Strain identifier

BacDive ID: 14109

Type strain: Yes

Species: Pedobacter steynii

Strain Designation: WB2.3-45

Strain history: <- S. Muurholm <- E. Brambilla <- O. Päuker; WB2.3-45

NCBI tax ID(s): 430522 (species)

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General

@ref: 7897

BacDive-ID: 14109

DSM-Number: 19110

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

description: Pedobacter steynii WB2.3-45 is a mesophilic, Gram-negative, motile bacterium that was isolated from stream water.

NCBI tax id

  • NCBI tax id: 430522
  • Matching level: species

strain history

  • @ref: 7897
  • history: <- S. Muurholm <- E. Brambilla <- O. Päuker; WB2.3-45

doi: 10.13145/bacdive14109.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/bacteroidota
  • domain: Bacteria
  • phylum: Bacteroidota
  • class: Sphingobacteriia
  • order: Sphingobacteriales
  • family: Sphingobacteriaceae
  • genus: Pedobacter
  • species: Pedobacter steynii
  • full scientific name: Pedobacter steynii Muurholm et al. 2007

@ref: 7897

domain: Bacteria

phylum: Bacteroidetes

class: Sphingobacteriia

order: Sphingobacteriales

family: Sphingobacteriaceae

genus: Pedobacter

species: Pedobacter steynii

full scientific name: Pedobacter steynii Muurholm et al. 2007

strain designation: WB2.3-45

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
32230negative2.73 µm0.83 µmrod-shapedyes
69480no90.201
69480negative99.988

pigmentation

  • @ref: 32230
  • production: no

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
7897R2A MEDIUM (DSMZ Medium 830)yeshttps://mediadive.dsmz.de/medium/830Name: 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
37317MEDIUM 566- Reasoner's 2A agar for Flavobacterium micromatiyesDistilled water make up to (1000.000 ml);R2A agar (18.200 g)

culture temp

@refgrowthtypetemperaturerange
7897positivegrowth25mesophilic
32230positivegrowth10-30
32230positiveoptimum26mesophilic
37317positivegrowth25mesophilic

culture pH

@refabilitytypepH
32230positivegrowth5.70-8.45
32230positiveoptimum7.08

Physiology and metabolism

spore formation

@refspore formationconfidence
32230no
69481no100
69480no99.985

halophily

@refsaltgrowthtested relationconcentration
32230NaClpositivegrowth0-4 %
32230NaClpositiveoptimum2 %

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3223040585alpha-cyclodextrin+carbon source
3223035391aspartate+carbon source
3223017057cellobiose+carbon source
3223023652dextrin+carbon source
3223028260galactose+carbon source
322305291gelatin+carbon source
3223017234glucose+carbon source
3223029987glutamate+carbon source
3223017754glycerol+carbon source
3223028087glycogen+carbon source
3223017716lactose+carbon source
3223017306maltose+carbon source
3223037684mannose+carbon source
3223028053melibiose+carbon source
3223037657methyl D-glucoside+carbon source
32230506227N-acetylglucosamine+carbon source
3223016634raffinose+carbon source
3223017814salicin+carbon source
3223017822serine+carbon source
3223026986threonine+carbon source
3223027082trehalose+carbon source
3223053426tween 80+carbon source
3223018222xylose+carbon source
322304853esculin+hydrolysis

enzymes

@refvalueactivityec
32230alkaline phosphatase+3.1.3.1
32230catalase+1.11.1.6
32230gelatinase+
32230cytochrome oxidase+1.9.3.1

Isolation, sampling and environmental information

isolation

  • @ref: 7897
  • sample type: stream water
  • geographic location: Lower Saxony, Westhöfer Bach
  • country: Germany
  • origin.country: DEU
  • continent: Europe

isolation source categories

  • Cat1: #Environmental
  • Cat2: #Aquatic
  • Cat3: #River (Creek)

taxonmaps

  • @ref: 69479
  • File name: preview.99_3245.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_115;96_319;97_404;98_463;99_3245&stattab=map
  • Last taxonomy: Pedobacter
  • 16S sequence: AM491372
  • Sequence Identity:
  • Total samples: 2263
  • soil counts: 673
  • aquatic counts: 488
  • animal counts: 754
  • plant counts: 348

Safety information

risk assessment

  • @ref: 7897
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 32230
  • description: Pedobacter steynii partial 16S rRNA gene, type strain WB2.3-45T
  • accession: AM491372
  • length: 1505
  • database: nuccore
  • NCBI tax ID: 430522

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Pedobacter steynii DSM 19110GCA_900103665scaffoldncbi430522
66792Pedobacter steynii strain DSM 19110430522.10wgspatric430522
66792Pedobacter steynii DSM 191102675903693draftimg430522

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileno84.037yes
flagellatedno96.231no
gram-positiveno97.224yes
anaerobicno99.288no
aerobicyes83.921no
halophileno96.917no
spore-formingno90.07yes
glucose-fermentno89.212no
thermophileno99.642yes
glucose-utilyes88.423yes

External links

@ref: 7897

culture collection no.: DSM 19110

straininfo link

  • @ref: 83276
  • straininfo: 310981

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny17911287Pedobacter duraquae sp. nov., Pedobacter westerhofensis sp. nov., Pedobacter metabolipauper sp. nov., Pedobacter hartonius sp. nov. and Pedobacter steynii sp. nov., isolated from a hard-water rivulet.Muurholm S, Cousin S, Pauker O, Brambilla E, Stackebrandt EInt J Syst Evol Microbiol10.1099/ijs.0.65166-02007Animals, Bacterial Typing Techniques, Bacteroidetes/chemistry/*classification/*isolation & purification, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis, Fresh Water/*microbiology, Genes, rRNA, Germany, Molecular Sequence Data, Organic Chemicals/metabolism, Phylogeny, Quinones/analysis, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sequence Homology, Nucleic AcidGenetics
Phylogeny24659428Pedobacter seoulensis sp. nov., isolated from soil of a bamboo field.Ngo HT, Son HM, Park SY, Kim KY, Yi THAntonie Van Leeuwenhoek10.1007/s10482-014-0154-z2014Bacterial Typing Techniques, Base Composition, Cluster Analysis, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis, Korea, Molecular Sequence Data, Nucleic Acid Hybridization, Pedobacter/*classification/genetics/*isolation & purification/physiology, Phospholipids/analysis, Phylogeny, Polyamines/analysis, Quinones/analysis, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil MicrobiologyGenetics
Phylogeny33502299Pedobacter gandavensis sp. nov., Pedobacter foliorum sp. nov. and Pedobacter planticolens sp. nov., isolated from leaves of Arabidopsis thaliana.Qi SS, Cnockaert M, Carlier A, Vandamme PInt J Syst Evol Microbiol10.1099/ijsem.0.0046672021

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmedjournal
7897Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 19110)https://www.dsmz.de/collection/catalogue/details/culture/DSM-19110
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
32230Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2847228776041
37317Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/7258
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
83276Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID310981.1StrainInfo: A central database for resolving microbial strain identifiers