New approaches to prokaryotic systematics:
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| Format: | Buch |
| Sprache: | English |
| Veröffentlicht: |
Amsterdam [u.a.]
Elsevier, Acad. Press
2014
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| Ausgabe: | 1. ed. |
| Schriftenreihe: | Methods in microbiology
41 |
| Schlagworte: | |
| Online-Zugang: | Inhaltsverzeichnis |
| Beschreibung: | XIX, 327 S., [10] Bl. Ill., graph. Darst. 24 cm |
| ISBN: | 9780128001769 |
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| 264 | 1 | |a Amsterdam [u.a.] |b Elsevier, Acad. Press |c 2014 | |
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Datensatz im Suchindex
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| adam_text | Methods in Microbiology
Volume 41
, New Approaches
to Prokaryotic
Systematics
Edited by
Michael Goodfellow
School of Biology, Newcastle University,
Newcastle upon Tyne, NE1 7RU, United Kingdom
lain Sutcliffe
Department of Applied Sciences, North urn bria University,
Newcastle upon Tyne, NE1 8ST, United Kingdom
Jongsik Chun
School of Biological Sciences, and Chun Lab Inc ,
Seoul National University, Seoul, Republic of Korea
ELSEVIER
AMSTERDAM • BOSTON • HEIDELBERG • LONDON
NEW YORK • OXFORD • PARIS • SAN DIEGO
SAN FRANCISCO • SINGAPORE * SYDNEY • TOKY(
Academic Press is an imprint of Eilsevier
Contents
Contributors xv
Preface xix
CHAPTER 1 The Need for Change: Embracing the Genome 1
Wiliiam B Whitman
1 A Brief History of Genomic Sequencing of Prokaryotes I
, 2 Why Sequence the Genomes of Prokaryotes? 3
3 The State-of-the-Art 6
4 Where we are Going 9
Acknowledgement 11
References 11
CHAPTER 2 An Introduction to Phylogenetics and the
Tree of Life 13
Tom A Williams, Sarah E Heaps
1 Introduction 13
2 Step 1: Posing a Question 16
3 Step 2: Choosing Relevant Sequences 16
3 1 Obtaining 16S rRNA Sequences for Bacteria,
Archaea and Eukarya 17
32A Note on the Availability and Use of
Data and Methods 18
4 Step 3: Aligning Sequences and Editing the Alignment 19
5 Step 4: The Theory of Fitting and Selecting a
Phylogenetic Model 22
5 1 Markov Nucleotide Substitution Models 22
5 2 Inferring Phylogenies under Markov Substitution
Models 25
5 3 Frequentist Inference 26
5 4 Bayesian Inference 27
5 5 Model Comparison and Assessment 28
5 6 Frequentist Methods 29
5 7 Bayesian Model Choice 30
6 Step 5: Inferring Trees—Practical Guidelines for
Fitting and Comparing Markov Substitution Models 31
6 1 Alignment Formats For Phylogeny Programs 31
6 2 Inferring Maximum Likelihood Phylogenies
using RAxML 32
viii Contents
6 3 Bayesian Analyses with PhyloBayes 32
6 4 Posterior Predictive Checks 34
7 Step 6: Interpreting the Phylogenetic Tree 35
Conclusions 40
Acknowledgements 41
References 41
i;
CHAPTER 3 The All-Species Living Tree Project 45
Pablo Yarza, Raul Munoz
1 Introduction 45
2 Sources of Information 46
2 1 Classification of Microbial Databases 46
3 Database Creation and Updating 50
4 Features of the Database 51
4 1 Optimized SSU and LSU Alignments 51
4 2 Curated Hierarchical Classification 51
4 3 Risk-Group Classification 53
4 4 Taxonomic Thresholds 54
5 Phylogenetic Trees 54
6 LTP as a Taxonomic Tool 55
Acknowledgements 57
References 57
CHAPTER 4 16S rRNA Gene-Based Identification of Bacteria
and Archaea using the EzTaxon Server 6i
Mincheol Kim, Jongsik Chun
1 Introduction 61
