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Bacterial Taxonomy

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J. M. Young – One of the best experts on this subject based on the ideXlab platform.

  • Classification, Naming, and Plant Pathogenic Bacteria — What is to be done?
    Plant Pathogenic Bacteria, 2020
    Co-Authors: J. M. Young

    Abstract:

    Recent developments in Bacterial Taxonomy are outlined with a discussion of alternative systems of classification, and with their implications for plant pathogenic bacteria. The status of pathovars and their application is discussed.

  • implications of alternative classifications and horizontal gene transfer for Bacterial Taxonomy
    International Journal of Systematic and Evolutionary Microbiology, 2001
    Co-Authors: J. M. Young

    Abstract:

    Following the publication of the Approved Lists, there has been a tendency to regard all subsequent revisions of classification as providing improved nomenclature, to be accepted without question. This takes no account of the fact that such revisions may be based on one of three alternative concepts, phenetic, phylogenetic or polyphasic classification, sometimes leading to different, valid, but incompatible nomenclature, or that some investigations are based only on subsets of relevant taxa and on limited data, leading to incomplete and sometimes confusing revisions of nomenclature. The polyphasic approach to classification has widespread support, although there appears to be a tendency to allow comparative sequence analyses of 16S rDNA to determine classification contrary to the indications of other data. In some cases, classification is based solely on 16S rDNA data. Examples are considered. Consideration is given to the criteria by which taxa are circumscribed, particularly at the level of genus and species. It is suggested that there is a need for reconciliation of the criteria by which taxa at these levels are circumscribed. Recent studies demonstrating the widespread occurrence of horizontal gene transfer suggest that there is a need for caution in monophyletic interpretations, especially when these are based on the analysis of single sequences.

Jean Swings – One of the best experts on this subject based on the ideXlab platform.

  • Towards a prokaryotic genomic Taxonomy.
    Fems Microbiology Reviews, 2005
    Co-Authors: Tom Coenye, Dirk Gevers, Peter Vandamme, Yves Van De Peer, Jean Swings

    Abstract:

    One of the most interesting developments in the field of modern-day microbiology is the ever increasing number of whole-genome sequences that is publicly available. There is an increasing interest in the use of these genome sequences to assess evolutionary relationships among microbial taxa, as it is anticipated that much additional taxonomic information can be extracted from these sequences. In a first part of the present review, mechanisms that are responsible for the evolution of genomes will be discussed. Subsequently, we will give an overview of approaches that are presently available to assess the taxonomic relationships between prokaryotic species based on complete genome sequences, followed by a brief discussion of the potential implications of these novel approaches for Bacterial Taxonomy in general and our thinking about the Bacterial species concept in particular.

  • Towards a prokaryotic genomic Taxonomy
    FEMS Microbiology Reviews, 2005
    Co-Authors: Tom Coenye, Dirk Gevers, Y. Van De Peer, Peter Vandamme, Jean Swings

    Abstract:

    One of the most interesting developments in the field of modern-day microbiology is the ever increasing number of whole-genome sequences that is publicly available. There is an increasing interest in the use of these genome sequences to assess evolutionary relationships among microbial taxa, as it is anticipated that much additional taxonomic information can be extracted from these sequences. In a first part of the present review, mechanisms that are responsible for the evolution of genomes will be discussed. Subsequently, we will give an overview of approaches that are presently available to assess the taxonomic relationships between prokaryotic species based on complete genome sequences, followed by a brief discussion of the potential implications of these novel approaches for Bacterial Taxonomy in general and our thinking about the Bacterial species concept in particular. © 2004 Federation of European Microbiological Societies. Published by Elsevier B.V. All rights reserved.

  • New Methods for the Analysis of Binarized BIOLOG GN Data of Vibrio species: Minimization of Stochastic Complexity and Cumulative Classification
    Systematic and Applied Microbiology, 2004
    Co-Authors: Mats Gyllenberg, Timo Koski, Tatu Lund, Peter Dawyndt, Fabiano L. Thompson, Brian Austin, Jean Swings

    Abstract:

    We apply minimization of stochastic complexity and the closely related method of cumulative classification to analyse the extensively studied BIOLOG GN data of Vibrio spp. Minimization of stochastic complexity provides an objective tool of Bacterial Taxonomy as it produces classifications that are optimal from the point of view of information theory. We compare the outcome of our results with previously published classifications of the same data set. Our results both confirm earlier detected relationships between species and discover new ones.

S T Koike – One of the best experts on this subject based on the ideXlab platform.

  • practical benefits of knowing the enemy modern molecular tools for diagnosing the etiology of Bacterial diseases and understanding the Taxonomy and diversity of plant pathogenic bacteria
    Annual Review of Phytopathology, 2015
    Co-Authors: Carolee T Bull, S T Koike

    Abstract:

    Knowing the identity of Bacterial plant pathogens is essential to strategic and sustainable disease management in agricultural systems. This knowledge is critical for growers, diagnosticians, extension agents, and others dealing with crops. However, such identifications are linked to Bacterial Taxonomy, a complicated and changing discipline that depends on methods and information that are often not used by those who are diagnosing field problems. Modern molecular tools for fingerprinting and sequencing allow for pathogen identification in the absence of distinguishing or conveniently tested phenotypic characteristics. These methods are also useful in studying the etiology and epidemiology of phytopathogenic bacteria from epidemics, as was done in numerous studies conducted in California’s Salinas Valley. Multilocus and whole-genome sequence analyses are becoming the cornerstones of studies of microbial diversity and Bacterial Taxonomy. Whole-genome sequence analysis needs to become adequately accessible, …