Bacterial taxonomics: finding the wood through the phylogenetic trees.

Bacterial taxonomy comprises systematics (theory of classification), nomenclature (formal process of naming), and identification. There are two basic approaches to classification. Similarities may be derived between microorganisms by numerical taxonomic methods based on a range of present-day observable characteristics (phenetics), drawing in particular on conventional morphological and physiological test characters as well as chemotaxonomic markers such as whole-cell protein profiles, mol% G+C content, and DNA-DNA homologies. By contrast, phylogenetics, the process of reconstructing possible evolutionary relationships, uses nucleotide sequences from conserved genes that act as molecular chronometers. A combination of both phenetics and phylogenetics is referred to as polyphasic taxonomy, and is the recommended strategy in description of new species and genera. Numerical analysis of small-subunit ribosomal RNA genes (rDNA) leading to the construction of branching trees representing the distance of divergence from a common ancestor has provided the mainstay of microbial phylogenetics. The approach has some limitations, particularly in the discrimination of closely related taxa, and there is a growing interest in the use of alternative loci as molecular chronometers, such as gyrA and RNAase P sequences. Comparison of the degree of congruence between phylogenetic trees derived from different genes provides a valuable test of the extent they represent gene trees or species trees. Rapid expansion in genome sequences will provide a rich source of data for future taxonomic analysis that should take into account population structure of taxa and novel methods for analysis of nonclonal bacterial populations.

[1]  W. Whitman,et al.  Report of the ad hoc committee for the re-evaluation of the species definition in bacteriology. , 2002, International journal of systematic and evolutionary microbiology.

[2]  K. Kakinuma,et al.  Phylogenetic Analysis of Salmonella, Shigella, and Escherichia coli Strains on the Basis of the gyrB Gene Sequence , 2002, Journal of Clinical Microbiology.

[3]  L. Pauling,et al.  Molecules as documents of evolutionary history. , 1965, Journal of theoretical biology.

[4]  S. Harayama,et al.  Phylogenetic analysis of Acinetobacter strains based on the nucleotide sequences of gyrB genes and on the amino acid sequences of their products. , 1996, International journal of systematic bacteriology.

[5]  M. Kimura A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences , 1980, Journal of Molecular Evolution.

[6]  M. Mulvey,et al.  Rapid Identification of Campylobacter,Arcobacter, and Helicobacter Isolates by PCR-Restriction Fragment Length Polymorphism Analysis of the 16S rRNA Gene , 1999, Journal of Clinical Microbiology.

[7]  S. T. Cowan,et al.  A Dictionary of Microbial Taxonomy. , 1978 .

[8]  Catherine Dauga,et al.  Evolution of the gyrB gene and the molecular phylogeny of Enterobacteriaceae: a model molecule for molecular systematic studies. , 2002, International journal of systematic and evolutionary microbiology.

[9]  R. Colwell Polyphasic Taxonomy of the Genus Vibrio: Numerical Taxonomy of Vibrio cholerae, Vibrio parahaemolyticus, and Related Vibrio Species , 1970, Journal of bacteriology.

[10]  Erko Stackebrandt,et al.  Taxonomic Note: A Place for DNA-DNA Reassociation and 16S rRNA Sequence Analysis in the Present Species Definition in Bacteriology , 1994 .

[11]  T. Jukes CHAPTER 24 – Evolution of Protein Molecules , 1969 .

[12]  P. Vandamme,et al.  Phylogenetic characterization of 'Candidatus Helicobacter bovis', a new gastric helicobacter in cattle. , 1999, International journal of systematic bacteriology.

[13]  C. Harrington,et al.  Extensive 16S rRNA gene sequence diversity in Campylobacter hyointestinalis strains: taxonomic and applied implications. , 1999, International journal of systematic bacteriology.

[14]  P. Vandamme,et al.  'Candidatus Helicobacter suis', a gastric helicobacter from pigs, and its phylogenetic relatedness to other gastrospirilla. , 1999, International journal of systematic bacteriology.

