Strain identifier

BacDive ID: 133504

Type strain: Yes

Species: Cobetia crustatorum

Strain Designation: JO1

Strain history: <- JW Bae, KRIBB

NCBI tax ID(s): 553385 (species)

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General

@ref: 29219

BacDive-ID: 133504

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

description: Cobetia crustatorum JO1 is an aerobe, Gram-negative, motile bacterium that was isolated from Fermented seafood.

NCBI tax id

  • NCBI tax id: 553385
  • Matching level: species

strain history

@refhistory
67770J.-W. Bae JO1.
67771<- JW Bae, KRIBB

doi: 10.13145/bacdive133504.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Gammaproteobacteria
  • order: Oceanospirillales
  • family: Halomonadaceae
  • genus: Cobetia
  • species: Cobetia crustatorum
  • full scientific name: Cobetia crustatorum Kim et al. 2010

@ref: 29219

domain: Bacteria

phylum: Proteobacteria

class: Gammaproteobacteria

order: Oceanospirillales

family: Halomonadaceae

genus: Cobetia

species: Cobetia crustatorum

strain designation: JO1

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotility
29219negative1.05 µm0.6 µmrod-shapedyes
67771negative

pigmentation

  • @ref: 29219
  • production: yes

Culture and growth conditions

culture temp

@refgrowthtypetemperaturerange
29219positivegrowth04-30
29219positiveoptimum25mesophilic
67770positivegrowth25mesophilic
67771positivegrowth25mesophilic

culture pH

@refabilitytypepHPH range
29219positivegrowth05-10alkaliphile
29219positiveoptimum5.5

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
29219aerobe
67771aerobe

halophily

@refsaltgrowthtested relationconcentration
29219NaClpositivegrowth3.5-11.5 %
29219NaClpositiveoptimum6.5 %

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
2921916449alanine+carbon source
2921922599arabinose+carbon source
2921922653asparagine+carbon source
2921916947citrate+carbon source
2921928757fructose+carbon source
2921928260galactose+carbon source
2921924265gluconate+carbon source
2921917234glucose+carbon source
2921929987glutamate+carbon source
2921917754glycerol+carbon source
2921924996lactate+carbon source
2921917306maltose+carbon source
2921929864mannitol+carbon source
2921937684mannose+carbon source
2921926271proline+carbon source
2921951850methyl pyruvate+carbon source
2921917822serine+carbon source
2921917992sucrose+carbon source
2921927082trehalose+carbon source
2921953426tween 80+carbon source

enzymes

@refvalueactivityec
29219acid phosphatase+3.1.3.2
29219alkaline phosphatase+3.1.3.1
29219catalase+1.11.1.6

Isolation, sampling and environmental information

isolation

@refsample typecountryorigin.countrycontinent
29219Fermented seafood
67770Jeotgal, traditional Korean fermented seafoodRepublic of KoreaKORAsia
67771From jogae jeotgalRepublic of KoreaKORAsia

isolation source categories

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

taxonmaps

  • @ref: 69479
  • File name: preview.99_1955.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_48;96_532;97_613;98_707;99_1955&stattab=map
  • Last taxonomy: Cobetia crustatorum
  • 16S sequence: EU909460
  • Sequence Identity:
  • Total samples: 1598
  • soil counts: 58
  • aquatic counts: 1196
  • animal counts: 321
  • plant counts: 23

Sequence information

16S sequences

  • @ref: 29219
  • description: Cobetia crustatorum strain JO1 16S ribosomal RNA gene, partial sequence
  • accession: EU909460
  • length: 1427
  • database: nuccore
  • NCBI tax ID: 553385

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Cobetia crustatorum JO12568526450draftimg553385
67770Cobetia crustatorum JO1GCA_000591415contigncbi553385

GC content

@refGC-contentmethod
2921961.4
6777061.4thermal denaturation, midpoint method (Tm)

External links

@ref: 29219

culture collection no.: KCTC 22486, JCM 15644, NRIC 0824

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny19654339Cobetia crustatorum sp. nov., a novel slightly halophilic bacterium isolated from traditional fermented seafood in Korea.Kim MS, Roh SW, Bae JWInt J Syst Evol Microbiol10.1099/ijs.0.008847-02009Animals, DNA, Bacterial/genetics, DNA, Ribosomal/genetics, Fatty Acids/chemistry/metabolism, *Fermentation, Halomonadaceae/*classification/genetics/*isolation & purification/metabolism, Korea, Molecular Sequence Data, Phylogeny, RNA, Ribosomal, 16S/genetics, Seafood/*microbiology, Sodium Chloride/*metabolismMetabolism
Phylogeny22427450Description of Cobetia amphilecti sp. nov., Cobetia litoralis sp. nov. and Cobetia pacifica sp. nov., classification of Halomonas halodurans as a later heterotypic synonym of Cobetia marina and emended descriptions of the genus Cobetia and Cobetia marina.Romanenko LA, Tanaka N, Svetashev VI, Falsen EInt J Syst Evol Microbiol10.1099/ijs.0.036863-02012Alaska, Bacterial Typing Techniques, DNA, Bacterial/genetics, Fatty Acids/analysis, Halomonadaceae/*classification/genetics/isolation & purification, Halomonas/classification/genetics/isolation & purification, Japan, Molecular Sequence Data, Nucleic Acid Hybridization, Oceans and Seas, *Phylogeny, RNA, Ribosomal, 16S/genetics, Seawater/microbiology, Sequence Analysis, DNA, *Water MicrobiologyEnzymology

Reference

@idauthorstitledoi/urlID_cross_referencepubmed
20215Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M.List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ10.1099/ijsem.0.004332
29219Barberan A, Caceres Velazquez H, Jones S, Fierer N.Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information10.1128/mSphere.00237-172564028776041
66792Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg OvermannAutomatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)https://diaspora-project.de/progress.html#genomes
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
67771Curators of the KCTChttps://kctc.kribb.re.kr/En/Kctc
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.MicrobeAtlas 1.0 betahttps://microbeatlas.org/