1;Title Page;2 2;Copyright Page;3 3;Preface;4 4;Table of Contents;6 5;Contributors;11 6;1 Exciting Times: The Challenge to be a Bacterial Systematist;13 6.1;1.1 Introduction;13 6.2;1.2 The Early Heroes (1860-1900);15 6.3;1.3 The Dawn of Microbial Ecology and the Continuing Struggle with Classification Systems (1900-1930);17 6.4;1.4 Encouragement and Frustration (The Era 1930-1950);19 6.5;1.5 Expanding the Range of Properties: The Genetic and Epigenetic Levels (1950-1980);22 6.6;1.6 Yet Another Exciting Time: Unravelling the Genealogy(ies) of Cultured and As-Yet Uncultured Prokaryotes;25 6.7;References;28 7;2 DNA-DNA Reassociation Methods Applied to Microbial Taxonomy and Their Critical Evaluation;34 7.1;2.1 Introduction;34 7.2;2.2 Semantic Considerations;37 7.3;2.3 DNA-DNA Reassociation Measurement, Parameters and Methods;40 7.4;2.4 Interpretation of Results and the Boundaries for Species Circumscription;50 7.5;2.5 The Impact of DNA-DNA Hybridizations on the Conception of a Species and Changes in the Concept and/or the Definition;53 7.6;2.6 Epilogue;55 7.7;References;57 8;3 DNA Fingerprinting Techniques Applied to the Identification, Taxonomy and Community Analysis of Prokaryotes;62 8.1;3.1 Introduction;62 8.2;3.2 DNA Typing Methods;64 8.2.1;3.2.1 DNA Typing Methods Targeting the Whole Genome of a Bacterial Strain;64 8.2.1.1;Pulsed Field Gel Electrophoresis for Macro-restriction of Total DNA;64 8.2.1.2;Random Amplified Polymorphic DNA Assay;65 8.2.1.3;Amplified Fragment Length Polymorphism Analysis;67 8.2.1.4;Amplification of Repetitive Elements Dispersed through the Whole Genome;68 8.2.2;3.2.2 DNA Typing Methods Targeting Gene Clusters (Operons);71 8.2.2.1;RFLP Analysis with Southern Blotting and Probe Hybridization (Ribotyping);71 8.2.2.2;Analysis of the 165-235 Ribosomal Intergenic Spacer Region;73 8.2.3;3.2.3 DNA Typing Methods Targeting the 16S rRNA Gene;75 8.2.3.1;Amplified Ribosomal rDNA Restriction Analysis;75 8.2.3.2;Terminal Restriction Fragment Length Polymorphism Analysis;76 8.2.3.3;Denaturing Gradient Electrophoresis and Temperature Gradient Gel Electrophoresis;77 8.2.3.4;PCR-based Single-stranded Confirmation Polymorphism;80 8.3;References;82 9;4 Multiple Locus VNTR (Variable Number of Tandem Repeat) Analysis;94 9.1;4.1 Introduction;94 9.2;4.2 MLVA Origins;94 9.3;4.3 MLVA Set-up and Enrichment;95 9.3.1;4.3.1 Evaluation of the Potential Interest of MLVA for a Given Species;96 9.3.2;4.3.2 MLVA Validation;97 9.3.3;4.3.3 Data Management;98 9.4;4.4 Existing First-generation MLVA Assays;99 9.4.1;4.4.1 Mycobacterium tuberculosis;102 9.4.2;4.4.2 Bacillus anthracis;104 9.4.3;4.4.3 Yersinia pestis;105 9.4.4;4.4.4 Brucella sp.;106 9.4.5;4.4.5 Legionella pneumophila;108 9.4.6;4.4.6 Other Bacteria;108 9.5;4.5 Validating and Analysing MLVA Data;108 9.6;4.6 MLVA Compared to Other Methods;111 9.7;References;112 10;5 Bacterial Phylogeny Reconstruction from Molecular Sequences;116 10.1;5.1 Introduction;116 10.2;5.2 Species Definition;117 10.3;5.3 Bacterial Diversity;119 10.4;5.4 Phylogenetic Analysis Based on 16S rDNA Sequences;121 10.5;5.5 Phylogenetic Analysis Based on Protein Sequences;126 10.5.1;5.5.1 Selection of Target Proteins;126 10.5.2;5.5.2 Design of PCR Primers for the Amplification of Protein-encoding Genes: A Case Study with gyrB;132 10.6;5.6 Limitations in Reconstructing Phylogenetic Trees;137 10.7;5.7 Conclusion and Future Perspective;140 10.8;References;142 11;6 Integrated Databasing and Analysis;151 11.1;6.1 Introduction;151 11.2;6.2 Classes of Data;152 11.3;6.3 Character Type Data;153 11.3.1;6.3.1 Definition;153 11.3.1.1;Open and Closed Data Sets;153 11.3.1.2;Binary, Numerical, and Categorical Data;154 11.3.2;6.3.2 Data Transformation;155 11.3.2.1;Standardization;155 11.3.2.1.1;A. Rows (Entries);157 11.3.2.1.2;B. Columns (Characters);157 11.3.2.2;Dealing with Missing Values;158 11.3.3;6.3.3 Cluster Analysis of Character Type Data;159 11.4;6.4 Fingerprint Type Data;159 11.4.1;6.4.1 Definition;159 11.4.2;6.4.2 Prep