Strain identifier

BacDive ID: 158033

Type strain: No

Species: Sphingobium yanoikuyae

Strain Designation: XLDN2-5

Strain history: <- P. Xu, Shanghai Jiao Tong Univ., China; XLDN2-5

NCBI tax ID(s): 13690 (species)

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General

@ref: 64606

BacDive-ID: 158033

DSM-Number: 28039

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

description: Sphingobium yanoikuyae XLDN2-5 is a mesophilic human pathogen that was isolated from petroleum polluted soil.

NCBI tax id

  • NCBI tax id: 13690
  • Matching level: species

strain history

  • @ref: 64606
  • history: <- P. Xu, Shanghai Jiao Tong Univ., China; XLDN2-5

doi: 10.13145/bacdive158033.20230509.8.1

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 yanoikuyae
  • full scientific name: Sphingobium yanoikuyae (Yabuuchi et al. 1990) Takeuchi et al. 2001

  • synonyms

    • @ref: 20215
    • synonym: Sphingomonas yanoikuyae

@ref: 64606

domain: Bacteria

phylum: Proteobacteria

class: Alphaproteobacteria

order: Pseudomonadales

family: Sphingomonadaceae

genus: Sphingobium

species: Sphingobium yanoikuyae

full scientific name: Sphingobium yanoikuyae (Yabuuchi et al. 1990) Takeuchi et al. 2001

strain designation: XLDN2-5

type strain: no

Morphology

multimedia

  • @ref: 64606
  • multimedia content: https://www.dsmz.de/microorganisms/photos/DSM_28039.jpg
  • intellectual property rights: © Leibniz-Institut DSMZ

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
64606TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535)yeshttps://mediadive.dsmz.de/medium/535Name: TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535) Composition: Trypticase soy broth 30.0 g/l Agar 15.0 g/l Distilled water
64606MINERAL MEDIUM (BRUNNER) (DSMZ Medium 457)yeshttps://mediadive.dsmz.de/medium/457Name: MINERAL MEDIUM (BRUNNER) (DSMZ Medium 457) Composition: Na2HPO4 2.44 g/l KH2PO4 1.52 g/l (NH4)2SO4 0.5 g/l MgSO4 x 7 H2O 0.2 g/l CaCl2 x 2 H2O 0.05 g/l EDTA 0.005 g/l FeSO4 x 7 H2O 0.002 g/l H3BO3 0.0003 g/l CoCl2 x 6 H2O 0.0002 g/l ZnSO4 x 7 H2O 0.0001 g/l MnCl2 x 4 H2O 3e-05 g/l Na2MoO4 x 2 H2O 3e-05 g/l NiCl2 x 6 H2O 2e-05 g/l CuCl2 x 2 H2O 1e-05 g/l Distilled water

culture temp

  • @ref: 64606
  • growth: positive
  • type: growth
  • temperature: 28
  • range: mesophilic

Physiology and metabolism

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
6836830849L-arabinose-fermentation
6836827613amygdalin-fermentation
6836828053melibiose-fermentation
6836817992sucrose-fermentation
6836862345L-rhamnose+fermentation
6836830911sorbitol-fermentation
6836817268myo-inositol-fermentation
6836816899D-mannitol-fermentation
6836817634D-glucose-fermentation
683685291gelatin-hydrolysis
6836827897tryptophan-energy source
6836816199urea-hydrolysis
6836816947citrate+assimilation
6836818257ornithine-degradation
6836825094lysine-degradation
6836829016arginine-hydrolysis

metabolite production

@refChebi-IDmetaboliteproduction
6836815688acetoinyes
6836835581indoleno
6836816136hydrogen sulfideno

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testindole test
6836815688acetoin+
6836835581indole-

enzymes

@refvalueactivityec
68368cytochrome oxidase-1.9.3.1
68368gelatinase-
68368tryptophan deaminase+4.1.99.1
68368urease-3.5.1.5
68368ornithine decarboxylase-4.1.1.17
68368lysine decarboxylase-4.1.1.18
68368arginine dihydrolase-3.5.3.6
68368beta-galactosidase+3.2.1.23

