New Approaches to Prokaryotic Systematics
- 1st Edition, Volume 41 - November 24, 2014
- Imprint: Academic Press
- Editors: Michael Goodfellow, Iain Sutcliffe, Jongsik Chun
- Language: English
- Hardback ISBN:9 7 8 - 0 - 1 2 - 8 0 0 1 7 6 - 9
- eBook ISBN:9 7 8 - 0 - 1 2 - 8 0 0 4 4 3 - 2
Volume 41 of Methods in Microbiology is a methods book designed to highlight procedures that will revitalize the purposes and practices of prokaryotic system… Read more
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Request a sales quoteVolume 41 of Methods in Microbiology is a methods book designed to highlight procedures that will revitalize the purposes and practices of prokaryotic systematics.
This volume will notably show that genomics and computational biology are pivotal to the new direction of travel and will emphasise that new developments need to be built upon historical good practices, notably the continued use of the nomenclatural type concept and the requirement to deposit type strains in at least two service culture collections in different countries.
This volume will notably show that genomics and computational biology are pivotal to the new direction of travel and will emphasise that new developments need to be built upon historical good practices, notably the continued use of the nomenclatural type concept and the requirement to deposit type strains in at least two service culture collections in different countries.
- Detailed protocols on cutting edge methods
- Prepared by leading international experts in the relevant fields
The microbiological community sensu lato with particular focus on ecology, evolutionary microbiology and clinical microbiology
Dedication
Preface
1: The Need for Change: Embracing the Genome
Abstract
1 A brief history of genomic sequencing of prokaryotes
2 Why sequence the genomes of prokaryotes?
3 The state-of-the-art
4 Where we are going
Acknowledgement
2: An Introduction to Phylogenetics and the Tree of Life
Abstract
1 Introduction
2 Step 1: posing a question
3 Step 2: choosing relevant sequences
4 Step 3: Aligning sequences and editing the alignment
5 Step 4: The theory of fitting and selecting a phylogenetic model
6 Step 5: inferring trees—practical guidelines for fitting and comparing markov substitution models
7 Step 6: Interpreting the phylogenetic tree
Conclusions
Acknowledgements
3: The All-Species Living Tree Project
Abstract
1 Introduction
2 Sources of information
3 Database creation and updating
4 Features of the database
5 Phylogenetic trees
6 LTP as a taxonomic tool
Acknowledgements
4: 16S rRNA Gene-Based Identification of Bacteria and Archaea using the EzTaxon Server
Abstract
1 Introduction
2 Use of 16S rRNA gene sequences in prokaryotic systematics
3 Identification of bacteria using the EzTaxon database
Concluding remarks
Acknowledgement
5: Revolutionizing Prokaryotic Systematics Through Next-Generation Sequencing
Abstract
1 Introduction
2 Sequencing approaches
3 Bioinformatic analyses
4 Applications of next-generation sequencing technology
Conclusions
Acknowledgements
6: Whole-Genome Analyses: Average Nucleotide Identity
Abstract
1 Introduction
2 Preparation and DNA Sequencing
3 ANI calculations using JSpecies
4 Interpretation and publication of results
5 Application to prokaryotic classification: case studies
Concluding remarks
Acknowledgements
7: Whole-Genome Sequencing for Rapid and Accurate Identification of Bacterial Transmission Pathways
Abstract
1 Introduction
2 The sequencing revolution
3 Bacterial typing with next-generation sequencing
4 Identifying transmission pathways using whole-genome sequencing – The toolkit
5 Combining genomic and epidemiological evidence
6 Future directions
8: Identification of Conserved Indels that are Useful for Classification and Evolutionary Studies
Abstract
1 Limitations of the phylogenetic trees for understanding microbial classification
2 Characteristics that are well-suited for classification
3 Conserved signature indels and Their usefulness for classification and evolutionary studies
4 Identification of conserved signature indels in protein sequences
5 Interpreting the significance of conserved indels
6 Correspondence of the results obtained from csis with rrna and other phylogenetic approaches
7 Importance of the discovered CSIs for understanding microbial classification and phylogeny
