Strain identifier

BacDive ID: 5853

Type strain: Yes

Species: Zooshikella ganghwensis

Strain Designation: JC2044

Strain history: CIP <- 2004, J. Chun, Seoul, Korea: strain JC2044

For citation purpose refer to the digital object identifier (doi) of the current version.
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General

@ref: 5784

BacDive-ID: 5853

DSM-Number: 15267

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

description: Zooshikella ganghwensis JC2044 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from sediment sample of getbol.

NCBI tax id

NCBI tax idMatching level
1123509strain
202772species

strain history

@refhistory
5784<- J. Chun; JC2044
374242004, J. Chun, Seoul, Korea: strain JC2044
67771<- J Chon, Seoul Nat. Univ.
119531CIP <- 2004, J. Chun, Seoul, Korea: strain JC2044

doi: 10.13145/bacdive5853.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Gammaproteobacteria
  • order: Oceanospirillales
  • family: Zooshikellaceae
  • genus: Zooshikella
  • species: Zooshikella ganghwensis
  • full scientific name: Zooshikella ganghwensis Yi et al. 2003
  • synonyms

    @refsynonym
    20215Zooshikella ganghwensis subsp. marina
    20215Zooshikella marina

@ref: 5784

domain: Bacteria

phylum: Proteobacteria

class: Gammaproteobacteria

order: Oceanospirillales

family: Hahellaceae

genus: Zooshikella

species: Zooshikella ganghwensis

full scientific name: Zooshikella ganghwensis Yi et al. 2003

strain designation: JC2044

type strain: yes

Morphology

cell morphology

@refgram stainmotilityconfidencecell shape
67771negative
69480yes94.947
69480negative99.897
119531negativeyesrod-shaped

multimedia

@refmultimedia contentcaptionintellectual property rights
66793EM_DSM_15267_1.jpgelectron microscopic image© HZI/Manfred Rohde
66793EM_DSM_15267_2.jpgelectron microscopic image© HZI/Manfred Rohde
66793EM_DSM_15267_3.jpgelectron microscopic image© HZI/Manfred Rohde
66793EM_DSM_15267_4.jpgelectron microscopic image© HZI/Manfred Rohde
66793EM_DSM_15267_5.jpgelectron microscopic image© HZI/Manfred Rohde

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
5784BACTO 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
37424Marine agar (MA)yesDistilled water make up to (1000.000 ml);Marine agar (55.100 g)
119531CIP Medium 13yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=13

culture temp

@refgrowthtypetemperaturerange
5784positivegrowth30mesophilic
37424positivegrowth30mesophilic
67771positivegrowth28mesophilic
119531positivegrowth22-37
119531nogrowth5psychrophilic
119531nogrowth15psychrophilic
119531nogrowth41thermophilic

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
67771aerobe
119531obligate aerobe

spore formation

@refspore formationconfidence
69481no94
69480no99.843

halophily

@refsaltgrowthtested relationconcentration
119531NaClpositivegrowth2-4 %
119531NaClnogrowth0 %
119531NaClnogrowth6 %
119531NaClnogrowth8 %
119531NaClnogrowth10 %

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
1195314853esculin-hydrolysis
11953117632nitrate-builds gas from
11953117632nitrate-reduction
11953116301nitrite-builds gas from
11953116301nitrite-reduction

metabolite production

  • @ref: 119531
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

enzymes

@refvalueactivityec
68382alpha-fucosidase-3.2.1.51
68382alpha-mannosidase-3.2.1.24
68382N-acetyl-beta-glucosaminidase-3.2.1.52
68382beta-glucosidase-3.2.1.21
68382alpha-glucosidase-3.2.1.20
68382beta-glucuronidase-3.2.1.31
68382beta-galactosidase-3.2.1.23
68382alpha-galactosidase-3.2.1.22
68382naphthol-AS-BI-phosphohydrolase-
68382acid phosphatase+3.1.3.2
68382alpha-chymotrypsin-3.4.21.1
68382trypsin-3.4.21.4
68382cystine arylamidase-3.4.11.3
68382valine arylamidase+
68382leucine arylamidase+3.4.11.1
68382lipase (C 14)-
68382esterase lipase (C 8)+
68382esterase (C 4)+
68382alkaline phosphatase+3.1.3.1
119531oxidase+
119531beta-galactosidase-3.2.1.23
119531alcohol dehydrogenase-1.1.1.1
119531gelatinase+
119531amylase+
119531caseinase+3.4.21.50
119531catalase+1.11.1.6
119531tween esterase+
119531gamma-glutamyltransferase+2.3.2.2
119531lecithinase+
119531lipase+
119531lysine decarboxylase-4.1.1.18
119531ornithine decarboxylase-4.1.1.17
119531phenylalanine ammonia-lyase-4.3.1.24
119531protease-
119531tryptophan deaminase-
119531urease-3.5.1.5