[15]  Dieter Naumann,et al.  Characterization and Identification of Micro-Organisms by FT-IR Spectroscopy and FT-IR Microscopy , 1994 .

[16]  D. Linton,et al.  Sequence similarities between large subunit ribosomal RNA gene intervening sequences from different Helicobacter species. , 1997, Gene.

[17]  N. Saitou,et al.  The neighbor-joining method: a new method for reconstructing phylogenetic trees. , 1987, Molecular biology and evolution.

[18]  H. Lior,et al.  Proposal of minimal standards for describing new species of the family Campylobacteraceae. , 1994, International journal of systematic bacteriology.

[19]  P. Vandamme,et al.  Interlaboratory comparative study of the numerical analysis of one‐dimensional sodium dodecyl sulphate‐polyacrylamide gel electrophoretic protein patterns of Campylobacter strains , 1990, Electrophoresis.

[20]  R. Owen,et al.  Current methods for estimating DNA base composition and levels of DNA-DNA hybridization , 1985 .

[21]  Thomas Huber,et al.  Chimeric 16S rDNA sequences of diverse origin are accumulating in the public databases. , 2003, International journal of systematic and evolutionary microbiology.

[22]  D. Falush,et al.  Recombination and mutation during long-term gastric colonization by Helicobacter pylori: Estimates of clock rates, recombination size, and minimal age , 2001, Proceedings of the National Academy of Sciences of the United States of America.

[23]  O. Kandler,et al.  International Committee on Systematic Bacteriology: announcement of the report of the ad hoc Committee on Reconciliation of Approaches to Bacterial Systematics. , 1987, Zentralblatt fur Bakteriologie, Mikrobiologie, und Hygiene. Series A, Medical microbiology, infectious diseases, virology, parasitology.

[24]  J. Ley,et al.  Intra- and Intergeneric Similarities of Agrobacterium Ribosomal Ribonucleic Acid Cistrons , 1977 .

[25]  R. Owen,et al.  A Rapid Identification Scheme for Helicobacter pylori and Other Species of Helicobacter Based on 23S , 1997 .

[26]  N. Pace,et al.  Evolutionary perspective on the structure and function of ribonuclease P, a ribozyme , 1995, Journal of bacteriology.

[27]  Mark Blaxter,et al.  Molecular systematics: Counting angels with DNA , 2003, Nature.

[28]  K. Kersters 13 – Numerical Methods in the Classification of Bacteria by Protein Electrophoresis , 1985 .

[29]  P. Vandamme,et al.  Analysis of electrophoretic whole organism protein fingerprints , 1994 .

[30]  P H Sneath,et al.  Evidence from Aeromonas for genetic crossing-over in ribosomal sequences. , 1993, International journal of systematic bacteriology.

[31]  R. Sokal,et al.  Principles of numerical taxonomy , 1965 .

[32]  H. Ogata,et al.  Phylogenetic classification of Bartonella species by comparing groEL sequences. , 2002, International journal of systematic and evolutionary microbiology.

[33]  J. Logan,et al.  Campylobacter hominis sp. nov., from the human gastrointestinal tract. , 2001, International journal of systematic and evolutionary microbiology.

[34]  A. J. Kluyver,et al.  Prospects for a Natural System of Classification of Bacteria. , 1936 .

[35]  P. Leopold,et al.  Phyloproteomics: species identification of Enterobacteriaceae using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry. , 2001, Journal of molecular microbiology and biotechnology.

[36]  F. Dewhirst,et al.  Helicobacter pullorum sp. nov.-genotype and phenotype of a new species isolated from poultry and from human patients with gastroenteritis. , 1994, Microbiology.

[37]  Conserved and variable domains within divergent rnase P RNA gene sequences of Prochlorococcus strains. , 2002, International journal of systematic and evolutionary microbiology.

[38]  P. Sneath,et al.  Approved lists of bacterial names. , 1980, The Medical journal of Australia.

