Strain identifier

BacDive ID: 14260

Type strain: Yes

Species: Sphingomonas hankookensis

Strain Designation: ODN7

Strain history: <- JH Yoon, KRIBB

NCBI tax ID(s): 563996 (species)

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General

@ref: 16799

BacDive-ID: 14260

DSM-Number: 23329

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

description: Sphingomonas hankookensis ODN7 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from wastewater treatment plant.

NCBI tax id

  • NCBI tax id: 563996
  • Matching level: species

strain history

@refhistory
16799<- KCTC <- J. H. Joon, KRIBB
67771<- JH Yoon, KRIBB

doi: 10.13145/bacdive14260.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Alphaproteobacteria
  • order: Sphingomonadales
  • family: Sphingomonadaceae
  • genus: Sphingomonas
  • species: Sphingomonas hankookensis
  • full scientific name: Sphingomonas hankookensis Yoon et al. 2009

@ref: 16799

domain: Bacteria

phylum: Proteobacteria

class: Alphaproteobacteria

order: Sphingomonadales

family: Sphingomonadaceae

genus: Sphingomonas

species: Sphingomonas hankookensis

full scientific name: Sphingomonas hankookensis Yoon et al. 2009

strain designation: ODN7

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotility
29210negative1.85 µm0.45 µmrod-shapedno
67771negative

colony morphology

  • @ref: 61355
  • incubation period: 7 days

Culture and growth conditions

culture medium

  • @ref: 16799
  • name: TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535)
  • growth: yes
  • link: https://mediadive.dsmz.de/medium/535
  • composition: Name: TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535) Composition: Trypticase soy broth 30.0 g/l Agar 15.0 g/l Distilled water

culture temp

@refgrowthtypetemperaturerange
16799positivegrowth28mesophilic
29210positivegrowth04-37
29210positiveoptimum30mesophilic
61355positivegrowth30mesophilic
67771positivegrowth30mesophilic

culture pH

@refabilitytypepHPH range
29210positivegrowth05-10alkaliphile
29210positiveoptimum7.5

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
61355aerobe
67771aerobe

halophily

@refsaltgrowthtested relationconcentration
29210NaClpositivegrowth0-1 %
29210NaClpositiveoptimum0.25 %

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
29210581435-dehydro-D-gluconate+carbon source
2921017128adipate+carbon source
2921022599arabinose+carbon source
2921016947citrate+carbon source
2921028757fructose+carbon source
2921033984fucose+carbon source
2921028260galactose+carbon source
2921024265gluconate+carbon source
2921017716lactose+carbon source
2921025115malate+carbon source
2921017306maltose+carbon source
2921037684mannose+carbon source
2921028053melibiose+carbon source
2921037657methyl D-glucoside+carbon source
29210506227N-acetylglucosamine+carbon source
2921016634raffinose+carbon source
2921026546rhamnose+carbon source
2921017814salicin+carbon source
2921017992sucrose+carbon source
2921053424tween 20+carbon source
2921053423tween 40+carbon source
2921053425tween 60+carbon source
2921018222xylose+carbon source
6836925115malate+assimilation
6836917128adipate-assimilation
6836927689decanoate-assimilation
6836924265gluconate+assimilation
6836917306maltose+assimilation
6836959640N-acetylglucosamine+assimilation
6836916899D-mannitol-assimilation
6836916024D-mannose+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
29210cytochrome oxidase+1.9.3.1
68369cytochrome oxidase+1.9.3.1
68369gelatinase-
68369beta-glucosidase+3.2.1.21
68369urease-3.5.1.5
68369arginine dihydrolase-3.5.3.6

API 20NE

@refNO3TRPGLU_ FermADH ArgUREESCGELPNPGGLU_ AssimARAMNEMANNAGMALGNTCAPADIMLTCITPACOX
16799-----+-++++-+++--++-+

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentsampling date
16799wastewater treatment plantTaejonRepublic of KoreaKORAsia
61355Waste treatment plantTaejonRepublic of KoreaKORAsia2006-01-01
67771From wastewaterDaejeonRepublic of KoreaKORAsia

isolation source categories

Cat1Cat2Cat3
#Engineered#Waste#Wastewater
#Engineered#Waste#Water treatment plant

taxonmaps

  • @ref: 69479
  • File name: preview.99_1423.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_20;96_348;97_957;98_1126;99_1423&stattab=map
  • Last taxonomy: Sphingomonas
  • 16S sequence: FJ194436
  • Sequence Identity:
  • Total samples: 894
  • soil counts: 63
  • aquatic counts: 171
  • animal counts: 508
  • plant counts: 152

Safety information

risk assessment

  • @ref: 16799
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 16799
  • description: Sphingomonas sp. ODN7 16S ribosomal RNA gene, partial sequence
  • accession: FJ194436
  • length: 1442
  • database: ena
  • NCBI tax ID: 563996

Genome sequences

  • @ref: 66792
  • description: Sphingomonas hankookensis KCTC 22579
  • accession: GCA_022664465
  • assembly level: scaffold
  • database: ncbi
  • NCBI tax ID: 563996

GC content

@refGC-contentmethod
1679967.2high performance liquid chromatography (HPLC)
2921067.2

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
flagellatedno84.496no
gram-positiveno97.161yes
anaerobicno99.351no
aerobicyes94.605yes
halophileno95.663yes
spore-formingno93.975no
motileyes74.416no
glucose-fermentno92.93yes
thermophileno98.858yes
glucose-utilyes90.175yes

External links

@ref: 16799

culture collection no.: DSM 23329, CCUG 57509, KCTC 22579

straininfo link

  • @ref: 83419
  • straininfo: 364661

literature

  • topic: Phylogeny
  • Pubmed-ID: 19625422
  • title: Sphingomonas hankookensis sp. nov., isolated from wastewater.
  • authors: Yoon JH, Park S, Kang SJ, Kim W, Oh TK
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijs.0.008680-0
  • year: 2009
  • mesh: DNA, Bacterial/genetics, DNA, Ribosomal/genetics, Fatty Acids/chemistry/metabolism, Fresh Water/*microbiology, Molecular Sequence Data, Phylogeny, RNA, Ribosomal, 16S/genetics, Sphingomonas/classification/genetics/*isolation & purification/metabolism
  • topic2: Metabolism

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmed
16799Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 23329)https://www.dsmz.de/collection/catalogue/details/culture/DSM-23329
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
29210Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2563128776041
61355Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 57509)https://www.ccug.se/strain?id=57509
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
83419Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID364661.1StrainInfo: A central database for resolving microbial strain identifiers