Acknowledgements
9: Reconciliation Approaches to Determining HGT, Duplications, and Losses in Gene Trees
Abstract
1 Introduction
2 Bacterial species tree
3 Gene family
4 Evolution of genes in bacterial genomes
5 Gene tree/species tree reconciliation
6 Analysis at the genome scale
Concluding Remarks
Acknowledgements
10: Multi-Locus Sequence Typing and the Gene-by-Gene Approach to Bacterial Classification and Analysis of Population Variation
Abstract
1 Introduction
2 Multi-locus sequence typing
3 Whole-genome data analyses
4 Examples of gene-by-gene analysis: neisseria
5 Examples of gene-by-gene analysis: campylobacter
Conclusions
11: Multi-locus Sequence Analysis: Taking Prokaryotic Systematics to the Next Level
Abstract
1 Introduction
2 Multi-Locus sequence analysis
3 Application of MLSAs in prokaryotic systematics
4 Detection of ecotypes based on MLSAs
5 MLSA based on whole genome sequences
12: Bacterial Typing and Identification By Genomic Analysis of 16S–23S rRNA Intergenic Transcribed Spacer (ITS) Sequences
Abstract
1 Introduction
2 Methods
3 Results
4 Discussion
13: MALDI-TOF Mass Spectrometry Applied to Classification and Identification of Bacteria
Abstract
1 Introduction
2 Sample Preparation
3 Optimisation of measurement conditions
4 Application of MALDI-TOF MS for classification and identification
Conclusions and Outlook
Acknowledgments
14: Continuing Importance of the “Phenotype” in the Genomic Era
Abstract
1 Phylogeny and genotype
2 The Phenotype
3 The ongoing importance of the phenotype in an organism based taxonomy
Conclusions and challenges
Index
Preface
1: The Need for Change: Embracing the Genome
Abstract
1 A brief history of genomic sequencing of prokaryotes
2 Why sequence the genomes of prokaryotes?
3 The state-of-the-art
4 Where we are going
Acknowledgement
2: An Introduction to Phylogenetics and the Tree of Life
Abstract
1 Introduction
2 Step 1: posing a question
3 Step 2: choosing relevant sequences
4 Step 3: Aligning sequences and editing the alignment
5 Step 4: The theory of fitting and selecting a phylogenetic model
6 Step 5: inferring trees—practical guidelines for fitting and comparing markov substitution models
7 Step 6: Interpreting the phylogenetic tree
Conclusions
Acknowledgements
3: The All-Species Living Tree Project
Abstract
1 Introduction
2 Sources of information
3 Database creation and updating
4 Features of the database
5 Phylogenetic trees
6 LTP as a taxonomic tool
Acknowledgements
4: 16S rRNA Gene-Based Identification of Bacteria and Archaea using the EzTaxon Server
Abstract
1 Introduction
2 Use of 16S rRNA gene sequences in prokaryotic systematics
3 Identification of bacteria using the EzTaxon database
Concluding remarks
Acknowledgement
5: Revolutionizing Prokaryotic Systematics Through Next-Generation Sequencing
Abstract
1 Introduction
2 Sequencing approaches
3 Bioinformatic analyses
4 Applications of next-generation sequencing technology
Conclusions
Acknowledgements
6: Whole-Genome Analyses: Average Nucleotide Identity
Abstract
1 Introduction
2 Preparation and DNA Sequencing
3 ANI calculations using JSpecies
4 Interpretation and publication of results
5 Application to prokaryotic classification: case studies
Concluding remarks
Acknowledgements
7: Whole-Genome Sequencing for Rapid and Accurate Identification of Bacterial Transmission Pathways
Abstract
1 Introduction
2 The sequencing revolution
3 Bacterial typing with next-generation sequencing
4 Identifying transmission pathways using whole-genome sequencing – The toolkit
5 Combining genomic and epidemiological evidence
6 Future directions
8: Identification of Conserved Indels that are Useful for Classification and Evolutionary Studies
Abstract
1 Limitations of the phylogenetic trees for understanding microbial classification
2 Characteristics that are well-suited for classification
3 Conserved signature indels and Their usefulness for classification and evolutionary studies
4 Identification of conserved signature indels in protein sequences
5 Interpreting the significance of conserved indels
6 Correspondence of the results obtained from csis with rrna and other phylogenetic approaches
7 Importance of the discovered CSIs for understanding microbial classification and phylogeny
Acknowledgements