[39]  S. N. Davey,et al.  The rapid identification of intact microorganisms using mass spectrometry , 1996, Nature Biotechnology.

[40]  J. Young,et al.  Implications of alternative classifications and horizontal gene transfer for bacterial taxonomy. , 2001, International journal of systematic and evolutionary microbiology.

[41]  P. Reeves,et al.  Intraspecies variation in bacterial genomes: the need for a species genome concept. , 2000, Trends in microbiology.

[42]  James W. Brown,et al.  Structure and evolution of ribonuclease P RNA in Gram-positive bacteria. , 1996, Nucleic acids research.

[43]  B. Holmes,et al.  Classification and Identification of Campylobacters, Helicobacters and Allied Taxa by Numerical Analysis of Phenotypic Characters , 1995 .

[44]  E. Stackebrandt,et al.  Nucleic acid techniques in bacterial systematics , 1991 .

[45]  T. Ezaki,et al.  A Rapid Method for Determining the Gmc Content of Bacterial Chromosomes by Monitoring Fluorescence Intensity during Dna Denaturation in a Capillary Tube , 2022 .

[46]  S. Orla-Jensen,et al.  THE MAIN LINES OF THE NATURAL BACTERIAL SYSTEM , 1921, Journal of bacteriology.

[47]  K. Schleifer,et al.  Bacterial phylogeny based on 16S and 23S rRNA sequence analysis. , 1994, FEMS microbiology reviews.

[48]  J. Logan,et al.  Genome Sequence-Based Fluorescent Amplified Fragment Length Polymorphism of Campylobacter jejuni, Its Relationship to Serotyping, and Its Implications for Epidemiological Analysis , 2001, Journal of Clinical Microbiology.

[49]  G. McCormack,et al.  The application of molecular phylogenetics to the analysis of viral genome diversity and evolution , 2002, Reviews in medical virology.

[50]  E. Stackebrandt,et al.  Taxonomic note: implementation of the provisional status Candidatus for incompletely described procaryotes. , 1995, International journal of systematic bacteriology.

[51]  D. Linton,et al.  16S rRNA gene sequences of 'Candidatus Campylobacter hominis', a novel uncultivated species, are found in the gastrointestinal tract of healthy humans. , 1998, Microbiology.

[52]  J. Marmur A procedure for the isolation of deoxyribonucleic acid from micro-organisms , 1961 .

[53]  G. Sachs,et al.  A H+-gated urea channel: the link between Helicobacter pylori urease and gastric colonization. , 2000, Science.

[54]  R. Amann,et al.  The species concept for prokaryotes. , 2013, FEMS microbiology reviews.

[55]  D. Minnikin,et al.  Chemical methods in bacterial systematics , 1985 .

[56]  P. Lio’,et al.  Molecular phylogenetics: state-of-the-art methods for looking into the past. , 2001, Trends in genetics : TIG.

[57]  P. de Vos,et al.  Polyphasic Taxonomy , a Consensus Approach to Bacterial Systematics , 1996 .

[58]  R A Clayton,et al.  Intraspecific variation in small-subunit rRNA sequences in GenBank: why single sequences may not adequately represent prokaryotic taxa. , 1995, International journal of systematic bacteriology.

[59]  M. Achtman,et al.  Evolution of Helicobacter pylori: the role of recombination. , 1999, Trends in microbiology.

[60]  Ross A. Overbeek,et al.  The RDP (Ribosomal Database Project) , 1997, Nucleic Acids Res..

[61]  Ernst Haeckel Generelle morphologie der organismen. Allgemeine grundzüge der organischen formen-wissenschaft, mechanisch begründet durch die von Charles Darwin reformirte descendenztheorie, von Ernst Haeckel , 1866 .

[62]  F. Dewhirst,et al.  Recommended minimal standards for describing new species of the genus Helicobacter. , 2000, International journal of systematic and evolutionary microbiology.