The Experts below are selected from a list of 285 Experts worldwide ranked by ideXlab platform
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, 2020Co-Authors: J. M. YoungAbstract: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, 2001Co-Authors: J. M. YoungAbstract: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, 2005Co-Authors: Tom Coenye, Dirk Gevers, Peter Vandamme, Yves Van De Peer, Jean SwingsAbstract: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, 2005Co-Authors: Tom Coenye, Y. Van De Peer, Dirk Gevers, Peter Vandamme, Jean SwingsAbstract: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, 2004Co-Authors: Mats Gyllenberg, Timo Koski, Brian Austin, Tatu Lund, Peter Dawyndt, Fabiano L. Thompson, Jean SwingsAbstract: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.
-
evaluation of the dna fingerprinting method aflp as a new tool in Bacterial Taxonomy
Microbiology, 1996Co-Authors: Paul Janssen, Jean Swings, Renata Coopman, Geert Huys, Marjo Bleeker, Marc Zabeau, Karel KerstersAbstract:We investigated the usefulness of a novel DNA fingerprinting technique, AFLP, which is based on the selective amplification of genomic restriction fragments by PCR, to differentiate Bacterial strains at the subgeneric level. In total, 147 Bacterial strains were subjected to AFLP fingerprinting: 36 Xanthomonas strains, including 23 pathovars of Xanthomonas axonopodis and six pathovars of Xanthomonas vasicola, one strain of Stenotrophomonas, 90 genotypically characterized strains comprising all 14 hybridization groups currently described in the genus Aeromonas, and four strains of each of the genera Clostridium, Bacillus, Acinetobacter, Pseudomonas and Vibrio. Depending on the genus, total genomic DNA of each bacterium was digested with a particular combination of two restriction endonucleases and the resulting fragments were ligated to restriction halfsite-specific adaptors. These adaptors served as primer-binding sites allowing the fragments to be amplified by selective PCR primers that extend beyond the adaptor and restriction site sequences. Following electrophoretic separation on 5% (w/v) polyacrylamide/8.3 M urea, amplified products could be visualized by autoradiography because one of the selective primers was radioactively labelled. The resulting banding patterns, containing approximately 30-50 visualized PCR products in the size range 80-550 bp, were captured by a high-resolution densitoscanner and further processed for computer-assisted analysis to determine band-based similarity coefficients. This study reveals extensive evidence for the applicability of AFLP in Bacterial Taxonomy through comparison of the newly obtained data with results previously obtained by well-established genotypic and chemotaxonomic methods such as DNA-DNA hybridization and cellular fatty acid analysis. In addition, this study clearly demonstrates the superior discriminative power of AFLP towards the differentiation of highly related Bacterial strains that belong to the same species or even biovar (i.e. to characterize strains at the infrasubspecific level), highlighting the potential of this novel fingerprinting method in epidemiological and evolutionary studies.
-
Polyphasic Taxonomy, a consensus approach to Bacterial systematics
Microbiological Reviews, 1996Co-Authors: Peter Vandamme, Mark Gillis, P. De Vos, Bruno Pot, Karel Kersters, Jean SwingsAbstract:Over the last 25 years, a much broader range of taxonomic studies of bacteria has gradually replaced the former reliance upon morphological, physiological, and biochemical characterization. This polyphasic Taxonomy takes into account all available phenotypic and genotypic data and integrates them in a consensus type of classification, framed in a general phylogeny derived from 16S rRNA sequence analysis. In some cases, the consensus classification is a compromise containing a minimum of contradictions. It is thought that the more parameters that will become available in the future, the more polyphasic classification will gain stability. In this review, the practice of polyphasic Taxonomy is discussed for four groups of bacteria chosen for their relevance, complexity, or both: the genera Xanthomonas and Campylobacter, the lactic acid bacteria, and the family Comamonadaceae. An evaluation of our present insights, the conclusions derived from it, and the perspectives of polyphasic Taxonomy are discussed, emphasizing the keystone role of the species. Taxonomists did not succeed in standardizing species delimitation by using percent DNA hybridization values. Together with the absence of another "gold standard" for species definition, this has an enormous repercussion on Bacterial Taxonomy. This problem is faced in polyphasic Taxonomy, which does not depend on a theory, a hypothesis, or a set of rules, presenting a pragmatic approach to a consensus type of Taxonomy, integrating all available data maximally. In the future, polyphasic Taxonomy will have to cope with (i) enormous amounts of data, (ii) large numbers of strains, and (iii) data fusion (data aggregation), which will demand efficient and centralized data storage. In the future, taxonomic studies will require collaborative efforts by specialized laboratories even more than now is the case. Whether these future developments will guarantee a more stable consensus classification remains an open question.