9: Reconciliation Approaches to Determining HGT, Duplications, and Losses in Gene Trees
Abstract
1 Introduction
2 Bacterial species tree
3 Gene family
4 Evolution of genes in bacterial genomes
5 Gene tree/species tree reconciliation
6 Analysis at the genome scale
Concluding Remarks
Acknowledgements
10: Multi-Locus Sequence Typing and the Gene-by-Gene Approach to Bacterial Classification and Analysis of Population Variation
Abstract
1 Introduction
2 Multi-locus sequence typing
3 Whole-genome data analyses
4 Examples of gene-by-gene analysis: neisseria
5 Examples of gene-by-gene analysis: campylobacter
Conclusions
11: Multi-locus Sequence Analysis: Taking Prokaryotic Systematics to the Next Level
Abstract
1 Introduction
2 Multi-Locus sequence analysis
3 Application of MLSAs in prokaryotic systematics
4 Detection of ecotypes based on MLSAs
5 MLSA based on whole genome sequences
12: Bacterial Typing and Identification By Genomic Analysis of 16S–23S rRNA Intergenic Transcribed Spacer (ITS) Sequences
Abstract
1 Introduction
2 Methods
3 Results
4 Discussion
13: MALDI-TOF Mass Spectrometry Applied to Classification and Identification of Bacteria
Abstract
1 Introduction
2 Sample Preparation
3 Optimisation of measurement conditions
4 Application of MALDI-TOF MS for classification and identification
Conclusions and Outlook
Acknowledgments
14: Continuing Importance of the “Phenotype” in the Genomic Era
Abstract
1 Phylogeny and genotype
2 The Phenotype
3 The ongoing importance of the phenotype in an organism based taxonomy
Conclusions and challenges
Index
- Edition: 1
- Volume: 41
- Published: November 24, 2014
- No. of pages (Hardback): 348
- No. of pages (eBook): 348
- Imprint: Academic Press
- Language: English
- Hardback ISBN: 9780128001769
- eBook ISBN: 9780128004432
MG
Michael Goodfellow
Professor Mike Goodfellow was awarded undergraduate and postgraduate degrees from the University of Liverpool where his life long interests in pure and applied microbial systematics began. He developed his expertise in actinobacterial systematics as an MRC Junior Research Fellow in the MRC Microbial Systematics Unit at the University of Leicester. At the University of Newcastle he helped pioneer the development of chemotaxonomic methods in prokaryotic systematics before focusing on the selective isolation, classification and screening of novel actinobacteria for new natural product leads drawing on financial support from industrial and governmental bodies. Until recently he was Chairman to the Board of Trustees of Bergey’s Manual Trust and was both senior editor and a major contributor to the Second Edition of Bergey’s Manual of Systematic Bacteriology which was devoted to The Actinobacteria.
Affiliations and expertise
Newcastle University, Newcastle upon Tyne, UKIS
Iain Sutcliffe
Prof Sutcliffe studied for his first degree in Biochemistry at the University of Newcastle upon Tyne, where he stayed on to complete a PhD in microbial membrane physiology, supervised by Dr Norman Shaw. Subsequent post-doctoral research notably included a Wellcome Trust Career Development Fellowship in Taxonomy (in the Department of Oral Biology, University of Newcastle upon Tyne) during which time his interested in cell envelope components as chemotaxonomic markers was developed. After a Senior Lectureship at the University of Sunderland (1996-2004) he moved to Northumbria University, where he is now Chair of Microbiology. His research focuses on the membrane-anchored molecules of bacteria, in particular bacterial lipoproteins (which appear to be a unique and ubiquitous feature of bacteria), lipoglycans and lipoteichoic acids. This work has been extended to using comparative genomics approaches to understand the diversity of microbial cell envelope structures at the phylum level, work underpinned by his interest in microbial systematics. Prof Sutcliffe is currently Editor-in-Chief of Antonie van Leeuwenhoek Journal of Microbiology and in this role has gained considerable experience of the procedures for describing new microbial taxa and the challenges facing microbial systematists.
Affiliations and expertise
Northumbria University, Newcastle upon Tyne, UKJC
Jongsik Chun
Affiliations and expertise
Seoul National University, Seoul, Republic of KoreaRead New Approaches to Prokaryotic Systematics on ScienceDirect