The Complete Genome Sequence of Pseudomonas putida NBRC 14164
            <sup>T</sup>
            Confirms High Intraspecies Variation

Ohji, Shoko; Yamazoe, Atsushi; Hosoyama, Akira; Tsuchikane, Keiko; Ezaki, Takayuki; Fujita, Nobuyuki

doi:10.1128/genomea.00029-14

Cited by 23 publications

(15 citation statements)

References 6 publications

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“…[10], [26] with 99%, 97%, 98%, and 99% DNA sequence identity, respectively with the type strain of P. putida NBRC14164 T ( Figure 1 ). It is interesting to notice that the closest relatives of W15Oct28 are the P. putida type strain NBRC 14164 T , and the recently sequenced strain H8234, a clinical isolate [27], confirming that our strain probably belongs to the species P. putida [28]. It appears also from the phylogenetic tree of Figure 1 that the other strains designated as P. putida probably represent other species.…”

Section: Resultssupporting

confidence: 70%

Draft Genome Sequence Analysis of a Pseudomonas putida W15Oct28 Strain with Antagonistic Activity to Gram-Positive and Pseudomonas sp. Pathogens

Hildebrand

Dingemans

et al. 2014

PLoS ONE

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Pseudomonas putida is a member of the fluorescent pseudomonads known to produce the yellow-green fluorescent pyoverdine siderophore. P. putida W15Oct28, isolated from a stream in Brussels, was found to produce compound(s) with antimicrobial activity against the opportunistic pathogens Staphylococcus aureus, Pseudomonas aeruginosa, and the plant pathogen Pseudomonas syringae, an unusual characteristic for P. putida. The active compound production only occurred in media with low iron content and without organic nitrogen sources. Transposon mutants which lost their antimicrobial activity had the majority of insertions in genes involved in the biosynthesis of pyoverdine, although purified pyoverdine was not responsible for the antagonism. Separation of compounds present in culture supernatants revealed the presence of two fractions containing highly hydrophobic molecules active against P. aeruginosa. Analysis of the draft genome confirmed the presence of putisolvin biosynthesis genes and the corresponding lipopeptides were found to contribute to the antimicrobial activity. One cluster of ten genes was detected, comprising a NAD-dependent epimerase, an acetylornithine aminotransferase, an acyl CoA dehydrogenase, a short chain dehydrogenase, a fatty acid desaturase and three genes for a RND efflux pump. P. putida W15Oct28 genome also contains 56 genes encoding TonB-dependent receptors, conferring a high capacity to utilize pyoverdines from other pseudomonads. One unique feature of W15Oct28 is also the presence of different secretion systems including a full set of genes for type IV secretion, and several genes for type VI secretion and their VgrG effectors.

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Section: Resultssupporting

confidence: 70%

Draft Genome Sequence Analysis of a Pseudomonas putida W15Oct28 Strain with Antagonistic Activity to Gram-Positive and Pseudomonas sp. Pathogens

Hildebrand

Dingemans

et al. 2014

PLoS ONE

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“…Intraspecies comparisons were characterized by ANIb values higher than 95%, which corresponds to MLSA values higher than 97% and GGDC values higher than 70%; these thresholds are considered the species boundaries by the three methods. However, the strains in the P. putida G assigned to the P. putida species were genomically very diverse, and some of those strains likely represent a new species, as has been proposed by Mulet et al ( 2013 ) and more recently by Ohji et al ( 2014 ).…”

Section: Discussionmentioning

confidence: 78%

Phylogenomics and systematics in Pseudomonas

et al. 2015

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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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“…aeruginosa , these include, the plant pathogens Pseudomonas syringae , also described as an opportunistic human pathogen [ 57 ], and Pseudomonas amygdali [ 58 ]; Enterobacteriaceae family; the harmful cyanobacteria Microcystis aeruginosa [ 59 ]; the fish pathogen Pseudomonas plecoglossicida [ 60 ]; and the clinical isolates P . putida NBRC 14164T [ 61 ] and Pseudomonas monteilii [ 62 ] ( Table 4 ). These clusters encode proteins involved in transport of ions (Mn ++ ) or peptides across the membrane (type I, II and IV secretion systems).…”

Section: Resultsmentioning

confidence: 99%

Specific Gene Loci of Clinical Pseudomonas putida Isolates

et al. 2016

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Pseudomonas putida are ubiquitous inhabitants of soils and clinical isolates of this species have been seldom described. Clinical isolates show significant variability in their ability to cause damage to hosts because some of them are able to modulate the host’s immune response. In the current study, comparisons between the genomes of different clinical and environmental strains of P. putida were done to identify genetic clusters shared by clinical isolates that are not present in environmental isolates. We show that in clinical strains specific genes are mostly present on transposons, and that this set of genes exhibit high identity with genes found in pathogens and opportunistic pathogens. The set of genes prevalent in P. putida clinical isolates, and absent in environmental isolates, are related with survival under oxidative stress conditions, resistance against biocides, amino acid metabolism and toxin/antitoxin (TA) systems. This set of functions have influence in colonization and survival within human tissues, since they avoid host immune response or enhance stress resistance. An in depth bioinformatic analysis was also carried out to identify genetic clusters that are exclusive to each of the clinical isolates and that correlate with phenotypical differences between them, a secretion system type III-like was found in one of these clinical strains, a determinant of pathogenicity in Gram-negative bacteria.

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The Complete Genome Sequence of Pseudomonas putida NBRC 14164 ^T Confirms High Intraspecies Variation

Cited by 23 publications

References 6 publications

Draft Genome Sequence Analysis of a Pseudomonas putida W15Oct28 Strain with Antagonistic Activity to Gram-Positive and Pseudomonas sp. Pathogens

Draft Genome Sequence Analysis of a Pseudomonas putida W15Oct28 Strain with Antagonistic Activity to Gram-Positive and Pseudomonas sp. Pathogens

Phylogenomics and systematics in Pseudomonas

Specific Gene Loci of Clinical Pseudomonas putida Isolates

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The Complete Genome Sequence of Pseudomonas putida NBRC 14164 T Confirms High Intraspecies Variation

Cited by 23 publications

References 6 publications

Draft Genome Sequence Analysis of a Pseudomonas putida W15Oct28 Strain with Antagonistic Activity to Gram-Positive and Pseudomonas sp. Pathogens

Draft Genome Sequence Analysis of a Pseudomonas putida W15Oct28 Strain with Antagonistic Activity to Gram-Positive and Pseudomonas sp. Pathogens

Phylogenomics and systematics in Pseudomonas

Specific Gene Loci of Clinical Pseudomonas putida Isolates

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The Complete Genome Sequence of Pseudomonas putida NBRC 14164 ^T Confirms High Intraspecies Variation