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2015 ; 6
(ä): 214
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Phylogenomics and systematics in Pseudomonas
#MMPMID26074881
Gomila M
; Peña A
; Mulet M
; Lalucat J
; García-Valdés E
Front Microbiol
2015[]; 6
(ä): 214
PMID26074881
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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.
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