Strain identifier

BacDive ID: 13132

Type strain: Yes

Species: Pseudomonas pohangensis

Strain Designation: H3-R18

Strain history: CIP <- 2006, DSMZ <- S.-W. Kwon: strain H3-R18 <- H.-Y. Weon et al.

NCBI tax ID(s): 364197 (species)

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General

@ref: 7212

BacDive-ID: 13132

DSM-Number: 17875

keywords: genome sequence, 16S sequence, Bacteria, aerobe, mesophilic, Gram-negative

description: Pseudomonas pohangensis H3-R18 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from sea shore sand.

NCBI tax id

  • NCBI tax id: 364197
  • Matching level: species

strain history

@refhistory
7212<- S.-W. Kwon; H3-R18 <- H.-Y. Weon et al.
375312006, DSMZ
67770KACC 11517 <-- S.-W. Kwon H3-R18.
121920CIP <- 2006, DSMZ <- S.-W. Kwon: strain H3-R18 <- H.-Y. Weon et al.

doi: 10.13145/bacdive13132.20230509.8.1

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 pohangensis
  • full scientific name: Pseudomonas pohangensis Weon et al. 2006

@ref: 7212

domain: Bacteria

phylum: Proteobacteria

class: Gammaproteobacteria

order: Pseudomonadales

family: Pseudomonadaceae

genus: Pseudomonas

species: Pseudomonas pohangensis

full scientific name: Pseudomonas pohangensis Weon et al. 2006 emend. Hameed et al. 2014

strain designation: H3-R18

type strain: yes

Morphology

cell morphology

@refgram stainconfidencecell shapemotility
69480negative99.995
121920negativerod-shapedno

colony morphology

  • @ref: 63627
  • incubation period: 3 days

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
7212REACTIVATION WITH LIQUID MEDIUM 514 (DSMZ Medium 514c)yeshttps://mediadive.dsmz.de/medium/514cName: REACTIVATION WITH LIQUID MEDIUM 514 (DSMZ Medium 514c) Composition: NaCl 19.45 g/l Agar 18.0 g/l MgCl2 5.9 g/l Bacto peptone 5.0 g/l Na2SO4 3.24 g/l CaCl2 1.8 g/l Yeast extract 1.0 g/l KCl 0.55 g/l Na2CO3 0.16 g/l Fe(III) citrate 0.1 g/l KBr 0.08 g/l SrCl2 0.034 g/l H3BO3 0.022 g/l Na2HPO4 0.008 g/l Na-silicate 0.004 g/l NaF 0.0024 g/l (NH4)NO3 0.0016 g/l Distilled water
37531MEDIUM 72- for trypto casein soja agaryesDistilled water make up to (1000.000 ml);Trypto casein soy agar (40.000 g)
121920CIP Medium 72yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72

culture temp

@refgrowthtypetemperaturerange
7212positivegrowth28mesophilic
37531positivegrowth30mesophilic
63627positivegrowth30mesophilic
67770positivegrowth30mesophilic

Physiology and metabolism

oxygen tolerance

  • @ref: 63627
  • oxygen tolerance: aerobe

spore formation

@refspore formationconfidence
69481no100
69480no100

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
12192017632nitrate+reduction
12192016301nitrite-reduction

metabolite production

@refChebi-IDmetaboliteproduction
6836935581indoleno
12192035581indoleno

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
121920oxidase+
121920catalase+1.11.1.6
121920urease+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
121920-+++-+----++--------

API 20NE

@refNO3TRPGLU_ FermADH ArgUREESCGELPNPGGLU_ AssimARAMNEMANNAGMALGNTCAPADIMLTCITPACOX
7212+--+---+-------+----+

Isolation, sampling and environmental information

isolation

@refsample typecountryorigin.countrycontinentgeographic location
7212sea shore sandRepublic of KoreaKORAsia
63627Seashore sandRepublic of KoreaKORAsiaPohang City,Homi Cape
67770Seashore sand from Homi capeRepublic of KoreaKORAsiaPohang City
121920Environment, Seashore sandRepublic of KoreaKORAsiaHomi cape, Pohang city

isolation source categories

Cat1Cat2Cat3
#Environmental#Aquatic#Marine
#Environmental#Terrestrial#Coast
#Environmental#Terrestrial#Sandy

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
72121Risk group (German classification)
1219201Risk group (French classification)

Sequence information

16S sequences

  • @ref: 7212
  • description: Pseudomonas pohangensis strain H3-R18 16S ribosomal RNA gene, partial sequence
  • accession: DQ339144
  • length: 1456
  • database: ena
  • NCBI tax ID: 364197

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Pseudomonas pohangensis DSM 17875GCA_900105995chromosomencbi364197
66792Pseudomonas pohangensis strain DSM 17875364197.3completepatric364197
66792Pseudomonas pohangensis DSM 178752667527387draftimg364197
67770Pseudomonas pohangensis strain DSM 17875 genome assembly, chromosome: ILT629785ncbi364197

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
gram-positiveno97.954no
anaerobicno98.424yes
halophileno62.636no
spore-formingno97.401no
glucose-utilno70.512yes
aerobicyes84.225yes
motileno75.683no
flagellatedno72.779no
thermophileno99.464yes
glucose-fermentno89.101yes

External links

@ref: 7212

culture collection no.: DSM 17875, KACC 11517, CCUG 69581, JCM 16393, CIP 109373

straininfo link

  • @ref: 82340
  • straininfo: 292704

literature

  • topic: Phylogeny
  • Pubmed-ID: 16957113
  • title: Pseudomonas pohangensis sp. nov., isolated from seashore sand in Korea.
  • authors: Weon HY, Kim BY, Yoo SH, Baek YK, Lee SY, Kwon SW, Go SJ, Stackebrandt E
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijs.0.64274-0
  • year: 2006
  • mesh: Bacterial Typing Techniques, Base Composition, DNA, Bacterial/analysis, DNA, Ribosomal/analysis, Korea, Molecular Sequence Data, Pseudomonas/classification/genetics/*isolation & purification, RNA, Ribosomal, 16S/*analysis, Silicon Dioxide, Soil Microbiology
  • topic2: Genetics

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
7212Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 17875)https://www.dsmz.de/collection/catalogue/details/culture/DSM-17875
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
37531Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/7107
63627Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 69581)https://www.ccug.se/strain?id=69581
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
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
82340Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID292704.1StrainInfo: A central database for resolving microbial strain identifiers
121920Curators of the CIPCollection of Institut Pasteur (CIP 109373)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20109373