| Exciting Times: The Challenge to be a Bacterial Systematist | p. 1 |
| Introduction | p. 1 |
| The Early Heroes (1860-1900) | p. 3 |
| The Dawn of Microbial Ecology and the Continuing Struggle with Classification Systems (1900-1930) | p. 5 |
| Encouragement and Frustration (The Era 1930-1950) | p. 7 |
| Expanding the Range of Properties: The Genetic and Epigenetic Levels (1950-1980) | p. 10 |
| Yet Another Exciting Time: Unravelling the Genealogy(ies) of Cultured and As-Yet Uncultured Prokaryotes | p. 13 |
| References | p. 16 |
| DNA-DNA Reassociation Methods Applied to Microbial Taxonomy and Their Critical Evaluation | p. 23 |
| Introduction | p. 23 |
| Semantic Considerations | p. 26 |
| DNA-DNA Reassociation Measurement, Parameters and Methods | p. 29 |
| Interpretation of Results and the Boundaries for Species Circumscription | p. 39 |
| The Impact of DNA-DNA Hybridizations on the Conception of a Species and Changes in the Concept and/or the Definition | p. 42 |
| Epilogue | p. 44 |
| References | p. 46 |
| DNA Fingerprinting Techniques Applied to the Identification, Taxonomy and Community Analysis of Prokaryotes | p. 51 |
| Introduction | p. 51 |
| DNA Typing Methods | p. 53 |
| DNA Typing Methods Targeting the Whole Genome of a Bacterial Strain | p. 53 |
| DNA Typing Methods Targeting Gene Clusters (Operons) | p. 60 |
| DNA Typing Methods Targeting the 16S rRNA Gene | p. 64 |
| References | p. 71 |
| Multiple Locus VNTR (Variable Number of Tandem Repeat) Analysis | p. 83 |
| Introduction | p. 83 |
| MLVA Origins | p. 83 |
| MLVA Set-up and Enrichment | p. 84 |
| Evaluation of the Potential Interest of MLVA for a Given Species | p. 85 |
| MLVA Validation | p. 86 |
| Data Management | p. 87 |
| Existing First-generation MLVA Assays | p. 88 |
| Mycobacterium tuberculosis | p. 91 |
| Bacillus anthracis | p. 93 |
| Yersinia pestis | p. 94 |
| Brucella sp. | p. 95 |
| Legionella pneumophila | p. 97 |
| Other Bacteria | p. 97 |
| Validating and Analysing MLVA Data | p. 97 |
| MLVA Compared to Other Methods | p. 100 |
| References | p. 101 |
| Bacterial Phylogeny Reconstruction from Molecular Sequences | p. 105 |
| Introduction | p. 105 |
| Species Definition | p. 106 |
| Bacterial Diversity | p. 108 |
| Phylogenetic Analysis Based on 16S rDNA Sequences | p. 110 |
| Phylogenetic Analysis Based on Protein Sequences | p. 115 |
| Selection of Target Proteins | p. 115 |
| Design of PCR Primers for the Amplification of Protein-encoding Genes: A Case Study with gyrB | p. 121 |
| Limitations in Reconstructing Phylogenetic Trees | p. 126 |
| Conclusion and Future Perspective | p. 129 |
| References | p. 131 |
| Integrated Databasing and Analysis | p. 141 |
| Introduction | p. 141 |
| Classes of Data | p. 142 |
| Character Type Data | p. 143 |
| Definition | p. 143 |
| Data Transformation | p. 145 |
| Cluster Analysis of Character Type Data | p. 149 |
| Fingerprint Type Data | p. 149 |
| Definition | p. 149 |
| Preprocessing of Fingerprint Data | p. 150 |
| Comparison of Fingerprint Data | p. 161 |
| Fingerprint Techniques That Require Special Analysis Methods | p. 172 |
| Sequence Type Data | p. 174 |
| Definition | p. 174 |
| Assembling Sequencer Trace Files into Consensus Sequences | p. 174 |
| Alignment of Sequences | p. 175 |
