Strain identifier

BacDive ID: 14188

Type strain: Yes

Species: Sphingobium olei

Strain history: <- A. F. Yassin, Univ. Bonn; IMMIB HF-1

NCBI tax ID(s): 420955 (species)

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General

@ref: 7823

BacDive-ID: 14188

DSM-Number: 18999

keywords: genome sequence, 16S sequence, Bacteria, mesophilic

description: Sphingobium olei DSM 18999 is a mesophilic bacterium that was isolated from oil contaminated soil.

NCBI tax id

  • NCBI tax id: 420955
  • Matching level: species

strain history

  • @ref: 7823
  • history: <- A. F. Yassin, Univ. Bonn; IMMIB HF-1

doi: 10.13145/bacdive14188.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Alphaproteobacteria
  • order: Sphingomonadales
  • family: Sphingomonadaceae
  • genus: Sphingobium
  • species: Sphingobium olei
  • full scientific name: Sphingobium olei Young et al. 2007

@ref: 7823

domain: Bacteria

phylum: Proteobacteria

class: Alphaproteobacteria

order: Sphingomonadales

family: Sphingomonadaceae

genus: Sphingobium

species: Sphingobium olei

full scientific name: Sphingobium olei Young et al. 2007

type strain: yes

Culture and growth conditions

culture medium

  • @ref: 7823
  • name: NUTRIENT AGAR (DSMZ Medium 1)
  • growth: yes
  • link: https://mediadive.dsmz.de/medium/1
  • composition: Name: NUTRIENT AGAR (DSMZ Medium 1) Composition: Agar 15.0 g/l Peptone 5.0 g/l Meat extract 3.0 g/l Distilled water

culture temp

  • @ref: 7823
  • growth: positive
  • type: growth
  • temperature: 28
  • range: mesophilic

Physiology and metabolism

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
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
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
7823--------+----+------+

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentsampling date
7823oil contaminated soilKaohsiung CountyTaiwanTWNAsia
60140Soil,oil-contaminatedKaohsiung CountyTaiwanTWNAsia2006

isolation source categories

Cat1Cat2Cat3
#Engineered#Contamination#Oil (Fuel)
#Environmental#Terrestrial#Soil

taxonmaps

  • @ref: 69479
  • File name: preview.99_1356.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_20;96_785;97_914;98_1071;99_1356&stattab=map
  • Last taxonomy: Sphingobium olei subclade
  • 16S sequence: AM489507
  • Sequence Identity:
  • Total samples: 877
  • soil counts: 28
  • aquatic counts: 577
  • animal counts: 211
  • plant counts: 61

Safety information

risk assessment

  • @ref: 7823
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 7823
  • description: Sphingobium olei partial 16S rRNA gene, strain IMMIB HF-1T
  • accession: AM489507
  • length: 1471
  • database: ena
  • NCBI tax ID: 420955

Genome sequences

  • @ref: 66792
  • description: Sphingobium olei DSM 18999
  • accession: 2828637024
  • assembly level: draft
  • database: img
  • NCBI tax ID: 420955

External links

@ref: 7823

culture collection no.: DSM 18999, CCUG 54329, IMMIB HF-1

straininfo link

  • @ref: 83351
  • straininfo: 404997

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny17978228Sphingobium olei sp. nov., isolated from oil-contaminated soil.Young CC, Ho MJ, Arun AB, Chen WM, Lai WA, Shen FT, Rekha PD, Yassin AFInt J Syst Evol Microbiol10.1099/ijs.0.65187-02007Bacterial Typing Techniques, DNA, Ribosomal/analysis, Fatty Acids/analysis, Genes, rRNA, Genotype, Molecular Sequence Data, *Petroleum, Phenotype, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, *Soil Pollutants, Sphingomonadaceae/chemistry/*classification/genetics/isolation & purification, TaiwanGenetics
Phylogeny19620380Sphingobium lactosutens sp. nov., isolated from a hexachlorocyclohexane dump site and Sphingobium abikonense sp. nov., isolated from oil-contaminated soil.Kumari H, Gupta SK, Jindal S, Katoch P, Lal RInt J Syst Evol Microbiol10.1099/ijs.0.004739-02009Bacterial Typing Techniques, Cluster Analysis, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis, Hexachlorocyclohexane/*metabolism, India, Molecular Sequence Data, Nucleic Acid Hybridization, Oils/*metabolism, Phospholipids/analysis, Phylogeny, Pigments, Biological/biosynthesis, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Soil Pollutants/*metabolism, Sphingomonadaceae/chemistry/*classification/genetics/*isolation & purificationMetabolism
Phylogeny28820116Sphingobium naphthae sp. nov., with the ability to degrade aliphatic hydrocarbons, isolated from oil-contaminated soil.Chaudhary DK, Jeong SW, Kim JInt J Syst Evol Microbiol10.1099/ijsem.0.0020642017Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Nepal, Nucleic Acid Hybridization, *Petroleum Pollution, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, *Soil Pollutants, Sphingomonadaceae/*classification/genetics/isolation & purification, Ubiquinone/chemistryTranscriptome

Reference

@idauthorscataloguedoi/urltitle
7823Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 18999)https://www.dsmz.de/collection/catalogue/details/culture/DSM-18999
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
60140Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 54329)https://www.ccug.se/strain?id=54329
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)
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
83351Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID404997.1StrainInfo: A central database for resolving microbial strain identifiers