2 Use of 16S rRNA Gene Sequences in Prokaryotic
Systematics 62
2 1 Sequencing of I6S rRNA Genes 62
2 2 Calc ulation of Nucleotide Sequence Similarity
Values of 16S rRNA Gene Sequences 64
3 Identification of Bacteria using the EzTaxon
Database 64
3 1 EzTaxon Database 64
3 2 Algorithm for EzTaxon Search 65
3 3 Overall Workflow from Sanger DNA Sequence Data 67
3 4 Assembly and Trimming of Sequences 67
3 5 Manual Editing of Sequences using the Secondary
Structure Information 69
Contents
3 6 Identification of Strains using the EzTaxon Server 71
3 7 Phylogenetic Analysis 72
Concluding Remarks 72
Acknowledgement 72
References 73
CHAPTER 5 Revolutionizing Prokaryotic Systematics Through
Next-Generation Sequencing 75
Vartul Sangal, Leena Nieminen, Nicholas P Tucker,
, Paul A Hoskisson
A
1 Introduction 75
2 Sequencing Approaches 76
3 Bioinformatic Analyses 78
3 1 De Novo Assembly and Mapping 78
3 2 Annotation 81
3 3 Comparative Genomic Analysis 83
3 4 SNP Extraction and Functional Characterislics 87
3 5 Phylogenetic Analyses 87
4 Applications of Next-Generation Sequencing Technology 88
4 1 Prokaryotic Systematics 88
4 2 Pathogen Evolution, Transmission and Adaptation 89
4 3 Genetic Basis of Phenotypic Characteristics 90
4 4 Metagenomics 90
4 5 Target Resequencing 91
4 6 RNA-Seq and Transcriptomics 91
Conclusions 93
Acknowledgements 93
References 93
CHAPTER 6 Whole-Genome Analyses: Average Nucleotide
Identity 103
David R Arahal
1 Introduction 103
1 1 Calculation of Average Nucleotide Identity 103
1 2 Theoretical Background: BLAST/MUMmei Software 105
2 Preparation and DNA Sequencing 106
2 1 Strain Cultivation 106
2 2 DNA Extraction and Quantification 107
2 3 Whole-Genome Sequencing 108
3 ANI Calculations using JSpecies 109
3 1 Installation 109
x Contents
3 2 Operation 110
3 3 Calculations On-Line 114
4 Interpretation and Publication of Results 114
5 Application to Prokaryotic Classification: Case Studies 114
Concluding Remarks 117
Acknowledgements 117
!, References ! 117
CHAPTER 7 Whole-Genome Sequencing for Rapid and
Accurate Identification of Bacterial
Transmission Pathways 123
Simon R Harris, Chinyere K Okoro
1 Introduction 123
2 The Sequencing Revolution 124
2 1 Second-Generation Sequencing Technologies 125
3 Bacterial Typing with Next-Generation Sequencing 128
4 Identifying Transmission Pathways Using Whole-Genome
Sequencing - The Toolkit 129
4 1 Mapping and Alignment of Whole Genomes 132
4 2 Dc novo Assembly and Genome Alignment 134
4 3 Identifying Variation from Whole-Genome Assemblies 137
4 4 Identifying Transmissions Using Whole-Genome
Variation 140
5 Combining Genomic and Epidemiological Evidence 144
6 Future Directions 145
References 147
CHAPTER 8 Identification of Conserved Indels that are
Useful for Classification and Evolutionary
Studies 153
Radhey S Gupta
1 Limitations of the Phylogenetic Trees for Understanding
Microbial Classification 153
2 Characteristics that are Well-Suited for Classification 154
3 Conserved Signature Indels and their Usefulness for
Classification and Evolutionary Studies 155
4 Identification of Conserved Signature Indels in Protein
Sequences 157
4 1 Creation of Multiple Sequence Alignments 158
4 2 Identification of Potential Conserved Indels
in the Sequence Alignments 159
Contents
4 3 Blast Searches 011 Potential Conserved Indels
