3.5.12 Coronaviruses, 216
3.5.13 SARS Virus, 216
3.5.14 Diarrheal Viruses, 216
3.5.15 Calicivirus (Sapovirus), 217
3.5.16 Enterovirus, 217
3.5.17 Poliomyelitis, 217
3.5.18 Coxsackie, 217
3.5.19 Echoviruses, 218
3.5.20 Mumps, 218
3.5.21 Measles Virus, 218
3.5.22 Rubella, 219
3.5.23 Parvovirus B, 219
3.5.24 Human Immunodeficiency Viruses, 220
3.5.25 Human T Cell Lymphotropic Viruses (HTLV), 222
3.5.26 Papillomaviruses, 222
3.5.27 Polyomaviruses, 223
3.5.28 Rabies, 223
3.5.29 Smallpox, 223
3.5.30 Monkeypox, 224
3.5.31 Vaccinia, 224
3.5.32 Cowpox, 224
3.5.33 Arthropodborne Viruses, 224
3.5.34 Lymphocytic Choriomenigitis Virus, 226
3.5.35 Filovirus, 226
3.5.36 Hantaviruses, 227
3.6 Prions 227
3.6.1 Kuru, 227
3.6.2 Creutzfeldt–Jacob Disease (CJD), 227
3.6.3 Gerstmann–Straussler Syndrome (GSS), 228
3.7 Parasitic Infections 228
3.7.1 Nematoda, 229
viii CONTENTS
3.7.2 Trematoda, 232
3.7.3 Cestoda, 234
3.7.4 Protozoan Parasites, 236
3.7.5 Skin Parasites, 248
3.8 Fungal Pathogen 249
3.8.1 Superficial Fungal Infections, 249
3.8.2 Systemic Fungal Infections, 250
3.9 Microbial Diagnostics 253
3.9.1 Immunodiagnostic Methods, 253
3.9.2 Molecular Diagnostic Approaches, 258
3.10Future Challenges: Promises of Pharmacogenomics 265
References 267
4
IDENTIFICATIONANDCLASSIFICATIONOFMICROBES 275
4.1 Prologue 275
4.2 Principles of Taxonomy 276
4.2.1 Strategies Used to Identify Microbes, 280
4.2.2 Methods for Bacterial Identification, 281
4.3 Using Phenotypic Characteristics to Identify Microbes 281
4.3.1 Microscopic Morphology, 283
4.3.2 Metabolic Differences, 288
4.3.3 Serology, 295
4.3.4 Fatty Acid Analysis (FAME), 298
4.4 Using Genotypic Character to Identify Microbes 299
4.4.1 Nucleic Acid Probes to Detect Specific Nucleotide
Sequence, 300
4.4.2 Amplifying Specific DNA Sequences Using PCR, 301
4.4.3 Sequencing Ribosomal RNA Genes, 302
4.5 Characterizing Strain Differences 306
4.5.1 Phenotypic Typing Methods, 306
4.5.2 Molecular Typing Methods, 315
4.6 Classification of Microbes on the Basis of Phenotypic Characteristics 319
4.6.1 Carbohydrate Utilization, 322
4.6.2 Enzyme Production, 322
4.6.3 Mode of Growth, 323
4.6.4 Motility, 323
4.6.5 Antigen and Phage Susceptibility, 324
4.7 Classification of Microbes on the Basis of Genotypic Characters 324
4.7.1 DNA Base Ratio (G+C Ratio), 325
4.7.2 DNA Hybridization, 326
4.7.3 Nucleotide Sequence Analysis, 330
4.7.4 Comparing the Sequence of 16S Ribosomal
Nucleic Acid, 331
4.8 Future Challenges: Aptamers for Detection of Pathogens 333
References 334