Strain identifier

BacDive ID: 14107

Type strain: Yes

Species: Pedobacter metabolipauper

Strain Designation: WB2.3-71

Strain history: <- S. Muurholm <- E. Brambilla <- O. Päuker; WB2.3-71

NCBI tax ID(s): 425513 (species)

For citation purpose refer to the digital object identifier (doi) of the current version.
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General

@ref: 7854

BacDive-ID: 14107

DSM-Number: 19035

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

description: Pedobacter metabolipauper WB2.3-71 is a mesophilic, Gram-negative, motile bacterium that was isolated from stream water.

NCBI tax id

  • NCBI tax id: 425513
  • Matching level: species

strain history

  • @ref: 7854
  • history: <- S. Muurholm <- E. Brambilla <- O. Päuker; WB2.3-71

doi: 10.13145/bacdive14107.20230509.8.1

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

@ref: 7854

domain: Bacteria

phylum: Bacteroidetes

class: Sphingobacteriia

order: Sphingobacteriales

family: Sphingobacteriaceae

genus: Pedobacter

species: Pedobacter metabolipauper

full scientific name: Pedobacter metabolipauper Muurholm et al. 2007

strain designation: WB2.3-71

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
32230negative2.2 µm0.83 µmrod-shapedyes
69480no90.154
69480negative99.982

pigmentation

  • @ref: 32230
  • production: no

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
7854R2A 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
33301MEDIUM 72- for trypto casein soja agaryesDistilled water make up to (1000.000 ml);Trypto casein soy agar (40.000 g)

culture temp

@refgrowthtypetemperaturerange
7854positivegrowth25mesophilic
32230positivegrowth08-31
32230positiveoptimum25mesophilic
33301positivegrowth15psychrophilic

culture pH

@refabilitytypepH
32230positivegrowth5.9-8.0
32230positiveoptimum6.95

Physiology and metabolism

spore formation

@refspore formationconfidence
32230no
69481no100
69480no99.979

halophily

@refsaltgrowthtested relationconcentration
32230NaClpositivegrowth<4 %
32230NaClpositiveoptimum2 %

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3223017057cellobiose+carbon source
3223017234glucose+carbon source
3223017716lactose+carbon source
3223017306maltose+carbon source
3223037684mannose+carbon source
3223028053melibiose+carbon source
3223017992sucrose+carbon source
3223027082trehalose+carbon source
3223053426tween 80+carbon source
322304853esculin+hydrolysis

enzymes

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

Isolation, sampling and environmental information

isolation

  • @ref: 7854
  • 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: 7854
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 32230
  • description: Pedobacter metabolipauper partial 16S rRNA gene, type strain WB2.3-71T
  • accession: AM491370
  • length: 1505
  • database: nuccore
  • NCBI tax ID: 425513

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Pedobacter metabolipauper DSM 19035GCA_004362715scaffoldncbi425513
66792Pedobacter metabolipauper strain DSM 19035425513.4wgspatric425513
66792Pedobacter metabolipauper DSM 190352636416080draftimg425513

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileno85.677yes
flagellatedno96.598no
gram-positiveno97.931yes
anaerobicno99.172no
aerobicyes87.6no
halophileno96.604no
spore-formingno95.979yes
glucose-utilyes90.182yes
thermophileno99.28yes
glucose-fermentno90.896no

External links

@ref: 7854

culture collection no.: DSM 19035

straininfo link

  • @ref: 83274
  • straininfo: 310980

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
Phylogeny25520261Pedobacter bambusae sp. nov., isolated from soil of a bamboo plantation.Won KH, Kook M, Yi THAntonie Van Leeuwenhoek10.1007/s10482-014-0352-82014Aerobiosis, Bacterial Typing Techniques, Base Composition, Cluster Analysis, Cytosol/chemistry, 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, Poaceae/growth & development, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Vitamin K 2/analysisGenetics

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmedjournal
7854Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 19035)https://www.dsmz.de/collection/catalogue/details/culture/DSM-19035
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
33301Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/7228
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
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
83274Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID310980.1StrainInfo: A central database for resolving microbial strain identifiers