Strain identifier

BacDive ID: 12869

Type strain: No

Species: Pseudomonas oleovorans

Strain Designation: X-59, X 59, 63

Strain history: CIP <- 1966, P. Thibault, Inst. Pasteur, Paris, France, Pseudomonas pseudoalcaligenes: strain X 59 <- Stanier, Inst. Pasteur, Paris, France: strain 63

NCBI tax ID(s): 301 (species)

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General

@ref: 12673

BacDive-ID: 12869

DSM-Number: 50188

keywords: genome sequence, 16S sequence, Bacteria, obligate aerobe, mesophilic, motile, human pathogen

description: Pseudomonas oleovorans X-59 is an obligate aerobe, mesophilic, motile human pathogen that was isolated from sinus discharge.

NCBI tax id

  • NCBI tax id: 301
  • Matching level: species

strain history

@refhistory
12673<- ICPB <- P. Thibault, X-59
67770Y. Kosako 85010 <-- Nissui Pharm. Co., Ltd. <-- ATCC 17440 <-- R. Y. Stanier 63 <-- P. Thibault X-59.
121412CIP <- 1966, P. Thibault, Inst. Pasteur, Paris, France, Pseudomonas pseudoalcaligenes: strain X 59 <- Stanier, Inst. Pasteur, Paris, France: strain 63

doi: 10.13145/bacdive12869.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Gammaproteobacteria
  • order: Pseudomonadales
  • family: Pseudomonadaceae
  • genus: Pseudomonas
  • species: Pseudomonas oleovorans
  • full scientific name: Pseudomonas oleovorans Lee and Chandler 1941 (Approved Lists 1980)

  • synonyms

    • @ref: 20215
    • synonym: Pseudomonas pseudoalcaligenes

@ref: 12673

domain: Bacteria

phylum: Proteobacteria

class: Gammaproteobacteria

order: Pseudomonadales

family: Pseudomonadaceae

genus: Pseudomonas

species: Pseudomonas oleovorans

full scientific name: Pseudomonas oleovorans Lee and Chandler 1941 emend. Saha et al. 2010

strain designation: X-59, X 59, 63

type strain: no

Morphology

cell morphology

@refmotilityconfidencegram staincell shape
69480yes99.181
6948099.999negative
121412nonegativerod-shaped

multimedia

  • @ref: 12673
  • multimedia content: https://www.dsmz.de/microorganisms/photos/DSM_50188.jpg
  • intellectual property rights: © Leibniz-Institut DSMZ

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
12673REACTIVATION WITH LIQUID MEDIUM 1 (DSMZ Medium 1a)yeshttps://mediadive.dsmz.de/medium/1aName: REACTIVATION WITH LIQUID MEDIUM 1 (DSMZ Medium 1a) Composition: Agar 15.0 g/l Peptone 5.0 g/l Meat extract 3.0 g/l Distilled water
35012MEDIUM 3 - Columbia agaryesColumbia agar (39.000 g);distilled water (1000.000 ml)
121412CIP Medium 3yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=3
121412CIP Medium 72yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72

culture temp

@refgrowthtypetemperaturerange
12673positivegrowth30mesophilic
35012positivegrowth30mesophilic
67770positivegrowth26mesophilic

Physiology and metabolism

oxygen tolerance

  • @ref: 121412
  • oxygen tolerance: obligate aerobe

spore formation

@refspore formationconfidence
69481no100
69480no99.995

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
6836925115malate+assimilation
6836917128adipate-assimilation
6836927689decanoate+assimilation
6836924265gluconate-assimilation
6836917306maltose-assimilation
6836959640N-acetylglucosamine-assimilation
6836916899D-mannitol-assimilation
6836916024D-mannose-assimilation
6836930849L-arabinose-assimilation
6836917634D-glucose-assimilation
683695291gelatin-hydrolysis
683694853esculin-hydrolysis
6836916199urea-hydrolysis
6836929016arginine-hydrolysis
6836917634D-glucose-fermentation
6836927897tryptophan-energy source
6836917632nitrate+reduction
12141217632nitrate+reduction
12141216301nitrite-reduction