| Multiple Alignment | p. 179 |
| Phylogenetic Clustering | p. 180 |
| Multi-locus Sequence Typing | p. 180 |
| Matrix Type Data | p. 183 |
| Trend Type Data | p. 184 |
| Two-dimensional Gel Type Data | p. 186 |
| Analyzing 2D Gels | p. 188 |
| The Integrated Database | p. 189 |
| Distributed Databases and Portability of Data | p. 189 |
| Hierarchical Cluster Analysis | p. 192 |
| Similarity- or Distance-based Clustering Techniques | p. 192 |
| Phylogenetic Clustering Methods | p. 198 |
| Minimum Spanning Trees | p. 198 |
| Consensus Grouping and Classification | p. 203 |
| Concatenation of Data Sets | p. 205 |
| Averaging Resemblance Matrices | p. 205 |
| Consensus Trees | p. 208 |
| Error on Dendrograms | p. 208 |
| Degeneracy of Dendrograms | p. 210 |
| Dealing with Dendrogram Degeneracies | p. 212 |
| References | p. 214 |
| Assessment of Microbial Phylogenetic Diversity Based on Environmental Nucleic Acids | p. 219 |
| Introduction | p. 219 |
| Microbial Phylogenetics and the 16S rRNA Gene | p. 220 |
| 16S rRNA and the Environment | p. 222 |
| Molecular Methodology in Microbial Ecology | p. 224 |
| General Considerations of Bias | p. 228 |
| Phylogenetic Assessment of Environmental Nucleic Acids | p. 232 |
| Fingerprinting | p. 233 |
| Denaturing Gradient Gel Electrophoresis | p. 234 |
| Temperature Gradient Gel Electrophoresis | p. 235 |
| Single-stranded Conformational Polymorphism | p. 236 |
| Terminal Restriction Fragment Length Polymorphism | p. 236 |
| Ribosomal Intergenic Spacer Analysis | p. 237 |
| Additional Considerations | p. 238 |
| Sequencing | p. 239 |
| 16S rRNA Gene Libraries | p. 239 |
| Serial Analysis of Ribosomal Sequence Tags | p. 241 |
| Metagenomics | p. 242 |
| Array Technology | p. 243 |
| Composite Methodologies | p. 245 |
| Conclusion | p. 246 |
| References | p. 247 |
| Metagenome Analyses | p. 261 |
| Introduction | p. 261 |
| Construction and Screening of Metagenome Libraries | p. 264 |
| Small and Large Insert Libraries | p. 265 |
| High-capacity Vectors: Cosmids, Fosmids or BACs? | p. 265 |
| Library Size | p. 267 |
| Isolation and Purification of HMW DNA | p. 268 |
| Construction of Large Insert Metagenomic Libraries | p. 269 |
| Storage of Metagenomic Libraries | p. 270 |
| Screening of Metagenomic Libraries | p. 271 |
| Sequencing of Large Insert Constructs | p. 272 |
| Sequence Analysis | p. 273 |
| Marker Genes | p. 273 |
| End-Sequences | p. 275 |
| Cosmids, Fosmids or BACs | p. 276 |
| Summary, Pitfalls and Outlook | p. 280 |
| References | p. 281 |
| DNA Microarrays for Bacterial Genotyping | p. 287 |
| Introduction | p. 287 |
| Technical Principles | p. 288 |
| Applications | p. 290 |
| Comparative Genome Hybridization | p. 290 |
| Diagnostic Detection of Virulence Genes | p. 295 |
| Diagnostic Detection of Resistance Determinants | p. 296 |
| Multi-locus Sequence Typing by Hybridization | p. 298 |
| Composite Gene Detection for Epidemiological Typing | p. 299 |
| Detection of Genes Associated with Metabolic Functions | p. 301 |
| Phylogenetic Identification | p. 303 |
| Random Hybridization Fingerprinting | p. 304 |
| Present Limitations and Future Prospects | p. 305 |
| References | p. 306 |
| Subject Index | p. 315 |
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