Abstract
The genus Pseudomonas currently contains 144 species, making it the genus of Gram-negative bacteria that contains the largest number of species. Currently, multilocus sequence analysis (MLSA) is the preferred method for establishing the phylogeny between species and genera. Four partial gene sequences of housekeeping genes (16S rRNA, gyrB, rpoB, and rpoD) were obtained from 112 complete or draft genomes of strains related to the genus Pseudomonas that were available in databases. These genes were analyzed together with the corresponding sequences of 133 Pseudomonas type strains of validly published species to assess their correct phylogenetic assignations. We confirmed that 30% of the sequenced genomes of non-type strains were not correctly assigned at the species level in the accepted taxonomy of the genus and that 20% of the strains were not identified at the species level. Most of these strains had been isolated and classified several years ago, and their taxonomic status has not been updated by modern techniques. MLSA was also compared with indices based on the analysis of whole-genome sequences that have been proposed for species delineation, such as tetranucleotide usage patterns (TETRA), average nucleotide identity (ANIm, based on MUMmer and ANIb, based on BLAST) and genome-to-genome distance (GGDC). TETRA was useful for discriminating Pseudomonas from other genera, whereas ANIb and GGDC clearly separated strains of different species. ANIb showed the strongest correlation with MLSA. The correct species classification is a prerequisite for most diversity and evolutionary studies. This work highlights the necessity for complete genomic sequences of type strains to build a phylogenomic taxonomy and that all new genome sequences submitted to databases should be correctly assigned to species to avoid taxonomic inconsistencies.
Highlights
The genus Pseudomonas is one of the most complex bacterial genera and is currently the genus of Gram-negative bacteria with the largest number of species; the number of species in the genus has increased every year (10 additional species in 2013 and six in 2014 through October)
Bacterial species are considered groups of strains that are characterized by a certain degree of phenotypic consistency, by a significant degree (70%) of DNA–DNA hybridisation (DDH; Wayne et al, 1987) and by over 98.7–99% of 16S ribosomal RNA gene sequence similarity (Stackebrandt and Ebers, 2006). 16S rRNA gene sequences are highly conserved among strains of the same bacterial species and are frequently used to identify and classify microorganisms
Taxonomic classifications based only on the analysis of the 16S rRNA gene can create misclassifications in some instances, and the additional analysis of other housekeeping gene sequences should be performed for a correct phylogenetic affiliation
Summary
The genus Pseudomonas is one of the most complex bacterial genera and is currently the genus of Gram-negative bacteria with the largest number of species; the number of species in the genus has increased every year (10 additional species in 2013 and six in 2014 through October). The current number of recognized and validly published species is 144, including 10 subspecies; these species are present in the List of Prokaryotic Names with Standing in Nomenclature (Parte, 2014). The five groups were recognized as being associated with the class Proteobacteria (De Vos and De Ley, 1983; De Vos et al, 1985, 1989; De Ley, 1992); the members of the genus Pseudomonas “sensu stricto” were shown to belong to rRNA-DNA group I in the subclass Gammaproteobacteria. The approved list of bacterial names (Skerman et al, 1980) included 96 Pseudomonas species; only 31 of those species are considered true species in the genus Pseudomonas in the accepted taxonomy
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