API zym

@refControlAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
119531-+++-++---+---------

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
119531++-+-----++--------+-----------+-----------------+---------+-------------------++---------++-+---+-

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
5784sediment sample of getbolKorea, Ganghwa islandRepublic of KoreaKORAsia
67771From Sediment sample of getbolGanghwa islandRepublic of KoreaKORAsia
119531Environment, Sediment sample of getbolRepublic of KoreaKORAsia

isolation source categories

Cat1Cat2Cat3
#Environmental#Aquatic#Sediment
#Environmental#Terrestrial#Tidal flat

taxonmaps

  • @ref: 69479
  • File name: preview.99_6836.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_202;96_3219;97_3951;98_5036;99_6836&stattab=map
  • Last taxonomy: Zooshikella
  • 16S sequence: AY130994
  • Sequence Identity:
  • Total samples: 1619
  • soil counts: 143
  • aquatic counts: 1307
  • animal counts: 154
  • plant counts: 15

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
57841Risk group (German classification)
1195311Risk group (French classification)

Sequence information

16S sequences

  • @ref: 5784
  • description: Zooshikella ganghwensis strain JC2044 16S ribosomal RNA gene, partial sequence
  • accession: AY130994
  • length: 1462
  • database: ena
  • NCBI tax ID: 202772

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Zooshikella ganghwensis DSM 15267GCA_000428585scaffoldncbi1123509
66792Zooshikella ganghwensis DSM 152671123509.3wgspatric1123509
66792Zooshikella ganghwensis DSM 152672524614643draftimg1123509

GC content

  • @ref: 5784
  • GC-content: 42

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno94no
motileyes88.657no
flagellatedyes82.559no
gram-positiveno98.562yes
anaerobicno96.223yes
aerobicyes78.939yes
halophileno76.523no
spore-formingno89.235no
glucose-utilyes89.409no
thermophileno98.527no
glucose-fermentno77.906no

External links

@ref: 5784

culture collection no.: DSM 15267, KCTC 12044, IMSNU 14003, CIP 108300

straininfo link

  • @ref: 75334
  • straininfo: 113586

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny26409875Zooshikella marina sp. nov. a cycloprodigiosin- and prodigiosin-producing marine bacterium isolated from beach sand.Ramaprasad EVV, Bharti D, Sasikala C, Ramana CVInt J Syst Evol Microbiol10.1099/ijsem.0.0006302015Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Gammaproteobacteria/*classification/genetics/isolation & purification, India, Indoles/*metabolism, Molecular Sequence Data, Nucleic Acid Hybridization/genetics, Phospholipids/chemistry, *Phylogeny, Pigmentation, Prodigiosin/*metabolism, Pyrroles/*metabolism, RNA, Ribosomal, 16S/genetics, Seawater/*microbiology, Sequence Analysis, DNA, Ubiquinone/chemistryMetabolism
Phylogeny34705624Proposal of Zooshikellaceae fam. nov. to accommodate the genera Zooshikella and Spartinivicinus and reclassification of Zooshikella marina as a later heterotypic synonym of Zooshikella ganghwensis based on whole genome sequence analysis.Huang Z, Su P, Lai QInt J Syst Evol Microbiol10.1099/ijsem.0.0050552021Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, *Gammaproteobacteria/classification/isolation & purification, Nucleic Acid Hybridization, *Phylogeny, Pigmentation, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Ubiquinone/chemistryTranscriptome

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
5784Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 15267)https://www.dsmz.de/collection/catalogue/details/culture/DSM-15267
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
37424Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/5908
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)
66793Mukherjee et al.10.1038/nbt.3886GEBA: 1,003 reference genomes of bacterial and archaeal isolates expand coverage of the tree of life 35: 676-683 201728604660
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
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
75334Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID113586.1StrainInfo: A central database for resolving microbial strain identifiers
119531Curators of the CIPCollection of Institut Pasteur (CIP 108300)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20108300