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New Approaches to Prokaryotic Systematics - 1st Edition - ISBN: 9780128001769, 9780128004432

New Approaches to Prokaryotic Systematics, Volume 41

1st Edition

Editors: Michael Goodfellow Iain Sutcliffe Jongsik Chun
Hardcover ISBN: 9780128001769
eBook ISBN: 9780128004432
Imprint: Academic Press
Published Date: 25th November 2014
Page Count: 348
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Table of Contents

  • Dedication
  • Preface
  • Chapter 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
  • Chapter 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
  • Chapter 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
  • Chapter 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
  • Chapter 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
  • Chapter 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
  • Chapter 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
  • Chapter 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
  • Chapter 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
  • Chapter 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
  • Chapter 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
  • Chapter 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
  • Chapter 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
  • Chapter 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


Volume 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.

Key Features

  • 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.


No. of pages:
© Academic Press 2014
25th November 2014
Academic Press
Hardcover ISBN:
eBook ISBN:

Ratings and Reviews

About the Editors

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, UK

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, UK

Jongsik Chun

Affiliations and Expertise

Seoul National University, Seoul, Republic of Korea