Strain identifier

BacDive ID: 23285

Type strain: Yes

Species: Stakelama sediminis

Strain Designation: CJ70

Strain history: C.-J. Cha CJ70.

NCBI tax ID(s): 463200 (species)

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

@ref: 19228

BacDive-ID: 23285

DSM-Number: 27203

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

description: Stakelama sediminis CJ70 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from tidal flat sediment.

NCBI tax id

  • NCBI tax id: 463200
  • Matching level: species

strain history

@refhistory
19228<- C.-J. Cha, Chung-Ang Univ., Seoul, Republic of Korea; CJ70 <- C. N. Thawng
67770C.-J. Cha CJ70.

doi: 10.13145/bacdive23285.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Alphaproteobacteria
  • order: Sphingomonadales
  • family: Sphingomonadaceae
  • genus: Stakelama
  • species: Stakelama sediminis
  • full scientific name: Stakelama sediminis Thawng et al. 2013

@ref: 19228

domain: Bacteria

phylum: Proteobacteria

class: Alphaproteobacteria

order: Sphingomonadales

family: Sphingomonadaceae

genus: Stakelama

species: Stakelama sediminis

full scientific name: Stakelama sediminis Thawng et al. 2013

strain designation: CJ70

type strain: yes

Morphology

cell morphology

@refgram staincell shapemotilityconfidence
30603negativerod-shapedno
69480negative99.907

pigmentation

  • @ref: 30603
  • production: yes

multimedia

  • @ref: 19228
  • multimedia content: https://www.dsmz.de/microorganisms/photos/DSM_27203.jpg
  • intellectual property rights: © Leibniz-Institut DSMZ

Culture and growth conditions

culture medium

  • @ref: 19228
  • name: R2A MEDIUM (DSMZ Medium 830)
  • growth: yes
  • link: https://mediadive.dsmz.de/medium/830
  • composition: Name: R2A MEDIUM (DSMZ Medium 830) Composition: Agar 15.0 g/l Casamino acids 0.5 g/l Starch 0.5 g/l Glucose 0.5 g/l Proteose peptone 0.5 g/l Yeast extract 0.5 g/l K2HPO4 0.3 g/l Na-pyruvate 0.3 g/l MgSO4 x 7 H2O 0.05 g/l Distilled water

culture temp

@refgrowthtypetemperaturerange
19228positivegrowth28mesophilic
30603positivegrowth20-37
30603positiveoptimum30mesophilic
67770positivegrowth30mesophilic

culture pH

@refabilitytypepHPH range
30603positivegrowth05-10alkaliphile
30603positiveoptimum6

Physiology and metabolism

oxygen tolerance

  • @ref: 30603
  • oxygen tolerance: aerobe

spore formation

@refspore formationconfidence
69481no100
69480no99.989

halophily

@refsaltgrowthtested relationconcentration
30603NaClpositivegrowth0-5 %
30603NaClpositiveoptimum0.5 %

observation

  • @ref: 67770
  • observation: quinones: Q-10

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3060321217L-alaninamide+carbon source
3060316449alanine+carbon source
3060322599arabinose+carbon source
3060317057cellobiose+carbon source
3060323652dextrin+carbon source
3060328757fructose+carbon source
3060328260galactose+carbon source
3060317234glucose+carbon source
3060332323glucuronamide+carbon source
3060329987glutamate+carbon source
3060324996lactate+carbon source
3060317306maltose+carbon source
3060337684mannose+carbon source
3060337657methyl D-glucoside+carbon source
3060326271proline+carbon source
3060351850methyl pyruvate+carbon source
3060317822serine+carbon source
3060330031succinate+carbon source
3060327082trehalose+carbon source
3060353426tween 80+carbon source
306034853esculin+hydrolysis
3060317632nitrate+reduction

enzymes

@refvalueactivityec
30603acid phosphatase+3.1.3.2
30603alkaline phosphatase+3.1.3.1
30603catalase+1.11.1.6
30603cytochrome oxidase+1.9.3.1
30603urease+3.5.1.5

Isolation, sampling and environmental information

isolation

@refsample typecountryorigin.countrycontinent
19228tidal flat sedimentRepublic of KoreaKORAsia
67770Tidal flat sedimentRepublic of KoreaKORAsia

isolation source categories

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

taxonmaps

  • @ref: 69479
  • File name: preview.99_116517.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_20;96_46188;97_59272;98_78722;99_116517&stattab=map
  • Last taxonomy: Stakelama sediminis subclade
  • 16S sequence: EU099873
  • Sequence Identity:
  • Total samples: 14
  • soil counts: 1
  • aquatic counts: 9
  • animal counts: 1
  • plant counts: 3

Safety information

risk assessment

  • @ref: 19228
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 19228
  • description: Stakelama sediminis strain CJ70 16S ribosomal RNA gene, partial sequence
  • accession: EU099873
  • length: 1410
  • database: ena
  • NCBI tax ID: 463200

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Stakelama sediminis DSM 27203GCA_014199335contigncbi463200
66792Stakelama sediminis strain DSM 27203463200.5wgspatric463200
66792Stakelama sediminis DSM 272032828395373draftimg463200

GC content

@refGC-contentmethod
1922861.4
6777061.4high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
gram-positiveno97.084no
anaerobicno99.134yes
halophileno91.467yes
spore-formingno94.694no
glucose-utilyes91.352yes
aerobicyes91.837yes
flagellatedno87.167yes
motileyes70.533yes
thermophileno94.819yes
glucose-fermentno90.837no

External links

@ref: 19228

culture collection no.: DSM 27203, JCM 18079, KACC 16559

straininfo link

  • @ref: 87506
  • straininfo: 397254

literature

  • topic: Phylogeny
  • Pubmed-ID: 22523167
  • title: Stakelama sediminis sp. nov., isolated from tidal flat sediment.
  • authors: Thawng CN, Park SJ, Cha JH, Cha CJ
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijs.0.039743-0
  • year: 2012
  • mesh: Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids, Geologic Sediments/*microbiology, Molecular Sequence Data, *Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, Seawater/*microbiology, Sequence Analysis, DNA, Sphingomonadaceae/*classification/genetics/isolation & purification, Ubiquinone/analysis
  • topic2: Genetics

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmed
19228Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 27203)https://www.dsmz.de/collection/catalogue/details/culture/DSM-27203
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
30603Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2693428776041
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/
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
87506Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID397254.1StrainInfo: A central database for resolving microbial strain identifiers