Strain identifier

BacDive ID: 14412

Type strain: Yes

Species: Jeotgalicoccus psychrophilus

Strain Designation: YKJ-115

Strain history: CIP <- 2003, JCM <- Y.H. Park: strain YKJ-115

NCBI tax ID(s): 1122129 (strain), 157228 (species)

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General

@ref: 7877

BacDive-ID: 14412

DSM-Number: 19085

keywords: genome sequence, 16S sequence, Bacteria, facultative anaerobe, mesophilic

description: Jeotgalicoccus psychrophilus YKJ-115 is a facultative anaerobe, mesophilic bacterium that was isolated from jeotgal, Korean fermented seafood.

NCBI tax id

NCBI tax idMatching level
157228species
1122129strain

strain history

@refhistory
7877<- JCM <-Y.-H. Park, strain YKJ-115
67770Y.-H. Park YKJ-115.
122031CIP <- 2003, JCM <- Y.H. Park: strain YKJ-115

doi: 10.13145/bacdive14412.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/bacillota
  • domain: Bacteria
  • phylum: Bacillota
  • class: Bacilli
  • order: Caryophanales
  • family: Staphylococcaceae
  • genus: Jeotgalicoccus
  • species: Jeotgalicoccus psychrophilus
  • full scientific name: Jeotgalicoccus psychrophilus Yoon et al. 2003

@ref: 7877

domain: Bacteria

phylum: Firmicutes

class: Bacilli

order: Bacillales

family: Staphylococcaceae

genus: Jeotgalicoccus

species: Jeotgalicoccus psychrophilus

full scientific name: Jeotgalicoccus psychrophilus Yoon et al. 2003

strain designation: YKJ-115

type strain: yes

Morphology

cell morphology

@refmotilityconfidencegram staincell shape
69480no93.935
69480100positive
122031nopositivecoccus-shaped

colony morphology

  • @ref: 122031

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
7877BACTO 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
39965Marine agar (MA)yesDistilled water make up to (1000.000 ml);Marine agar (55.100 g)
122031CIP Medium 13yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=13

culture temp

@refgrowthtypetemperaturerange
7877positivegrowth28mesophilic
39965positivegrowth30mesophilic
67770positivegrowth25mesophilic
122031positivegrowth10-37
122031nogrowth41thermophilic
122031nogrowth45thermophilic

Physiology and metabolism

oxygen tolerance

  • @ref: 122031
  • oxygen tolerance: facultative anaerobe

spore formation

  • @ref: 69480
  • spore formation: no
  • confidence: 99.923

observation

  • @ref: 67770
  • observation: quinones: MK-7

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
122031606565hippurate-hydrolysis
12203117632nitrate-reduction
12203116301nitrite-reduction

metabolite production

  • @ref: 122031
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testmethylred-test
12203115688acetoin-
12203117234glucose-

enzymes

@refvalueactivityec
122031oxidase+
122031beta-galactosidase-3.2.1.23
122031alcohol dehydrogenase-1.1.1.1
122031gelatinase-
122031amylase-
122031DNase-
122031caseinase-3.4.21.50
122031catalase+1.11.1.6
122031tween esterase-
122031gamma-glutamyltransferase-2.3.2.2
122031lysine decarboxylase-4.1.1.18
122031ornithine decarboxylase-4.1.1.17
122031phenylalanine ammonia-lyase+4.3.1.24
122031urease-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
122031-+++-+---+-+--------

Isolation, sampling and environmental information

isolation

@refsample typecountryorigin.countrycontinentisolation date
7877jeotgal, Korean fermented seafoodRepublic of KoreaKORAsia
57844Jeotgal (traditional Korean fermented seafood)
67770Jeotgal, traditional Korean fermented seafoodRepublic of KoreaKORAsia
122031Food, Fermented seafood jeotgalRepublic of KoreaKORAsia1999

isolation source categories

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

taxonmaps

  • @ref: 69479
  • File name: preview.99_6097.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_3;96_2904;97_3572;98_4523;99_6097&stattab=map
  • Last taxonomy: Jeotgalicoccus psychrophilus
  • 16S sequence: AY028926
  • Sequence Identity:
  • Total samples: 4833
  • soil counts: 504
  • aquatic counts: 353
  • animal counts: 3842
  • plant counts: 134

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
78771Risk group (German classification)
1220311Risk group (French classification)

Sequence information

16S sequences

  • @ref: 7877
  • description: Jeotgalicoccus psychrophilus 16S ribosomal RNA gene, partial sequence
  • accession: AY028926
  • length: 1507
  • database: ena
  • NCBI tax ID: 157228

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Jeotgalicoccus psychrophilus DSM 190851122129.3wgspatric1122129
66792Jeotgalicoccus psychrophilus DSM 190852524614585draftimg1122129
67770Jeotgalicoccus psychrophilus DSM 19085GCA_000425845scaffoldncbi1122129

GC content

@refGC-contentmethod
787742
6777042high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingyes79no
motileno89.539no
flagellatedno95.714no
gram-positiveyes91.362no
anaerobicno99.345no
halophileyes98.145no
spore-formingno88.321no
thermophileno99.858yes
glucose-utilyes83.626no
aerobicyes95.91no
glucose-fermentno71.772no

External links

@ref: 7877

culture collection no.: DSM 19085, JCM 11199, KCCM 41449, CCUG 47729, CCM 7136, CGMCC 1.6772, CIP 107952

straininfo link

  • @ref: 83556
  • straininfo: 100702

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny12710632Jeotgalicoccus halotolerans gen. nov., sp. nov. and Jeotgalicoccus psychrophilus sp. nov., isolated from the traditional Korean fermented seafood jeotgal.Yoon JH, Lee KC, Weiss N, Kang KH, Park YHInt J Syst Evol Microbiol10.1099/ijs.0.02132-02003Fatty Acids/analysis, Fermentation, Korea, Molecular Sequence Data, Phylogeny, RNA, Ribosomal, 16S/*analysis/genetics, Seafood/*microbiology, Sequence Analysis, DNA, Staphylococcaceae/*classification/genetics/isolation & purification/*physiologyGenetics
Phylogeny20802063Jeotgalicoccus halophilus sp. nov., isolated from salt lakes.Liu WY, Jiang LL, Guo CJ, Yang SSInt J Syst Evol Microbiol10.1099/ijs.0.022251-02010Bacterial Typing Techniques, Base Composition, Cell Wall/chemistry, China, DNA, Bacterial/genetics, Fatty Acids/chemistry, Lakes/*microbiology, Molecular Sequence Data, Nucleic Acid Hybridization, *Phylogeny, Pigmentation, RNA, Ribosomal, 16S/genetics, Salinity, Sequence Analysis, DNA, Staphylococcaceae/*classification/genetics/isolation & purification, Vitamin K 2/analogs & derivatives/chemistryGenetics

Reference

@idauthorscataloguedoi/urltitle
7877Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 19085)https://www.dsmz.de/collection/catalogue/details/culture/DSM-19085
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
39965Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/5520
57844Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 47729)https://www.ccug.se/strain?id=47729
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/
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)
83556Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID100702.1StrainInfo: A central database for resolving microbial strain identifiers
122031Curators of the CIPCollection of Institut Pasteur (CIP 107952)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20107952