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, 2015Co-Authors: Carolee T Bull, S T KoikeAbstract: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, ...
Philip Hugenholtz - One of the best experts on this subject based on the ideXlab platform.
-
a standardized Bacterial Taxonomy based on genome phylogeny substantially revises the tree of life
Nature Biotechnology, 2018Co-Authors: Donovan H Parks, Maria Chuvochina, David W Waite, Christian Rinke, Adam Skarshewski, Pierrealain Chaumeil, Philip HugenholtzAbstract:Interpretation of microbial genome data will be improved by a fully revised Bacterial Taxonomy.
-
a proposal for a standardized Bacterial Taxonomy based on genome phylogeny
bioRxiv, 2018Co-Authors: Donovan H Parks, Maria Chuvochina, David W Waite, Christian Rinke, Adam Skarshewski, Pierrealain Chaumeil, Philip HugenholtzAbstract:Taxonomy is a fundamental organizing principle of biology, which ideally should be based on evolutionary relationships. Microbial Taxonomy has been greatly restricted by the inability to obtain most microorganisms in pure culture and, to a lesser degree, the historical use of phenotypic properties as the basis for classification. However, we are now at the point of obtaining genome sequences broadly representative of microbial diversity by using culture-independent techniques, which provide the opportunity to develop a comprehensive genome-based Taxonomy. Here we propose a standardized Bacterial Taxonomy based on a concatenated protein phylogeny that conservatively removes polyphyletic groups and normalizes ranks based on relative evolutionary divergence. From 94,759 Bacterial genomes, 99 phyla are described including six major normalized monophyletic units from the subdivision of the Proteobacteria, and amalgamation of the Candidate Phyla Radiation into the single phylum Patescibacteria. In total, 73% of taxa had one or more changes to their existing Taxonomy.
Brian Austin - One of the best experts on this subject based on the ideXlab platform.
-
Taxonomy of Bacterial fish pathogens
Veterinary Research, 2011Co-Authors: Brian AustinAbstract:Bacterial Taxonomy has progressed from reliance on highly artificial culture-dependent techniques involving the study of phenotype (including morphological, biochemical and physiological data) to the modern applications of molecular biology, most recently 16S rRNA gene sequencing, which gives an insight into evolutionary pathways (= phylogenetics). The latter is applicable to culture-independent approaches, and has led directly to the recognition of new uncultured Bacterial groups, i.e. "Candidatus", which have been associated as the cause of some fish diseases, including rainbow trout summer enteritic syndrome. One immediate benefit is that 16S rRNA gene sequencing has led to increased confidence in the accuracy of names allocated to Bacterial pathogens. This is in marked contrast to the previous dominance of phenotyping, and identifications, which have been subsequently challenged in the light of 16S rRNA gene sequencing. To date, there has been some fluidity over the names of Bacterial fish pathogens, with some, for example Vibrio anguillarum, being divided into two separate entities (V. anguillarum and V. ordalii). Others have been combined, for example V. carchariae, V. harveyi and V. trachuri as V. harveyi. Confusion may result with some organisms recognized by more than one name; V. anguillarum was reclassified as Beneckea and Listonella, with Vibrio and Listonella persisting in the scientific literature. Notwithstanding, modern methods have permitted real progress in the understanding of the taxonomic relationships of many Bacterial fish pathogens.
-
New Methods for the Analysis of Binarized BIOLOG GN Data of Vibrio species: Minimization of Stochastic Complexity and Cumulative Classification
Systematic and Applied Microbiology, 2004Co-Authors: Mats Gyllenberg, Timo Koski, Brian Austin, Tatu Lund, Peter Dawyndt, Fabiano L. Thompson, Jean SwingsAbstract: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.
