Strain identifier

BacDive ID: 13100

Type strain: Yes

Species: Pseudomonas jinjuensis

Strain history: CIP <- 2005, KACC <- Nat. Inst. Agricult. Biotechn., Korea: strain Pss 26

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General

@ref: 6522

BacDive-ID: 13100

DSM-Number: 16612

keywords: genome sequence, 16S sequence, Bacteria, aerobe, mesophilic, motile

description: Pseudomonas jinjuensis CCUG 69580 is an aerobe, mesophilic, motile bacterium that was isolated from agricultural soil.

NCBI tax id

NCBI tax idMatching level
198616species
1215105strain

strain history

@refhistory
6522<- S. W. Kwon; Pss 26
67770IAM 15166 <-- LMG 21316 <-- S.-W. Kwon Pss 26.
120352CIP <- 2005, KACC <- Nat. Inst. Agricult. Biotechn., Korea: strain Pss 26

doi: 10.13145/bacdive13100.20230509.8.1

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 jinjuensis
  • full scientific name: Pseudomonas jinjuensis Kwon et al. 2003

@ref: 6522

domain: Bacteria

phylum: Proteobacteria

class: Gammaproteobacteria

order: Pseudomonadales

family: Pseudomonadaceae

genus: Pseudomonas

species: Pseudomonas jinjuensis

full scientific name: Pseudomonas jinjuensis Kwon et al. 2003

type strain: yes

Morphology

cell morphology

@refmotilityconfidencegram staincell shape
69480yes94.68
6948099.991negative
120352yesnegativerod-shaped

pigmentation

  • @ref: 120352
  • production: no
  • name: Pyocyanin

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
6522CASO AGAR (MERCK 105458) (DSMZ Medium 220)yeshttps://mediadive.dsmz.de/medium/220Name: CASO AGAR (Merck 105458) (DSMZ Medium 220) Composition: Agar 15.0 g/l Casein peptone 15.0 g/l NaCl 5.0 g/l Soy peptone 5.0 g/l Distilled water
38284MEDIUM 72- for trypto casein soja agaryesDistilled water make up to (1000.000 ml);Trypto casein soy agar (40.000 g)
120352CIP Medium 72yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72

culture temp

@refgrowthtypetemperaturerange
6522positivegrowth30mesophilic
38284positivegrowth30mesophilic
63626positivegrowth30mesophilic
67770positivegrowth30mesophilic
120352positivegrowth10-41
120352nogrowth5psychrophilic

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
63626aerobe
120352obligate aerobe

spore formation

@refspore formationconfidence
69481no100
69480no99.978

halophily

@refsaltgrowthtested relationconcentration
120352NaClpositivegrowth0-4 %
120352NaClnogrowth6 %
120352NaClnogrowth8 %
120352NaClnogrowth10 %

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
12035216947citrate+carbon source
1203524853esculin-hydrolysis
12035217632nitrate+reduction
12035216301nitrite+reduction
12035217632nitrate+respiration

antibiotic resistance

  • @ref: 120352
  • metabolite: 0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)
  • is antibiotic: yes
  • is sensitive: no
  • is resistant: yes

metabolite production

@refChebi-IDmetaboliteproduction
6836935581indoleno
12035235581indoleno

metabolite tests

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

enzymes

@refvalueactivityec
68369cytochrome oxidase+1.9.3.1
68369gelatinase-
68369beta-glucosidase-3.2.1.21
68369urease-3.5.1.5
68369arginine dihydrolase+3.5.3.6
120352oxidase+
120352beta-galactosidase-3.2.1.23
120352alcohol dehydrogenase+1.1.1.1
120352gelatinase-
120352amylase-
120352DNase-
120352caseinase-3.4.21.50
120352catalase+1.11.1.6
120352tween esterase-
120352lecithinase-
120352lipase-
120352lysine decarboxylase-4.1.1.18
120352ornithine decarboxylase-4.1.1.17
120352protease-
120352tryptophan deaminase-
120352urease-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
120352-+++-+----++--------

API 20NE

@refNO3TRPGLU_ FermADH ArgUREESCGELPNPGGLU_ AssimARAMNEMANNAGMALGNTCAPADIMLTCITPACOX
6522+--+----+-----+++++++

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
120352++-----------------------------+-------------+-++++--+--+---+++++--+--++++++++++++-+---++++++++-+++

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentisolation date
6522agricultural soilJinju regionRepublic of KoreaKORAsia
63626Agricultural soilJinju RegionRepublic of KoreaKORAsia
67770Soil
120352Environment, SoilJinju regionRepublic of KoreaKORAsia2000

isolation source categories

Cat1Cat2Cat3
#Engineered#Agriculture
#Environmental#Terrestrial#Soil

taxonmaps

  • @ref: 69479
  • File name: preview.99_5527.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_23;96_203;97_221;98_4126;99_5527&stattab=map
  • Last taxonomy: Pseudomonas jinjuensis subclade
  • 16S sequence: AF468448
  • Sequence Identity:
  • Total samples: 135
  • soil counts: 62
  • aquatic counts: 28
  • animal counts: 39
  • plant counts: 6

