Stackebrandt Molecular Identification, Systematics, and Population Structure of Prokaryotes

1. Auflage 2010
ISBN: 978-3-540-31292-5
Verlag: Springer-Verlag
Format: PDF
Kopierschutz: Wasserzeichen (»Systemvoraussetzungen)

E-Book, Englisch, 320 Seiten

Systematic biology has a far wider application than merely the provision of a reliable classification scheme for new strains. With the framework of the hierarchic system stabilizing, genomes, noncoding regions, and genes and their products can now be evaluated in an evolutionary context. This book summarizes recent developments in the molecular characterization of cultured and as-yet uncultured prokaryotes, emphasizing the strengths and weaknesses of individual approaches. The chapters of the book are compiled to stimulate students to enter the field of bacterial diversity, presenting a broad spectrum of fascinating multifaceted disciplines that illuminate the paths to ecosystem functioning, communication within communities, symbiosis, life in extreme environments, astrobiology, and more.

Autoren/Hrsg.

Stackebrandt, Erko

Inhaltsverzeichnis

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 Preprocessing of Fingerprint Data;160
11.4.2.1;Step 1. Import and Preprocessing of the Gel Image;160
11.4.2.2;Step 2. Extracting Densitometric Curves from the Gel Image Lanes;164
11.4.2.3;Step 3. Normalization;165
11.4.2.4;Step 4. Detection of Bands/Peaks;169
11.4.3;6.4.3 Comparison of Fingerprint Data;171
11.4.3.1;Comparison of Densitometric Curves;172
11.4.3.2;Comparison of Band/Peak Positions;174
11.4.3.3;Dealing with Uncertain Bands;177
11.4.3.4;Optimization of Pattern Alignment;177
11.4.3.5;Choosing the Most Appropriate Coefficient;178
11.4.4;6.4.4 Fingerprint Techniques That Require Special Analysis Methods;182
11.4.4.1;Variable Number Tandem Repeats;182
11.5;6.5 Sequence Type Data;184
11.5.1;6.5.1 Definition;184
11.5.2;6.5.2 Assembling Sequencer Trace Files into Consensus Sequences;184
11.5.3;6.5.3 Alignment of Sequences;185
11.5.4;6.5.4 Multiple Alignment;189
11.5.5;6.5.5 Phylogenetic Clustering;190
11.5.6;6.5.6 Multi-locus Sequence Typing;190
11.5.6.1;Analysis of MLST Data;192
11.6;6.6 Matrix Type Data;193
11.7;6.7 Trend Type Data;194
11.8;6.8 Two-dimensional Gel Type Data;196
11.8.1;6.8.1 Analyzing 2D Gels;198
11.9;6.9 The Integrated Database;199
11.9.1;6.9.1 Distributed Databases and Portability of Data;199
11.10;6.10 Hierarchical Cluster Analysis;202
11.10.1;6.10.1 Similarity- or Distance-based Clustering Techniques;202
11.10.1.1;UPGMA and Related Clustering Algorithms;204
11.10.1.2;Neighbor Joining Technique;206
11.10.2;6.10.2 Phylogenetic Clustering Methods;208
11.10.3;6.10.3 Minimum Spanning Trees;208
11.10.3.1;MSTs and Population Genetics;210
11.11;6.11 Consensus Grouping and Classification;213
11.11.1;6.11.1 Concatenation of Data Sets;215
11.11.2;6.11.2 Averaging Resemblance Matrices;215
11.11.2.1;Harmonization of Distance Matrices;216
11.11.3;6.11.3 Consensus Trees;218
11.12;6.12 Error on Dendrograms;218
11.12.1;6.12.1 Degeneracy of Dendrograms;220
11.12.2;6.12.2 Dealing with Dendrogram Degeneracies;222
11.13;References;224
12;7 Assessment of Microbial Phylogenetic Diversity Based on Environmental Nucleic Acids;228
12.1;7.1 Introduction;228
12.2;7.2 Microbial Phylogenetics and the 16S rRNA Gene;229
12.3;7.3 16S rRNA and the Environment;231
12.4;7.4 Molecular Methodology in Microbial Ecology;233
12.5;7.5 General Considerations of Bias;237
12.6;7.6 Phylogenetic Assessment of Environmental Nucleic Acids;241
12.7;7.7 Fingerprinting;242
12.7.1;7.7.1 Denaturing Gradient Gel Electrophoresis;243
12.7.2;7.7.2 Temperature Gradient Gel Electrophoresis;244
12.7.3;7.7.3 Single-stranded Conformational Polymorphism;245
12.7.4;7.7.4 Terminal Restriction Fragment Length Polymorphism;245
12.7.5;7.7.5 Ribosomal lntergenic Spacer Analysis;246
12.7.6;7.7.6 Additional Considerations;247
12.8;7.8 Sequencing;248
12.8.1;7.8.1 16S rRNA Gene Libraries;248
12.8.2;7.8.2 Serial Analysis of Ribosomal Sequence Tags;250
12.9;7.9 Metagenomics;251
12.10;7.10 Array Technology;252
12.11;7.11 Composite Methodologies;254
12.12;7.12 Conclusion;255
12.13;References;256
13;8 Metagenome Analyses;269
13.1;8.1 Introduction;269
13.2;8.2 Construction and Screening of Metagenome Libraries;272
13.2.1;8.2.1 Small and Large Insert Libraries;273
13.2.2;8.2.2 High-capacity Vectors: Cosmids, Fosmids or BACs?;273
13.2.3;8.2.3 Library Size;275
13.2.4;8.2.4 Isolation and Purification of HMW DNA;276
13.2.5;8.2.5 Construction of Large Insert Metagenomic Libraries;277
13.2.6;8.2.6 Storage of Metagenomic Libraries;278
13.2.7;8.2.7 Screening of Metagenomic Libraries;279
13.2.8;8.2.8 Sequencing of Large Insert Constructs;280
13.3;8.3 Sequence Analysis;281
13.3.1;8.3.1 Marker Genes;281
13.3.2;8.3.2 End-Sequences;283
13.3.3;8.3.3 Cosmids, Fosmids or BACs;284
13.3.3.1;Correlation of Metagenomic Fragments;284
13.3.3.2;Functional Annotation;285
13.4;8.4 Summary, Pitfalls and Outlook;288
13.5;References;289
14;9 DNA Microarrays for Bacterial Genotyping;295
14.1;9.1 Introduction;295
14.2;9.2 Technical Principles;296
14.3;9.3 Applications;298
14.3.1;9.3.1 Comparative Genome Hybridization;298
14.3.2;9.3.2 Diagnostic Detection of Virulence Genes;303
14.3.3;9.3.3 Diagnostic Detection of Resistance Determinants;304
14.3.3.1;Detection of Resistance Genes;304
14.3.3.2;Analysis of Resistance-mediating Point Mutations;305
14.3.4;9.3.4 Multi-locus Sequence Typing by Hybridization;306
14.3.5;9.3.5 Composite Gene Detection for Epidemiological Typing;307
14.3.6;9.3.6 Detection of Genes Associated with Metabolic Functions;309
14.3.7;9.3.7 Phylogenetic Identification;311
14.3.8;9.3.8 Random Hybridization Fingerprinting;312
14.4;9.4 Present Limitations and Future Prospects;313
14.5;References;314
15;Subject Index;322