Strain identifier

BacDive ID: 14129

Type strain: Yes

Species: Sphingobacterium wenxiniae

Strain Designation: LQY-18

Strain history: <- J. Zhang, Nanjing Agric. Univ., China; LQY-18

NCBI tax ID(s): 683125 (species)

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General

@ref: 16519

BacDive-ID: 14129

DSM-Number: 22789

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

description: Sphingobacterium wenxiniae LQY-18 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from activated sludge of a wastewater treatment plant in a synthetic pyrethroid-manufacturing facility.

NCBI tax id

  • NCBI tax id: 683125
  • Matching level: species

strain history

  • @ref: 16519
  • history: <- J. Zhang, Nanjing Agric. Univ., China; LQY-18

doi: 10.13145/bacdive14129.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/bacteroidota
  • domain: Bacteria
  • phylum: Bacteroidota
  • class: Sphingobacteriia
  • order: Sphingobacteriales
  • family: Sphingobacteriaceae
  • genus: Sphingobacterium
  • species: Sphingobacterium wenxiniae
  • full scientific name: Sphingobacterium wenxiniae Zhang et al. 2012

@ref: 16519

domain: Bacteria

phylum: Bacteroidetes

class: Sphingobacteriia

order: Sphingobacteriales

family: Sphingobacteriaceae

genus: Sphingobacterium

species: Sphingobacterium wenxiniae

full scientific name: Sphingobacterium wenxiniae Zhang et al. 2012

strain designation: LQY-18

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
30307negative0.6-1.4 µm0.3-0.6 µmrod-shapedno
69480no92.09
69480negative99.997

pigmentation

  • @ref: 30307
  • production: yes

Culture and growth conditions

culture medium

  • @ref: 16519
  • name: TRYPTONE SOYA BROTH (TSB) (DSMZ Medium 545)
  • growth: yes
  • link: https://mediadive.dsmz.de/medium/545
  • composition: Name: TRYPTONE SOYA BROTH (TSB) (DSMZ Medium 545) Composition: Casein peptone 17.0 g/l NaCl 5.0 g/l Soy peptone 3.0 g/l D(+)-Glucose 2.5 g/l K2HPO4 2.5 g/l Distilled water

culture temp

@refgrowthtypetemperaturerange
16519positivegrowth28mesophilic
30307positivegrowth08-40
30307positiveoptimum30mesophilic

culture pH

@refabilitytypepHPH range
30307positivegrowth05-10alkaliphile
30307positiveoptimum07-08

Physiology and metabolism

oxygen tolerance

  • @ref: 30307
  • oxygen tolerance: aerobe

spore formation

@refspore formationconfidence
30307no
69481no100
69480no99.988

halophily

@refsaltgrowthtested relationconcentration
30307NaClpositivegrowth0-5 %
30307NaClpositiveoptimum1 %

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3030733984fucose+carbon source
3030728087glycogen+carbon source
3030726271proline+carbon source
3030727082trehalose+carbon source
3030753424tween 20+carbon source
3030753426tween 80+carbon source
303074853esculin+hydrolysis

enzymes

@refvalueactivityec
30307acid phosphatase+3.1.3.2
30307alkaline phosphatase+3.1.3.1
30307alpha-galactosidase+3.2.1.22
30307catalase+1.11.1.6
30307cytochrome oxidase+1.9.3.1

Isolation, sampling and environmental information

isolation

  • @ref: 16519
  • sample type: activated sludge of a wastewater treatment plant in a synthetic pyrethroid-manufacturing facility
  • geographic location: Jiangsu Province, Yangzhou
  • country: China
  • origin.country: CHN
  • continent: Asia

isolation source categories

Cat1Cat2Cat3
#Engineered#Industrial
#Engineered#Waste#Activated sludge
#Engineered#Waste#Industrial wastewater
#Engineered#Waste#Water treatment plant

taxonmaps

  • @ref: 69479
  • File name: preview.99_39802.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_15366;96_18642;97_23065;98_29087;99_39802&stattab=map
  • Last taxonomy: Sphingobacterium wenxiniae subclade
  • 16S sequence: GQ988781
  • Sequence Identity:
  • Total samples: 1264
  • soil counts: 270
  • aquatic counts: 226
  • animal counts: 682
  • plant counts: 86

Safety information

risk assessment

  • @ref: 16519
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 16519
  • description: Sphingobacterium wenxiniae strain LQY-18 16S ribosomal RNA gene, partial sequence
  • accession: GQ988781
  • length: 1453
  • database: ena
  • NCBI tax ID: 683125

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Sphingobacterium wenxiniae DSM 22789GCA_900116225scaffoldncbi683125
66792Sphingobacterium wenxiniae strain DSM 22789683125.3wgspatric683125
66792Sphingobacterium wenxiniae DSM 227892634166295draftimg683125

GC content

@refGC-contentmethod
1651940.3thermal denaturation, midpoint method (Tm)
3030740.3

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileno92.828yes
flagellatedno95.324yes
gram-positiveno98.355no
anaerobicno98.929no
aerobicyes89.773yes
halophileno91.898yes
spore-formingno96.301no
glucose-fermentno91.001no
thermophileno99.121yes
glucose-utilyes88.71no

External links

@ref: 16519

culture collection no.: DSM 22789, ACCC 05410, CCTCC AB 2010005, KCTC 23009

straininfo link

  • @ref: 83294
  • straininfo: 402443

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny21551333Sphingobacterium wenxiniae sp. nov., a cypermethrin-degrading species from activated sludge.Zhang J, Zheng JW, Cho BC, Hwang CY, Fang C, He J, Li SPInt J Syst Evol Microbiol10.1099/ijs.0.033118-02011Bacterial Typing Techniques, Base Composition, China, Cluster Analysis, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis, Hydrogen-Ion Concentration, Molecular Sequence Data, Phylogeny, Pyrethrins/*metabolism, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sewage/*microbiology, Sodium Chloride/metabolism, Sphingobacterium/*classification/genetics/*isolation & purification/metabolism, Temperature, Vitamin K 2/analysisMetabolism
Phylogeny26374401Sphingobacterium suaedae sp. nov., isolated from the rhizosphere soil of Suaeda corniculata.Sun JQ, Liu M, Wang XY, Xu L, Wu XLInt J Syst Evol Microbiol10.1099/ijsem.0.0006002015Bacterial Typing Techniques, Base Composition, Chenopodiaceae/*microbiology, China, DNA, Bacterial/genetics, Fatty Acids/chemistry, Lakes, Molecular Sequence Data, *Phylogeny, RNA, Ribosomal, 16S/genetics, *Rhizosphere, Sequence Analysis, DNA, *Soil Microbiology, Sphingobacterium/*classification/genetics/isolation & purification, Vitamin K 2/analogs & derivatives/chemistryGenetics
33998126Organoarsenical tolerance in Sphingobacterium wenxiniae, a bacterium isolated from activated sludge.Chen J, Zhang J, Rosen BPEnviron Microbiol10.1111/1462-2920.155992021Animals, *Arsenic, *Arsenicals, *Roxarsone/chemistry, Sewage, *Sphingobacterium/genetics, Swine

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmedjournal
16519Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 22789)https://www.dsmz.de/collection/catalogue/details/culture/DSM-22789
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
30307Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2664828776041
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)
66794Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg10.1093/nar/gkaa1025BRENDA, the ELIXIR core data resource in 2021: new developments and updates33211880Nucleic Acids Res. 49: D498-D508 2020
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
83294Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID402443.1StrainInfo: A central database for resolving microbial strain identifiers