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Polyphasic taxonomy

Polyphasic taxonomy refers to the currently accepted approach to classify bacteria. This approach aids in use of major paradigms in differentiating bacterial species, such as use of phenotypic properties, including morphological and biochemical properties, chemical markers and molecular based differences. The introduction of polyphasic approach in bacterial systematics has aided in resolving taxonomical position of several microbial taxa.

Early species concept for bacteria - morphospecies
Before the inclusion of polyphasic approach to taxonomy the definition of species in bacteria has been a source of confusion at various taxonomic hierarchies i.e., phylum, family, genus, species and clonal populations. The biological species concept introduced were not applicable to bacteria since sexual reproduction is not known in bacteria. Although genetic transfer between bacteria is known, the exchange of genetic elements can occur even between evolutionarily unrelated strains. Morphological species has been popular in the early days of microbial systematics and is still widely used for filamentous fungi. Morphological species concept has been found to be highly laborious and results might not reflect the phylogeny of the strains. Moreover, morphological similarity between different distinct bacterial species is also not uncommon.

Chemical markers
Bacterial cells, like most other cellular organisms, are rich in macromolecules such as amino acids, peptides, proteins, enzymes, lipids, polysaccharides and other related polymeric molecules, like isoprenoid quinones and sterols (Goodfellow, 2000). The break through in bacterial species identification was made with the realisation that these chemical markers were different amongst members of different taxa (Goodfellow & O'Donnell, 1994). The use of such information for classification and identification of bacteria is known as chemotaxonomy (Goodfellow & O'Donnell, 1994: Goodfellow, 2000). Chemotaxonomic analyses of macromolecules, particularly amino acids and peptides (e.g. from peptidoglycan and pseudomurein), lipids (e.g. fatty acids, lipo- polysaccharides, mycolic acids and polar lipids), polysaccharides and related polymers (e.g. teichoic and teichuronic acids, wall sugars), proteins (whole-organism protein patterns), enzymes (e.g. hydrolases, lyases) and other complex polymeric compounds, such as isoprenoid quinones, sterols provide valuable chemical data. The determination of the amino acid, major wall sugar composition and peptidoglycan structure prompted a radical reappraisal of bacterial systematics (Goodfellow & O'Donnell, 1994; Goodfellow, 2000). In general, good congruence has been found between the distribution of chemical markers and phyletic lineages in all major taxa (Chun & Goodfellow, 1995; Ward & Goodfellow, 2004).

Numerical taxonomy for bacteria
Numerical taxonomy aims in achieving sound classification by defining the various phenotypes within a phenome of a bacterium. Numerical taxonomy uses biochemical, cultural, morphological, nutritional and physiological characters to represent a phenome. The analysis aims in accomplishing defined clades to represent a single species. The minimum unit attained in such a classification is referred to as operational taxonomic unit (or OUT). The analysis employs defining each property with as 1 or + and the absence of it as 0 or -. The similarities and the differences between expressions of the phenotypes are expressed as cladograms. Cladograms can be obtained either by use of either Jacard coefficients or SSM coefficients. Where SSM takes into consideration of all the data as true (Sneath & Sokal, 1973; Stackebrandt et al., 1999), Jacard discards properties with all negatives as unreliable (Jaccard, 1908). Numerical taxonomic studies have tended to go out of fashion as they are seen to be time-consuming and laborious. However, high-throughput phenotypic screening using commercially available 96 well phenotypic array plates overcome these limitations (Biolog plc, Harvard, CA, USA; Bochner et al., 2001), as does the use of rapid enzyme tests based on 4-methylumbelliferone and 7-amino-4-methyl-coumarin (Goodfellow, 1991; Manafi, 1996; Trujillo et al., 2003). These methods are also applicable for analysing microbial communities present in natural habitats (Marx et al., 2001;Vepsäläinen et al., 2001; Stemmer, 2004).