Strain identifier

BacDive ID: 14108

Type strain: Yes

Species: Pedobacter westerhofensis

Strain Designation: WB3.3-22

Strain history: <- S. Muurholm <- E. Brambilla <- O. Päuker; WB3.3-22

NCBI tax ID(s): 425512 (species)

« back to strain detail view
For citation purpose refer to the digital object identifier (doi) of the current version.
Archive
version 9.3 (current version):
version 9.2:
version 9.1:
version 9:
version 8.1:
version 8:
version 7.1:
version 7:
version 6:
version 5:
version 4.1:
version 4:
version 3:
version 2.1:
version 2:
version 1:
version 9.3 (current version)

General

@ref: 7855

BacDive-ID: 14108

DSM-Number: 19036

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

description: Pedobacter westerhofensis WB3.3-22 is a mesophilic, Gram-negative, motile bacterium that was isolated from stream water.

NCBI tax id

  • NCBI tax id: 425512
  • Matching level: species

strain history

  • @ref: 7855
  • history: <- S. Muurholm <- E. Brambilla <- O. Päuker; WB3.3-22

doi: 10.13145/bacdive14108.20250331.9.3

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 westerhofensis
  • full scientific name: Pedobacter westerhofensis Muurholm et al. 2007

@ref: 7855

domain: Bacteria

phylum: Bacteroidetes

class: Sphingobacteriia

order: Sphingobacteriales

family: Sphingobacteriaceae

genus: Pedobacter

species: Pedobacter westerhofensis

full scientific name: Pedobacter westerhofensis Muurholm et al. 2007

strain designation: WB3.3-22

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
32230negative2.1 µm0.915 µmrod-shapedyes
125439negative99.3
125438negative94.25

pigmentation

  • @ref: 32230
  • production: no

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
7855R2A 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
42248MEDIUM 566- Reasoner's 2A agar for Flavobacterium micromatiyesDistilled water make up to (1000.000 ml);R2A agar (18.200 g)

culture temp

@refgrowthtypetemperature
7855positivegrowth25
32230positivegrowth09-28
32230positiveoptimum23
42248positivegrowth15

culture pH

@refabilitytypepH
32230positivegrowth5.3-7.8
32230positiveoptimum6.55

Physiology and metabolism

oxygen tolerance

  • @ref: 125439
  • oxygen tolerance: obligate aerobe
  • confidence: 91.5

spore formation

@refspore formationconfidence
32230no
125439no98.5

halophily

@refsaltgrowthtested relationconcentration
32230NaClpositivegrowth<4 %
32230NaClpositiveoptimum2 %

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3223040585alpha-cyclodextrin+carbon source
3223022599arabinose+carbon source
3223017057cellobiose+carbon source
3223023652dextrin+carbon source
3223028757fructose+carbon source
3223028260galactose+carbon source
322305291gelatin+carbon source
3223017234glucose+carbon source
3223017754glycerol+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
3223026546rhamnose+carbon source
3223017822serine+carbon source
3223017992sucrose+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: 7855
  • 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)

Safety information

risk assessment

  • @ref: 7855
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 32230
  • description: Pedobacter westerhofensis partial 16S rRNA gene, type strain WB3.3-22T
  • accession: AM491369
  • length: 1503
  • database: nuccore
  • NCBI tax ID: 425512

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Pedobacter westerhofensis DSM 19036GCA_900182595scaffoldncbi425512
66792Pedobacter westerhofensis strain DSM 19036425512.3wgspatric425512
66792Pedobacter westerhofensis DSM 190362724679782draftimg425512

Genome-based predictions

predictions

@refmodeltraitdescriptionpredictionconfidencetraining_data
125438gram-positivegram-positivePositive reaction to Gram-stainingno94.25no
125438anaerobicanaerobicAbility to grow under anoxygenic conditions (including facultative anaerobes)no96.443no
125438aerobicaerobicAbility to grow under oxygenic conditions (including facultative aerobes)yes87.678no
125438spore-formingspore-formingAbility to form endo- or exosporesno84.027yes
125438thermophilethermophilicAbility to grow at temperatures above or equal to 45°Cno96.472no
125438motile2+flagellatedAbility to perform flagellated movementno88.5no
125439BacteriaNetspore_formationAbility to form endo- or exosporesno98.5
125439BacteriaNetmotilityAbility to perform movementno72.5
125439BacteriaNetgram_stainReaction to gram-stainingnegative99.3
125439BacteriaNetoxygen_toleranceOxygenic conditions needed for growthobligate aerobe91.5

External links

@ref: 7855

culture collection no.: DSM 19036

straininfo link

  • @ref: 83275
  • straininfo: 310977

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
Phylogeny28109203Pedobacter lusitanus sp. nov., isolated from sludge of a deactivated uranium mine.Covas C, Caetano T, Cruz A, Santos T, Dias L, Klein G, Abdulmawjood A, Rodriguez-Alcala LM, Pimentel LL, Gomes A, Freitas AC, Garcia-Serrano A, Fontecha J, Mendo SInt J Syst Evol Microbiol10.1099/ijsem.0.0018142017Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, DNA, Ribosomal Spacer/genetics, Fatty Acids/chemistry, Genes, Bacterial, *Mining, Nucleic Acid Hybridization, Pedobacter/*classification/genetics/isolation & purification, Phospholipids/chemistry, *Phylogeny, Portugal, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sewage/*microbiology, Sphingolipids, *Uranium, Vitamin K 2/analogs & derivatives/chemistryTranscriptome

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmed
7855Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 19036)https://www.dsmz.de/collection/catalogue/details/culture/DSM-19036
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
42248Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/7227
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)
83275Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID310977.1StrainInfo: A central database for resolving microbial strain identifiers
125438Julia Koblitz, Lorenz Christian Reimer, Rüdiger Pukall, Jörg Overmann10.1101/2024.08.12.607695Predicting bacterial phenotypic traits through improved machine learning using high-quality, curated datasets
125439Philipp Münch, René Mreches, Martin Binder, Hüseyin Anil Gündüz, Xiao-Yin To, Alice McHardyhttps://github.com/GenomeNet/deepGdeepG: Deep Learning for Genome Sequence Data. R package version 0.3.1