ReviewMultilocus sequence analysis (MLSA) in prokaryotic taxonomy
Section snippets
Background
Genotypic methods are playing a key role in phylogenetic classification and identification at various taxonomic levels, as well as for diversity analyses of prokaryotic taxa. Tremendous changes have been seen in microbial taxonomy since Sanger et al. [56] described the didesoxy sequencing technology in the 1970s, Woese and Fox [70] and others introduced small subunit ribosomal RNA (rRNA) gene-based phylogeny,1
Origin of MLSA
MLSA is based on multilocus sequence typing (MLST), which was first introduced by Maiden et al. in 1998 as a microbial typing method for epidemiological and population genetic studies of pathogenic bacteria (species) [38]. A high infra-species resolution and the determination of the clonality of strains were key points of these studies [21]. MLST itself is based on the concept of multi-locus enzyme electrophoresis, a molecular typing method applied to populations and epidemiological studies of
Historical overview of the establishment of MLSA in prokaryotic taxonomy
In the statement given by the ad hoc committee for the re-evaluation of the species definition in bacteriology [59], MLST was mentioned as a method mainly applied in epidemiology and population studies, although it was envisaged as a method which had “brought a new dimension into the elucidation of genomic relatedness at the inter- and intra-specific” level. Stackebrandt et al. [59] pointed out that MLST provided microbiologists with a tool to search for phylogenetic markers independently of
Selection of genes
A critical point for MLSA studies is the selection of genes. It is clear that housekeeping genes coding for proteins with important functions should be considered because they are stable with respect to rapid genetic modifications. However, a universal set of genes that allows the hierarchical classification of all prokaryotes must be congruent with the best set of genes in order to distinguish closely related taxa [22]. Therefore, genes are often selected independently for each new taxon
Authors’ recommendations
16S rRNA gene sequence-based phylogenies cannot provide sufficient resolutions down to the species level (and below this taxonomic rank), but should remain the basic approach used in prokaryotic taxonomy because they reflect the overall relationships of prokaryotes. They enable the phylogenetic placement of both cultured and as yet uncultured bacteria, provide an initial genus assignment in most cases, and can reflect overall phylogenetic diversity. Clear recommendations with regard to sequence
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