Strain identifier

BacDive ID: 23239

Type strain: Yes

Species: Celeribacter baekdonensis

Strain Designation: L-6

Strain history: <- JH Yoon, KRIBB

NCBI tax ID(s): 875171 (species)

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General

@ref: 19149

BacDive-ID: 23239

DSM-Number: 27375

keywords: genome sequence, 16S sequence, Bacteria, anaerobe, mesophilic, Gram-negative, ovoid-shaped

description: Celeribacter baekdonensis L-6 is an anaerobe, mesophilic, Gram-negative bacterium that was isolated from seawater.

NCBI tax id

  • NCBI tax id: 875171
  • Matching level: species

strain history

@refhistory
19149<- KCTC <- J. H. Joon <- S. Y. Lee, KRIBB; L-6
67771<- JH Yoon, KRIBB

doi: 10.13145/bacdive23239.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Alphaproteobacteria
  • order: Rhodobacterales
  • family: Roseobacteraceae
  • genus: Celeribacter
  • species: Celeribacter baekdonensis
  • full scientific name: Celeribacter baekdonensis Lee et al. 2012

@ref: 19149

domain: Bacteria

phylum: Proteobacteria

class: Alphaproteobacteria

order: Rhodobacterales

family: Rhodobacteraceae

genus: Celeribacter

species: Celeribacter baekdonensis

full scientific name: Celeribacter baekdonensis Lee et al. 2012

strain designation: L-6

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapeconfidence
30275negative2 µm0.8 µmovoid-shaped
67771negative
69480negative99.997

colony morphology

@refincubation period
191492-3 days
624421-2 days

pigmentation

  • @ref: 30275
  • production: yes

Culture and growth conditions

culture medium

  • @ref: 19149
  • 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
19149positivegrowth30mesophilic
30275positivegrowth04-37
30275positiveoptimum30mesophilic
62442positivegrowth30mesophilic
67771positivegrowth30mesophilic

culture pH

@refabilitytypepH
30275positivegrowth05-08
30275positiveoptimum7.75

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
30275anaerobe
62442aerobe
67771aerobe

spore formation

@refspore formationconfidence
69481no100
69480no99.995

halophily

@refsaltgrowthtested relationconcentration
30275NaClpositivegrowth0-13 %
30275NaClpositiveoptimum2 %

observation

  • @ref: 67771
  • observation: quinones: Q-10

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3027522599arabinose+carbon source
3027528260galactose+carbon source
3027517306maltose+carbon source
3027517814salicin+carbon source
3027527082trehalose+carbon source
302754853esculin+hydrolysis
6836925115malate+assimilation
6836917128adipate-assimilation
6836927689decanoate-assimilation
6836924265gluconate-assimilation
6836917306maltose+assimilation
6836959640N-acetylglucosamine-assimilation
6836916899D-mannitol+assimilation
6836930849L-arabinose+assimilation
6836917634D-glucose+assimilation
683695291gelatin+hydrolysis
683694853esculin+hydrolysis
6836916199urea-hydrolysis
6836929016arginine-hydrolysis
6836917634D-glucose-fermentation
6836927897tryptophan-energy source
6836917632nitrate-reduction

metabolite production

  • @ref: 68369
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

metabolite tests

  • @ref: 68369
  • Chebi-ID: 35581
  • metabolite: indole
  • indole test: -

enzymes

@refvalueactivityec
19149catalase+1.11.1.6
19149cytochrome-c oxidase+1.9.3.1
30275catalase+1.11.1.6
30275gelatinase+
30275cytochrome oxidase+1.9.3.1
30275urease+3.5.1.5
68369gelatinase+
68369beta-glucosidase+3.2.1.21
68369urease-3.5.1.5
68369arginine dihydrolase-3.5.3.6

API 20NE

@refNO3TRPGLU_ FermADH ArgUREESCGELPNPGGLU_ AssimARAMNEMANNAGMALGNTCAPADIMLTCITPAC
19149-----++++++/-+-+---++-

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentsampling date
19149seawaterEast Sea, Baekdo-harbourRepublic of KoreaKORAsia
62442SeawaterEast Sea,Baekdo HarbourRepublic of KoreaKORAsia2007
67771From seawate of Baekdo-harborEast SeaRepublic of KoreaKORAsia

isolation source categories

  • Cat1: #Environmental
  • Cat2: #Aquatic
  • Cat3: #Marine

taxonmaps

  • @ref: 69479
  • File name: preview.99_333.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_19;96_233;97_255;98_284;99_333&stattab=map
  • Last taxonomy: Celeribacter baekdonensis
  • 16S sequence: HM997022
  • Sequence Identity:
  • Total samples: 6946
  • soil counts: 161
  • aquatic counts: 6090
  • animal counts: 658
  • plant counts: 37

Safety information

risk assessment

  • @ref: 19149
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 19149
  • description: Celeribacter baekdonensis strain L-6 16S ribosomal RNA gene, partial sequence
  • accession: HM997022
  • length: 1423
  • database: ena
  • NCBI tax ID: 875171

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Celeribacter baekdonensis DSM 27375GCA_900102315scaffoldncbi875171
66792Celeribacter baekdonensis strain DSM 27375875171.3wgspatric875171
66792Celeribacter baekdonensis DSM 273752616644820draftimg875171

GC content

@refGC-contentmethod
1914960.9high performance liquid chromatography (HPLC)
3027560.9

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
flagellatedno74.405no
gram-positiveno98.98no
anaerobicno96.85no
aerobicyes77.463no
halophileyes54.788no
spore-formingno97.315no
glucose-fermentno90.361no
thermophileno97.836yes
glucose-utilyes89.881yes
motileno56.225no

External links

@ref: 19149

culture collection no.: DSM 27375, CCUG 60799, KCTC 23497

straininfo link

  • @ref: 87465
  • straininfo: 405340

literature

  • topic: Phylogeny
  • Pubmed-ID: 21828017
  • title: Celeribacter baekdonensis sp. nov., isolated from seawater, and emended description of the genus Celeribacter Ivanova et al. 2010.
  • authors: Lee SY, Park S, Oh TK, Yoon JH
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijs.0.032227-0
  • year: 2011
  • mesh: Base Composition, DNA, Bacterial/genetics, Fatty Acids/metabolism, Molecular Sequence Data, Phylogeny, RNA, Ribosomal, 16S/genetics, Rhodobacteraceae/classification/genetics/*isolation & purification, Seawater/*microbiology
  • topic2: Genetics

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmed
19149Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 27375)https://www.dsmz.de/collection/catalogue/details/culture/DSM-27375
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
30275Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2661628776041
62442Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 60799)https://www.ccug.se/strain?id=60799
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
68369Automatically annotated from API 20NE
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
87465Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID405340.1StrainInfo: A central database for resolving microbial strain identifiers