New Approaches to Prokaryotic Systematics

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.

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