Strain identifier

BacDive ID: 24556

Type strain: Yes

Species: Sphingobium jiangsuense

Strain Designation: BA-3

Strain history: <- J. He, Key Lab. of Microbiological Engineering of Agricultural Environment, Nanjing Agricultural University; BA-3 <- X.-Q. Duan, Nanjing Agric. Univ., China

NCBI tax ID(s): 870476 (species)

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General

@ref: 20814

BacDive-ID: 24556

DSM-Number: 26189

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

description: Sphingobium jiangsuense BA-3 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from activated sludge of a pyrethroid manufactoring facility.

NCBI tax id

  • NCBI tax id: 870476
  • Matching level: species

strain history

  • @ref: 20814
  • history: <- J. He, Key Lab. of Microbiological Engineering of Agricultural Environment, Nanjing Agricultural University; BA-3 <- X.-Q. Duan, Nanjing Agric. Univ., China

doi: 10.13145/bacdive24556.20230509.8.1

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 jiangsuense
  • full scientific name: Sphingobium jiangsuense Zhang et al. 2012

@ref: 20814

domain: Bacteria

phylum: Proteobacteria

class: Alphaproteobacteria

order: Pseudomonadales

family: Sphingomonadaceae

genus: Sphingobium

species: Sphingobium jiangsuense

full scientific name: Sphingobium jiangsuense Zhang et al. 2012

strain designation: BA-3

type strain: yes

Morphology

cell morphology

  • @ref: 30137
  • gram stain: negative
  • cell length: 1-1.2 µm
  • cell width: 0.6-0.8 µm
  • motility: no

pigmentation

  • @ref: 30137
  • production: yes

Culture and growth conditions

culture medium

  • @ref: 20814
  • 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
20814positivegrowth28mesophilic
30137positivegrowth10-37
30137positiveoptimum28mesophilic

culture pH

@refabilitytypepHPH range
30137positivegrowth5.5-9alkaliphile
30137positiveoptimum7

Physiology and metabolism

oxygen tolerance

  • @ref: 30137
  • oxygen tolerance: aerobe

spore formation

  • @ref: 30137
  • spore formation: no

halophily

@refsaltgrowthtested relationconcentration
30137NaClpositivegrowth0-2 %
30137NaClpositiveoptimum0.50 %

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3013717234glucose+carbon source
3013729864mannitol+carbon source
3013726546rhamnose+carbon source
301374853esculin+hydrolysis
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
30137urease+3.5.1.5
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
20814-----+-+++----------+

Isolation, sampling and environmental information

isolation

  • @ref: 20814
  • sample type: activated sludge of a pyrethroid manufactoring facility
  • geographic location: Jiangsu Prov., Yangzhou
  • country: China
  • origin.country: CHN
  • continent: Asia
  • latitude: 32.4
  • longitude: 119.433

isolation source categories

Cat1Cat2Cat3
#Engineered#Industrial
#Engineered#Waste#Activated sludge
#Engineered#Waste#Industrial wastewater

Safety information

risk assessment

  • @ref: 20814
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 20814
  • description: Sphingobium jiangsuense strain BA-3 16S ribosomal RNA gene, partial sequence
  • accession: HM748834
  • length: 1445
  • database: ena
  • NCBI tax ID: 870476

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Sphingobium jiangsuense DSM 26189GCA_014196495scaffoldncbi870476
66792Sphingobium jiangsuense strain DSM 26189870476.3wgspatric870476
66792Sphingobium jiangsuense DSM 261892829898683draftimg870476

GC content

  • @ref: 30137
  • GC-content: 63.8

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
flagellatedno87.554yes
gram-positiveno95.753no
anaerobicno98.962no
aerobicyes95.488yes
halophileno94.093no
spore-formingno93.831yes
glucose-utilyes73.315no
thermophileno97.453yes
motileyes58.587yes
glucose-fermentno91.721yes

External links

@ref: 20814

culture collection no.: DSM 26189, CCTCC AB 201217, KACC 16433, KCTC 23196

straininfo link

  • @ref: 88411
  • straininfo: 407790

literature

  • topic: Phylogeny
  • Pubmed-ID: 21571933
  • title: Sphingobium jiangsuense sp. nov., a 3-phenoxybenzoic acid-degrading bacterium isolated from a wastewater treatment system.
  • authors: Zhang J, Lang ZF, Zheng JW, Hang BJ, Duan XQ, He J, Li SP
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijs.0.029827-0
  • year: 2011
  • mesh: Bacterial Typing Techniques, Base Composition, Benzoates, DNA, Bacterial/genetics, Fatty Acids/chemistry, Molecular Sequence Data, Nucleic Acid Hybridization, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sewage/*microbiology, Spermidine/chemistry, Sphingomonadaceae/*classification/genetics/metabolism, Ubiquinone/chemistry, Waste Disposal, Fluid
  • topic2: Genetics

Reference

@idauthorstitledoi/urlcatalogueID_cross_referencepubmed
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
20814Curators of the DSMZhttps://www.dsmz.de/collection/catalogue/details/culture/DSM-26189Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 26189)
30137Barberan A, Caceres Velazquez H, Jones S, Fierer N.Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information10.1128/mSphere.00237-172648828776041
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
68369Automatically annotated from API 20NE
88411Reimer, 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-ID407790.1