metabolite production

@refChebi-IDmetaboliteproduction
6836935581indoleno
12141235581indoleno

metabolite tests

  • @ref: 68369
  • Chebi-ID: 35581
  • metabolite: indole
  • indole test: -

enzymes

@refvalueactivityec
68369gelatinase-
68369beta-glucosidase-3.2.1.21
68369urease-3.5.1.5
68369arginine dihydrolase-3.5.3.6
121412oxidase+
121412catalase+1.11.1.6
121412urease-3.5.1.5
68382alkaline phosphatase-3.1.3.1
68382esterase (C 4)+
68382esterase lipase (C 8)+
68382lipase (C 14)-
68382leucine arylamidase+3.4.11.1
68382valine arylamidase-
68382cystine arylamidase-3.4.11.3
68382trypsin+3.4.21.4
68382alpha-chymotrypsin-3.4.21.1
68382acid phosphatase+3.1.3.2
68382naphthol-AS-BI-phosphohydrolase+
68382alpha-galactosidase-3.2.1.22
68382beta-galactosidase-3.2.1.23
68382beta-glucuronidase-3.2.1.31
68382alpha-glucosidase-3.2.1.20
68382beta-glucosidase-3.2.1.21
68382N-acetyl-beta-glucosaminidase-3.2.1.52
68382alpha-mannosidase-3.2.1.24
68382alpha-fucosidase-3.2.1.51

API zym

@refControlAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
121412--++-+--+-++--------

API 20NE

@refNO3TRPGLU_ FermADH ArgUREESCGELPNPGGLU_ AssimARAMNEMANNAGMALGNTCAPADIMLTCITPACOX
12673+--------------+-++-+/-

Isolation, sampling and environmental information

isolation

@refsample typecountryorigin.countrycontinentisolation date
12673sinus discharge
67770Sinus drainage
121412Human, Sinus drainageFranceFRAEurope1956

isolation source categories

Cat1Cat2Cat3
#Host Body-Site#Oral cavity and airways#Airways
#Host Body Product#Fluids

taxonmaps

  • @ref: 69479
  • File name: preview.99_2828.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_23;96_61;97_64;98_1532;99_2828&stattab=map
  • Last taxonomy: Pseudomonas
  • 16S sequence: LC462171
  • Sequence Identity:
  • Total samples: 7465
  • soil counts: 769
  • aquatic counts: 2670
  • animal counts: 2451
  • plant counts: 1575

Safety information

risk assessment

@refpathogenicity humanpathogenicity plantbiosafety levelbiosafety level comment
12673yes, in single casesyes1Risk group (German classification)
1214121Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Pseudomonas pseudoalcaligenes gene for 16S rRNA, strain: JCM 5968AB0213791511ena330
67770Pseudomonas oleovorans subsp. oleovorans JCM 5968 gene for 16S ribosomal RNA, partial sequenceLC4621711459ena1218129
67770P.pseudoalcaligenes (strain LMG 1225T) 16S rRNA geneZ766661492ena301

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Pseudomonas oleovorans NCTC10860GCA_900455635contigncbi301
66792Pseudomonas oleovorans NBRC 14167GCA_002091775contigncbi1215116
66792Pseudomonas pseudoalcaligenes NBRC 14167 strain NBRC 141671215116.3wgspatric1215116
66792Pseudomonas pseudoalcaligenes strain NCTC10860330.60wgspatric301
66792Pseudomonas pseudoalcaligenes NBRC 141672758568623draftimg1215116
66792Pseudomonas oleovorans NCTC 108602917173859draftimg301

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileyes88.225no
gram-positiveno98.769no
anaerobicno97.646no
aerobicyes88.339no
halophileno81.862no
spore-formingno95.981no
thermophileno99.463yes
glucose-utilyes82.215no
flagellatedyes88.264no
glucose-fermentno91.413yes

External links

@ref: 12673

culture collection no.: DSM 50188, ATCC 17440, ICPB 2750-63, IMET 11177, JCM 5968, NCIB 9946, NCTC 10860, BCRC 11902, CCM 3467, CCUG 51525, CCUG 726, CECT 318, CFBP 2435, CGMCC 1.1806, CIP 66.14, ICPB 3982, IFO 14167, LMG 1225, NBRC 14167, NCAIM B.01176, NCCB 76045, NCIMB 9946, NCPPB 1971, VKM B-1300, VTT E-012029