to Identify Useful Conserved Indels 163
4 4 Formatting of the Conserved Indels 164
5 Interpreting the Significance of Conserved Indels 167
6 Correspondence of the Results Obtained from CSIs with
rRNA and Other Phylogenetic Approaches 170
7 Importance of the Discovered CSIs for Understanding
Microbial Classification and Phylogeny 173
Acknowledgements 175
• References 175
CHAPTER 9 Reconciliation Approaches to Determining HGT,
Duplications, and Losses in Gene Trees 183
Olga K Kamneva, Naomi L Ward
1 Introduction 183
2 Bacterial Species Tree 184
3 Gene Family 185
4 Evolution of Genes in Bacterial Genomes 186
5 Gene Tree/Species Tree Reconciliation 188
5 1 Protocol for Running AnGST 191
5 2 Interpreting the Results of AnGST Analyses 192
6 Analysis at the Genome Scale 193
6 1 Protocol for Running COUNT 193
Concluding Remarks 195
Acknowledgements 197
References 198
CHAPTER 10 Multi-Locus Sequence Typing and the
Gene-by-Gene Approach to Bacterial
Classification and Analysis of Population
Variation 201
Alison J Cody, Julia S Bennett, Martin C J Maiden
1 Introduction 201
1 1 Historical Perspective 201
1 2 Multi-Locus Population Analyses 201
2 Multi-Locus Sequence Typing 202
3 Whole-Genome Data Analyses 203
3 1 Gene-by-Gene Analysis of WGS Data 204
3 2 The Bacterial Isolate Genome Sequence Database 204
3 3 Isolate and Sequence Databases 204
3 4 Reference Sequence and Profile Definitions Database 207
Contents
3 5 Database Integrity 207
3 6 Gene Nomenclature 209
3 7 Typing and Analysis Schemes 209
4 Examples of Gene-by-Gene Analysis: Neisseria 209
4 1 Ribosomal Multi-Locus Sequence Typing 210
4 2 Neisseria rplF Assay 211
5 Examples of Gene-by-Gene Analysis: Campylobacter 213
5 1 Core Genome Multi-Locus Sequence Typing 213
5 2 Whole-Genome Multi-Locus Sequence Typing 213
Conclusions 214
References 216
CHAPTER 11 Multi-locus Sequence Analysis: Taking
Prokaryotic Systematics to the Next Level 221
Xiaoying Rong, Ying Huang
1 Introduction 221
2 Multi-locus Sequence Analysis 222
2 1 Underlying Concepts 222
2 2 Selection of Gene Loci 223
2 3 Generating Sequences 223
2 4 Data Analysis 225
2 5 Comparison with Other Taxonomic Methods 227
2 6 MLS As: Advantages and Disadvantages 228
2 7 MLSA Databases 229
3 Application of MLSAs in Prokaryotic Systematics 229
3 1 The Genus Streptomyces 229
3 2 Classification of the S pratensis Phylogroup 239
3 3 MLSA of Phytopathogenic Streptomyces Species 242
3 4 MLSA: Actinobacteria 242
4 Detection of Ecotypes Based on MLSAs 243
5 MLSA Based on Whole Genome Sequences 245
References 246
CHAPTER 12 Bacterial Typing and Identification By Genomic
Analysis of 16S-23S rRNA Intergenic
Transcribed Spacer (ITS) Sequences 253
Volker Giirtler, Gangavarapu Stibrahmanyam,
Malathi Shekar, Biswajit Maiti, Indrani Karunasagar
1 Introduction 254
2 Methods 259
2 1 Search and Download Bacterial Whole-Genome
Sequences 259
Contents xiii
2 2 Annotation of r rn Alleles 260
2 3 Extraction of the Gene Components (I6S, 23S
and 5S) and Extra Genie Regions (ITS I, ITS2,
pre-16S and post-5S) that Make Up mi Alleles 260
2 4 Alignment of mi Gene Components and
Extra Genie Regions 263
25, Editing of mi Gene Components and Extra
Genie Region Alignment Files 263
2 6 Exporting Annotations and Associated Data from
i Geneious to Excel 266
2 7 Exporting and Drawing Genome, Restriction
and Alignment Maps in Illustrator 266
