New Approaches to Prokaryotic Systematics: Volume 41(Volume 41 Methods in Microbiology)

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.

Table of Contents:
1. The Need for Change: Embracing the Genome William B. Whitman 2. An Introduction to Phylogenetics and The Tree of Life1 Tom A. Williams and Sarah E. Heap 3. The All-Species Living Tree Project Pablo Yarza and Raul Munoz 4. 16S rRNA Gene-based Identification of Bacteria and Archaea using the EzTaxon Server Mincheol Kim and Jongsik Chun 5. Revolutionising Prokaryotic Systematics Through Next-Generation Sequencing Vartul Sangal, Leena Nieminen, Nicholas P. Tucker and Paul A. Hoskisson 6. Whole Genome Analyses: Average Nucleotide Identity David R. Arahal 7. Whole-Genome Sequencing for Rapid and Accurate Identification of Bacterial Transmission Pathways Simon R. Harris and Chinyere K. Okoro 8. Identification of Conserved Indels that are useful for Classification and Evolutionary Studies Radhey S. Gupta 9. Reconciliation Approaches to Determining HGT, Duplications, and Losses in Gene Trees Olga K.Kamneva and Naomi L. Ward 10. Multi-locus Sequence Typing and the Gene-by-Gene Approach to Bacterial Classification and Analysis of Population Variation Alison J. Cody, Julia S. Bennett and Martin C.J. Maiden 11. Multilocus Sequence Analysis: Bringing Bacterial Systematics to the Next Level Xiaoying Rong and Ying Huang 12. Bacterial Typing and Identification by Genomic Analysis of 16s-23s rRNA Intergenic Spacer (ITS) Sequences Volker Gürtler, Gangavarapu Subrahmanyam, Malathi Shakar, Biswajit Maiti and Indrani Karunasagar 13. MALDI-TOF Mass Spectrometry Applied to Classification and Identification of Bacteria Peter Schumann and Thomas Maier 14. Continuing Importance of the “Phenotype” in the Genomic Era Peter Kämpfer

About the Author :
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. 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.