straininfo link

  • @ref: 82081
  • straininfo: 13743

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Metabolism1883229Pyrimidine base and ribonucleoside utilization by the Pseudomonas alcaligenes group.West TPAntonie Van Leeuwenhoek10.1007/BF005836791991Amidohydrolases/metabolism, Culture Media, Cytosine Deaminase, Dihydrouracil Dehydrogenase (NADP), N-Glycosyl Hydrolases/metabolism, Nucleoside Deaminases/metabolism, Oxidoreductases/metabolism, Pseudomonas/*metabolism, Pyrimidines/*metabolism, Ribonucleosides/*metabolismCultivation
Metabolism7916185Control of the pyrimidine biosynthetic pathway in Pseudomonas pseudoalcaligenes.West TPArch Microbiol10.1007/BF002643761994Aspartate Carbamoyltransferase/*metabolism, Dihydroorotase/metabolism, Dihydroorotate Dehydrogenase, Orotate Phosphoribosyltransferase/metabolism, Orotidine-5'-Phosphate Decarboxylase/metabolism, Oxidoreductases/metabolism, *Oxidoreductases Acting on CH-CH Group Donors, Pseudomonas/enzymology/*metabolism, Pyrimidines/*biosynthesis, Time FactorsEnzymology
Phylogeny19126738Pseudomonas tuomuerensis sp. nov., isolated from a bird's nest.Xin YH, Zhang DC, Liu HC, Zhou HL, Zhou YGInt J Syst Evol Microbiol10.1099/ijs.0.000547-02009Animals, Bacterial Typing Techniques, Base Composition, *Birds, China, DNA, Bacterial/analysis, DNA, Ribosomal/analysis, Fatty Acids/analysis, Genes, rRNA, *Housing, Animal, Nucleic Acid Hybridization, Phenotype, Phylogeny, Pseudomonas/*classification/genetics/*isolation & purification/physiology, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Species SpecificityPhenotype
Phylogeny19622647Pseudomonas caeni sp. nov., a denitrifying bacterium isolated from the sludge of an anaerobic ammonium-oxidizing bioreactor.Xiao YP, Hui W, Wang Q, Roh SW, Shi XQ, Shi JH, Quan ZXInt J Syst Evol Microbiol10.1099/ijs.0.005108-02009Anaerobiosis, Bioreactors/*microbiology, DNA, Bacterial/genetics, DNA, Ribosomal/genetics, Molecular Sequence Data, Nitrites/*metabolism, Oxidation-Reduction, Phylogeny, Pseudomonas/classification/genetics/*isolation & purification/*metabolism, Quaternary Ammonium Compounds/*metabolism, RNA, Ribosomal, 16S/genetics, Sewage/*microbiologyMetabolism
Phylogeny19936829Pseudomonas oleovorans subsp. lubricantis subsp. nov., and reclassification of Pseudomonas pseudoalcaligenes ATCC 17440T as later synonym of Pseudomonas oleovorans ATCC 8062 T.Saha R, Sproer C, Beck B, Bagley SCurr Microbiol10.1007/s00284-009-9540-62009Bacterial Proteins/genetics, Bacterial Typing Techniques, Base Composition, DNA Gyrase/genetics, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, DNA-Directed RNA Polymerases/genetics, Fatty Acids/analysis, *Industrial Waste, Molecular Sequence Data, Nucleic Acid Hybridization, Pseudomonas oleovorans/chemistry/*classification/*genetics/isolation & purification, Pseudomonas pseudoalcaligenes/*classification/*genetics, RNA, Ribosomal, 16S/genetics, Ribotyping, Sequence Analysis, DNA, Sigma Factor/geneticsGenetics
Phylogeny23918786Pseudomonas guguanensis sp. nov., a gammaproteobacterium isolated from a hot spring.Liu YC, Young LS, Lin SY, Hameed A, Hsu YH, Lai WA, Shen FT, Young CCInt J Syst Evol Microbiol10.1099/ijs.0.047712-02013Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Genes, Bacterial, Hot Springs/*microbiology, Molecular Sequence Data, Nucleic Acid Hybridization, *Phylogeny, Pseudomonas/*classification/genetics/isolation & purification, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Taiwan, Ubiquinone/chemistryGenetics

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
12673Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 50188)https://www.dsmz.de/collection/catalogue/details/culture/DSM-50188
20215Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M.10.1099/ijsem.0.004332List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ
20218Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P.10.1016/j.syapm.2013.11.002StrainInfo introduces electronic passports for microorganisms.Syst Appl Microbiol. 37: 42-50 201424321274
35012Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/10236
66792Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmannhttps://diaspora-project.de/progress.html#genomesAutomatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
68369Automatically annotated from API 20NE
68382Automatically annotated from API zym
69479João F Matias Rodrigues, Janko Tackmann,Gregor Rot, Thomas SB Schmidt, Lukas Malfertheiner, Mihai Danaila,Marija Dmitrijeva, Daniela Gaio, Nicolas Näpflin and Christian von Mering. University of Zurich.https://microbeatlas.org/MicrobeAtlas 1.0 beta
69480Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmannhttps://diaspora-project.de/progress.html#genomesPredictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)
69481Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch10.21203/rs.3.rs-2527258/v1Predictions based on the model GenomeNet Sporulation v. 1
82081Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID13743.1StrainInfo: A central database for resolving microbial strain identifiers
121412Curators of the CIPCollection of Institut Pasteur (CIP 66.14)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%2066.14