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
65221Risk group (German classification)
1203521Risk group (French classification)

Sequence information

16S sequences

  • @ref: 6522
  • description: Pseudomonas sp. Pss 26 16S ribosomal RNA gene, partial sequence
  • accession: AF468448
  • length: 1454
  • database: ena
  • NCBI tax ID: 198616

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Pseudomonas jinjuensis NBRC 103047 strain NBRC 1030471215105.3wgspatric1215105
66792Pseudomonas jinjuensis strain JCM 21621198616.7wgspatric198616
66792Pseudomonas jinjuensis JCM 216212663762768draftimg198616
67770Pseudomonas jinjuensis NBRC 103047GCA_002091655contigncbi1215105
67770Pseudomonas jinjuensis JCM 21621GCA_900103845scaffoldncbi198616

GC content

  • @ref: 67770
  • GC-content: 66.9
  • method: high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileyes90.149no
gram-positiveno97.935no
anaerobicno97.798yes
aerobicyes90.465yes
halophileno82.743no
spore-formingno95.268no
thermophileno99.389yes
glucose-utilyes85.127no
flagellatedyes67.098no
glucose-fermentno90.378yes

External links

@ref: 6522

culture collection no.: CCUG 69580, DSM 16612, KACC 10760, LMG 21316, Pss 26, JCM 21621, IAM 15166, NBRC 103047, CIP 108617

straininfo link

  • @ref: 82310
  • straininfo: 86036

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny12656147Pseudomonas koreensis sp. nov., Pseudomonas umsongensis sp. nov. and Pseudomonas jinjuensis sp. nov., novel species from farm soils in Korea.Kwon SW, Kim JS, Park IC, Yoon SH, Park DH, Lim CK, Go SJInt J Syst Evol Microbiol10.1099/ijs.0.02326-02003Agriculture, DNA, Bacterial/genetics, DNA, Ribosomal/genetics, Korea, Microscopy, Electron, Molecular Sequence Data, Nucleic Acid Hybridization, Phylogeny, Pseudomonas/*classification/genetics/*isolation & purification/metabolism, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, *Soil Microbiology, Species SpecificityGenetics
Phylogeny17329778Pseudomonas delhiensis sp. nov., from a fly ash dumping site of a thermal power plant.Prakash O, Kumari K, Lal RInt J Syst Evol Microbiol10.1099/ijs.0.64456-02007Acyclic Monoterpenes, *Carbon, Coal Ash, DNA, Bacterial/genetics, DNA, Ribosomal/genetics, India, Molecular Sequence Data, Monoterpenes/metabolism, *Particulate Matter, Phenanthrenes/metabolism, Phylogeny, *Power Plants, Pseudomonas/*classification/genetics/isolation & purification/metabolism, RNA, Ribosomal, 16S/geneticsMetabolism
Phylogeny17329787Pseudomonas knackmussii sp. nov.Stolz A, Busse HJ, Kampfer PInt J Syst Evol Microbiol10.1099/ijs.0.64761-02007DNA, Bacterial/genetics, DNA, Ribosomal/genetics, Fatty Acids/analysis, Molecular Sequence Data, Pseudomonas/chemistry/*classification/genetics/physiology, RNA, Ribosomal, 16S/geneticsGenetics
Phylogeny18523175Pseudomonas panipatensis sp. nov., isolated from an oil-contaminated site.Gupta SK, Kumari R, Prakash O, Lal RInt J Syst Evol Microbiol10.1099/ijs.0.65401-02008Bacterial Typing Techniques, Base Sequence, DNA, Bacterial/analysis, DNA, Ribosomal/analysis, Fatty Acids/analysis, Genes, rRNA, India, Molecular Sequence Data, Nucleic Acid Hybridization, *Petroleum, Phenotype, Phylogeny, Pseudomonas/*classification/genetics/*isolation & purification/physiology, RNA, Ribosomal, 16S/chemistry/genetics, Sequence Analysis, DNA, *Soil Microbiology, *Soil Pollutants, Species SpecificityGenetics

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
6522Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 16612)https://www.dsmz.de/collection/catalogue/details/culture/DSM-16612
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
38284Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/6266
63626Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 69580)https://www.ccug.se/strain?id=69580
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)
66794Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg10.1093/nar/gkaa1025BRENDA, the ELIXIR core data resource in 2021: new developments and updatesNucleic Acids Res. 49: D498-D508 202033211880
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
82310Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID86036.1StrainInfo: A central database for resolving microbial strain identifiers
120352Curators of the CIPCollection of Institut Pasteur (CIP 108617)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20108617