Strain identifier

BacDive ID: 6197

Type strain: Yes

Species: Cucumibacter marinus

Strain Designation: CL-GR60

Strain history: <- B. C. Cho, Seoul Natl. Univ., Republic of Korea; CL-GR60

NCBI tax ID(s): 422296 (strain), 1121252 (species)

« back to strain detail view
For citation purpose refer to the digital object identifier (doi) of the current version.
Archive
version 8.1 (current version):
version 8:
version 7.1:
version 7:
version 6:
version 5:
version 4.1:
version 4:
version 3:
version 2.1:
version 2:
version 1:
version 8.1 (current version)

General

@ref: 7820

BacDive-ID: 6197

DSM-Number: 18995

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

description: Cucumibacter marinus CL-GR60 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from coastal seawater.

NCBI tax id

NCBI tax idMatching level
1121252species
422296strain

strain history

  • @ref: 7820
  • history: <- B. C. Cho, Seoul Natl. Univ., Republic of Korea; CL-GR60

doi: 10.13145/bacdive6197.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Alphaproteobacteria
  • order: Hyphomicrobiales
  • family: Devosiaceae
  • genus: Cucumibacter
  • species: Cucumibacter marinus
  • full scientific name: Cucumibacter marinus Hwang and Cho 2008

@ref: 7820

domain: Bacteria

phylum: Proteobacteria

class: Alphaproteobacteria

order: Rhizobiales

family: Devosiaceae

genus: Cucumibacter

species: Cucumibacter marinus

full scientific name: Cucumibacter marinus Hwang and Cho 2008

strain designation: CL-GR60

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
32499negative1.5-2 µm0.4-0.6 µmrod-shapedyes
69480negative99.979

pigmentation

  • @ref: 32499
  • production: yes

multimedia

@refmultimedia contentcaptionintellectual property rights
66793EM_DSM_18995_1.jpgelectron microscopic image© HZI/Manfred Rohde
66793EM_DSM_18995_2.jpgelectron microscopic image© HZI/Manfred Rohde
66793EM_DSM_18995_3.jpgelectron microscopic image© HZI/Manfred Rohde
66793EM_DSM_18995_4.jpgelectron microscopic image© HZI/Manfred Rohde
66793EM_DSM_18995_5.jpgelectron microscopic image© HZI/Manfred Rohde

Culture and growth conditions

culture medium

  • @ref: 7820
  • name: BACTO MARINE BROTH (DIFCO 2216) (DSMZ Medium 514)
  • growth: yes
  • link: https://mediadive.dsmz.de/medium/514
  • composition: Name: 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

culture temp

@refgrowthtypetemperaturerange
7820positivegrowth28mesophilic
32499positivegrowth15-40
32499positiveoptimum30-35mesophilic

culture pH

@refabilitytypepHPH range
32499positivegrowth06-09alkaliphile
32499positiveoptimum7

Physiology and metabolism

oxygen tolerance

  • @ref: 32499
  • oxygen tolerance: aerobe

spore formation

@refspore formationconfidence
32499no
69481no100
69480no99.986

halophily

@refsaltgrowthtested relationconcentration
32499NaClpositivegrowth01-03 %
32499NaClpositiveoptimum2 %

observation

  • @ref: 32499
  • observation: aggregates in chains

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3249922599arabinose+carbon source
3249929016arginine+carbon source
3249922653asparagine+carbon source
3249928757fructose+carbon source
3249928260galactose+carbon source
3249917234glucose+carbon source
3249929987glutamate+carbon source
3249917754glycerol+carbon source
3249917716lactose+carbon source
3249925017leucine+carbon source
3249929864mannitol+carbon source
3249937684mannose+carbon source
3249915361pyruvate+carbon source
3249917992sucrose+carbon source
3249927082trehalose+carbon source

enzymes

@refvalueactivityec
32499acid phosphatase+3.1.3.2
32499alkaline phosphatase+3.1.3.1
32499catalase+1.11.1.6
32499gelatinase+
32499cytochrome oxidase+1.9.3.1

Isolation, sampling and environmental information

isolation

  • @ref: 7820
  • sample type: coastal seawater
  • geographic location: Busan, East Sea
  • country: Republic of Korea
  • origin.country: KOR
  • continent: Asia

isolation source categories

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

taxonmaps

  • @ref: 69479
  • File name: preview.99_2875.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_5;96_1524;97_1818;98_2225;99_2875&stattab=map
  • Last taxonomy: Cucumibacter marinus subclade
  • 16S sequence: EF211830
  • Sequence Identity:
  • Total samples: 1392
  • soil counts: 348
  • aquatic counts: 894
  • animal counts: 116
  • plant counts: 34

Safety information

risk assessment

  • @ref: 7820
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 7820
  • description: Cucumibacter marinus DSM 18995 strain CL-GR60 16S ribosomal RNA gene, partial sequence
  • accession: EF211830
  • length: 1358
  • database: ena
  • NCBI tax ID: 422296

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Cucumibacter marinus DSM 18995GCA_000429865scaffoldncbi422296
66792Cucumibacter marinus DSM 18995422296.3wgspatric422296
66792Cucumibacter marinus DSM 189952524614806draftimg422296

GC content

  • @ref: 7820
  • GC-content: 62.9

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileyes87.165yes
flagellatedno57.12no
gram-positiveno97.119no
anaerobicno98.301yes
aerobicyes86.892yes
halophileno72.484no
spore-formingno96.754no
thermophileno89.938no
glucose-utilyes89.439yes
glucose-fermentno90.451no

External links

@ref: 7820

culture collection no.: DSM 18995, KCCM 90027

straininfo link

  • @ref: 75677
  • straininfo: 402276

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny18599700Cucumibacter marinus gen. nov., sp. nov., a marine bacterium in the family Hyphomicrobiaceae.Hwang CY, Cho BCInt J Syst Evol Microbiol10.1099/ijs.0.65587-02008Fatty Acids/metabolism, Hyphomicrobiaceae/chemistry/*classification/genetics/ultrastructure, Korea, Microscopy, Electron, Transmission, Molecular Sequence Data, Phylogeny, RNA, Ribosomal, 16S/genetics, Seawater/*microbiology, Species SpecificityGenetics
Phylogeny19620375Zhangella mobilis gen. nov., sp. nov., a new member of the family Hyphomicrobiaceae isolated from coastal seawater.Xu HY, Chen LP, Fu SZ, Fan HX, Zhou YG, Liu SJ, Liu ZPInt J Syst Evol Microbiol10.1099/ijs.0.004366-02009Bacterial Typing Techniques, Base Composition, Catalase/metabolism, China, Cluster Analysis, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis, Flagella/physiology, Hyphomicrobiaceae/*classification/genetics/*isolation & purification/physiology, Locomotion, Molecular Sequence Data, Nitrates/metabolism, Oxidation-Reduction, Oxidoreductases/metabolism, Phylogeny, Pigments, Biological/biosynthesis, RNA, Ribosomal, 16S/genetics, Seawater/*microbiology, Sequence Analysis, DNA, Sodium Chloride/metabolism, Ubiquinone/analysisMetabolism

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmedjournal
7820Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 18995)https://www.dsmz.de/collection/catalogue/details/culture/DSM-18995
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
32499Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2871928776041
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 life28604660 35: 676-683 2017
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
75677Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID402276.1StrainInfo: A central database for resolving microbial strain identifiers