API 20E

@refONPGADH ArgLDC LysODCCITH2SURETDA TrpINDVPGELGLUMANINOSorRHASACMELAMYARAOX
64606+---+--+-+-----+-----

Isolation, sampling and environmental information

isolation

  • @ref: 64606
  • sample type: petroleum polluted soil
  • geographic location: Shandong Province, Jinan
  • country: China
  • origin.country: CHN
  • continent: Asia

isolation source categories

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

taxonmaps

  • @ref: 69479
  • File name: preview.99_1339.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_20;96_774;97_902;98_1058;99_1339&stattab=map
  • Last taxonomy: Sphingobium yanoikuyae
  • 16S sequence: EF062503
  • Sequence Identity:
  • Total samples: 130321
  • soil counts: 32411
  • aquatic counts: 35267
  • animal counts: 53023
  • plant counts: 9620

Safety information

risk assessment

  • @ref: 64606
  • pathogenicity human: yes, in single cases
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 64606
  • description: Sphingomonas sp. XLDN2-5 16S ribosomal RNA gene, partial sequence
  • accession: EF062503
  • length: 1384
  • database: ena
  • NCBI tax ID: 411925

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Sphingobium yanoikuyae XLDN2-5GCA_000224695contigncbi1074493
66792Sphingobium yanoikuyae XLDN2-51074493.3wgspatric1074493
66792Sphingobium yanoikuyae XLDN2-52548876536draftimg1074493

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
motileyes60.472no
flagellatedno89.372no
gram-positiveno97.204no
anaerobicno99.054no
aerobicyes93.781no
halophileno95.449no
spore-formingno95.765no
thermophileno98.22no
glucose-utilyes87.656no
glucose-fermentno93.349yes

External links

@ref: 64606

culture collection no.: DSM 28039

straininfo link

  • @ref: 110878
  • straininfo: 397936

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Genetics22038966Genome sequence of Sphingobium yanoikuyae XLDN2-5, an efficient carbazole-degrading strain.Gai Z, Wang X, Tang H, Tai C, Tao F, Wu G, Xu PJ Bacteriol10.1128/JB.06050-112011Base Sequence, Carbazoles/*metabolism, *Genome, Bacterial, Molecular Sequence Data, Sphingomonadaceae/*genetics/metabolism, Xenobiotics/*metabolismMetabolism
Metabolism22745775Carotenoids play a positive role in the degradation of heterocycles by Sphingobium yanoikuyae.Liu X, Gai Z, Tao F, Tang H, Xu PPLoS One10.1371/journal.pone.00395222012Carotenoids/*metabolism, Cryptoxanthins, Heterocyclic Compounds/*metabolism, Oxidative Stress/physiology, Sphingomonadaceae/*metabolism, Xanthophylls/metabolism, Zeaxanthins, beta Carotene/metabolism
Metabolism30390601Highly sensitive microbial biosensor based on recombinant Escherichia coli overexpressing catechol 2,3-dioxygenase for reliable detection of catechol.Liu Z, Zhang Y, Bian C, Xia T, Gao Y, Zhang X, Wang H, Ma H, Hu Y, Wang XBiosens Bioelectron10.1016/j.bios.2018.10.0502018Biosensing Techniques/*methods, Catechol 2,3-Dioxygenase/*genetics/metabolism, Catechols/*analysis/metabolism, Electrodes, Escherichia coli/*genetics/metabolism, Limit of Detection, Recombinant Proteins/genetics/metabolism, Sphingomonadaceae/*enzymology/*genetics/metabolism, Up-RegulationEnzymology
Metabolism35970217Efficient bioelectricity generation and carbazole biodegradation using an electrochemically active bacterium Sphingobium yanoikuyae XLDN2-5.Wang H, Qi X, Zhang L, Zhang X, Xu P, Wang XChemosphere10.1016/j.chemosphere.2022.1359862022*Bioelectric Energy Sources/microbiology, Carbazoles/metabolism, Electricity, Electrodes, *Environmental Pollutants/metabolism, Oxygen/metabolism, *Sphingomonadaceae/metabolism

Reference

@idauthorstitledoi/urlcatalogue
20215Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M.List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ10.1099/ijsem.0.004332
64606Curators of the DSMZhttps://www.dsmz.de/collection/catalogue/details/culture/DSM-28039Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 28039)
66792Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg OvermannAutomatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)https://diaspora-project.de/progress.html#genomes
68368Automatically annotated from API 20E
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.MicrobeAtlas 1.0 betahttps://microbeatlas.org/
110878Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.StrainInfo: A central database for resolving microbial strain identifiers10.60712/SI-ID397936.1