2 8 Design of Excel Tables for FileMaker Database
Construction 267
2 9 Construction of FileMaker Database from
Excel Tables 267
2 10 Design of FileMaker Statistical and Graphical
Reports 267
2 11 A New Way of Reporting Large Amounts
of Statistical and Graphical Information
in FileMaker Go 268
3 Results 268
3 1 Sequence Acquisition and Preparation 268
3 2 Extraction of mi Operon Genes and Sequence
Alignment 268
3 3 Annotation of Sequence Differences in the r rn
Operons 269
3 4 Graphical Presentation of Alignments, Operon
Restriction Maps and Whole-Genome Maps 269
3 5 Statistical Presentation of Annotation and Metadata,
Linking Alignments, Whole Genomes, r rn
Operon Alleles, Strains and Organotypes 270
4 Discussion 270
References 271
CHAPTER 13 MALDI-T0F Mass Spectrometry Applied to
Classification and Identification of Bacteria 275
Peter Schumann, Thomas Maier
1 Introduction 275
2 Sample Preparation 276
2 1 Cultivation of Bacteria 276
xiv Contents
2 2 Selection of the Matrix and Composition of the
Matrix Solution 277
2 3 Direct Colony Transfer 281
2 4 Extraction Methods 282
2 5 Organism-Specific Sample Preparation 284
2 6 MALD1-TOF MS-Based Identification of Bacteria
in Complex Biological Matrices 286
• 3 Optimisation of Measurement Conditions 289
3 1 MALDI-TOF MS Library Creation 290
4 Application of MALDI-TOF MS for Classification and
Identification 291
4 1 Software Used for Taxonomic Evaluation of
MALDI-TOF Mass Spectra 291
4 2 Classification and Taxonomic Resolution 292
4 3 Identification 297
4 4 MALDI-TOF MS and Discovery of Novel Organisms 298
Conclusions and Outlook 299
Acknowledgements 300
References 300
CHAPTER 14 Continuing Importance of the Phenotype
in the Genomic Era 307
Peter Kampfer
1 Phylogeny and Genotype 307
2 The Phenotype 312
3 The Ongoing Importance of the Phenotype in an
Organism Based Taxonomy 313
Conclusions and Challenges 315
References 315
Index 321
|
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| spelling | New approaches to prokaryotic systematics ed. by Michael Goodfellow ... 1. ed. Amsterdam [u.a.] Elsevier, Acad. Press 2014 XIX, 327 S., [10] Bl. Ill., graph. Darst. 24 cm txt rdacontent n rdamedia nc rdacarrier Methods in microbiology 41 Prokaryotes Goodfellow, Michael 1941- (DE-588)1067508635 edt Methods in microbiology 41 (DE-604)BV000899780 41 HEBIS Datenaustausch application/pdf http://bvbr.bib-bvb.de:8991/F?func=service&doc_library=BVB01&local_base=BVB01&doc_number=027727611&sequence=000002&line_number=0001&func_code=DB_RECORDS&service_type=MEDIA Inhaltsverzeichnis |
| spellingShingle | New approaches to prokaryotic systematics Methods in microbiology Prokaryotes |
| title | New approaches to prokaryotic systematics |
| title_auth | New approaches to prokaryotic systematics |
| title_exact_search | New approaches to prokaryotic systematics |
| title_full | New approaches to prokaryotic systematics ed. by Michael Goodfellow ... |
| title_fullStr | New approaches to prokaryotic systematics ed. by Michael Goodfellow ... |
| title_full_unstemmed | New approaches to prokaryotic systematics ed. by Michael Goodfellow ... |
| title_short | New approaches to prokaryotic systematics |
| title_sort | new approaches to prokaryotic systematics |
| topic | Prokaryotes |
| topic_facet | Prokaryotes |
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