Strain identifier

BacDive ID: 8194

Type strain: Yes

Species: Psychrobacter cibarius

Strain Designation: JG-219

Strain history: CIP <- 2005, KCTC <- J. H. Yoon, KRIBB: strain JG-219

NCBI tax ID(s): 282669 (species)

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General

@ref: 6369

BacDive-ID: 8194

DSM-Number: 16327

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

description: Psychrobacter cibarius JG-219 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from jeotgal, a traditional Korean fermented seafood.

NCBI tax id

  • NCBI tax id: 282669
  • Matching level: species

strain history

@refhistory
6369<- J.-H. Yoon; JG-219
67771<- J.H. Yoon
118273CIP <- 2005, KCTC <- J. H. Yoon, KRIBB: strain JG-219

doi: 10.13145/bacdive8194.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Gammaproteobacteria
  • order: Pseudomonadales
  • family: Moraxellaceae
  • genus: Psychrobacter
  • species: Psychrobacter cibarius
  • full scientific name: Psychrobacter cibarius Jung et al. 2005

@ref: 6369

domain: Bacteria

phylum: Proteobacteria

class: Gammaproteobacteria

order: Pseudomonadales

family: Moraxellaceae

genus: Psychrobacter

species: Psychrobacter cibarius

full scientific name: Psychrobacter cibarius Jung et al. 2005

strain designation: JG-219

type strain: yes

Morphology

cell morphology

@refgram staincell shapemotilityconfidence
31359negativerod-shapedno
67771negative
69480no95.763
69480positive100
118273negativeoval-shapedno

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
6369BACTO MARINE BROTH (DIFCO 2216) (DSMZ Medium 514)yeshttps://mediadive.dsmz.de/medium/514Name: BACTO MARINE BROTH (DIFCO 2216) (DSMZ Medium 514) Composition: NaCl 19.45 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 NaHCO3 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
41750Marine agar (MA)yesDistilled water make up to (1000.000 ml);Marine agar (55.100 g)
118273CIP Medium 13yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=13
118273CIP Medium 72yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72

culture temp

@refgrowthtypetemperaturerange
6369positivegrowth30mesophilic
31359positivegrowth04-32
31359positiveoptimum27.5mesophilic
41750positivegrowth30mesophilic
67771positivegrowth30mesophilic
118273positivegrowth22-30
118273nogrowth37mesophilic
118273nogrowth41thermophilic

culture pH

@refabilitytypepH
31359positivegrowth05-08
31359positiveoptimum7.5

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
31359aerobe
67771aerobe
118273obligate aerobe

spore formation

@refspore formationconfidence
69481no91
69480no99.999

halophily

@refsaltgrowthtested relationconcentration
31359NaClpositivegrowth<11 %
31359NaClpositiveoptimum3.5 %

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3135930089acetate+carbon source
3135916449alanine+carbon source
3135925115malate+carbon source
3135915361pyruvate+carbon source
3135917822serine+carbon source
3135930031succinate+carbon source
3135953426tween 80+carbon source
3135917632nitrate+reduction
11827317632nitrate+reduction
11827316301nitrite-reduction
11827317632nitrate-respiration

enzymes

@refvalueactivityec
31359alkaline phosphatase+3.1.3.1
118273oxidase+
118273alcohol dehydrogenase-1.1.1.1
118273catalase+1.11.1.6
118273lysine decarboxylase-4.1.1.18
118273ornithine decarboxylase-4.1.1.17
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
118273---+-++----+--------

Isolation, sampling and environmental information

isolation

@refsample typecountryorigin.countrycontinent
6369jeotgal, a traditional Korean fermented seafoodRepublic of KoreaKORAsia
67771From Jeotgal, a traditional Korean fermented seafoodRepublic of KoreaKORAsia
118273Food, Jeotgal, a traditional Korean fermented seafoodRepublic of KoreaKORAsia

isolation source categories

Cat1Cat2Cat3
#Engineered#Food production#Seafood
#Engineered#Food production#Fermented

taxonmaps

  • @ref: 69479
  • File name: preview.99_279.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_80;96_193;97_209;98_234;99_279&stattab=map
  • Last taxonomy: Psychrobacter
  • 16S sequence: AY639871
  • Sequence Identity:
  • Total samples: 7634
  • soil counts: 925
  • aquatic counts: 3187
  • animal counts: 3350
  • plant counts: 172

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
63691Risk group (German classification)
1182731Risk group (French classification)

Sequence information

16S sequences

  • @ref: 6369
  • description: Psychrobacter cibarius strain JG-219 16S ribosomal RNA gene, partial sequence
  • accession: AY639871
  • length: 1494
  • database: ena
  • NCBI tax ID: 282669

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Psychrobacter cibarius DSM 16327GCA_016107535contigncbi282669
66792Psychrobacter cibarius strain DSM 16327282669.8wgspatric282669

GC content

  • @ref: 6369
  • GC-content: 43.5

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno91no
motileno87.027yes
gram-positiveno98.045no
anaerobicno98.609yes
halophileyes84.351yes
spore-formingno96.853no
glucose-utilno51.174no
flagellatedno90.906yes
aerobicyes89.746yes
thermophileno99.603no
glucose-fermentno93.231no

External links

@ref: 6369

culture collection no.: DSM 16327, KCTC 12256, CIP 108733

straininfo link

  • @ref: 77597
  • straininfo: 138036

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny15774627Psychrobacter cibarius sp. nov., isolated from jeotgal, a traditional Korean fermented seafood.Jung SY, Lee MH, Oh TK, Park YH, Yoon JHInt J Syst Evol Microbiol10.1099/ijs.0.63398-02005Bacterial Typing Techniques, Base Composition, DNA, Bacterial/analysis, DNA, Ribosomal/analysis, Fermentation, Genes, rRNA, Korea, Molecular Sequence Data, Nucleic Acid Hybridization, Phenotype, Phylogeny, Psychrobacter/*classification/*genetics/growth & development/isolation & purification, RNA, Ribosomal, 16S/genetics, Seafood/*microbiology, Sequence Analysis, DNAGenetics
Phylogeny19502339Psychrobacter fulvigenes sp. nov., isolated from a marine crustacean from the Sea of Japan.Romanenko LA, Tanaka N, Frolova GM, Mikhailov VVInt J Syst Evol Microbiol10.1099/ijs.0.007195-02009Animals, Bacterial Typing Techniques, Base Composition, Crustacea/*microbiology, DNA Gyrase/genetics, DNA, Bacterial/analysis, DNA, Ribosomal/analysis, Japan, Molecular Sequence Data, Nucleic Acid Hybridization, Oceans and Seas, Phenotype, Phylogeny, Polymerase Chain Reaction/methods, Psychrobacter/*classification/genetics/*isolation & purification/physiology, RNA, Ribosomal, 16S/genetics, Seawater, Sequence Analysis, DNA, Species SpecificityGenetics

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmed
6369Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 16327)https://www.dsmz.de/collection/catalogue/details/culture/DSM-16327
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
31359Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2767228776041
41750Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/6394
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)
67771Curators of the KCTChttps://kctc.kribb.re.kr/En/Kctc
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
77597Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID138036.1StrainInfo: A central database for resolving microbial strain identifiers
118273Curators of the CIPCollection of Institut Pasteur (CIP 108733)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20108733