Strain identifier

BacDive ID: 5578

Type strain: Yes

Species: Flavobacterium swingsii

Strain Designation: WB2.3-68

Strain history: CIP <- 2008, DSMZ <- Dr. Tindall, Germany: strain WB2.3-68

NCBI tax ID(s): 1121900 (strain), 498292 (species)

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General

@ref: 15952

BacDive-ID: 5578

DSM-Number: 21789

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

description: Flavobacterium swingsii WB2.3-68 is an aerobe, psychrophilic, Gram-negative bacterium that was isolated from water of a hardwater creek.

NCBI tax id

NCBI tax idMatching level
1121900strain
498292species

strain history

@refhistory
15952<- Z. Ali, DSMZ; WB 2.3-68 <- O. Päuker and E. Brambilla, DSMZ
123396CIP <- 2008, DSMZ <- Dr. Tindall, Germany: strain WB2.3-68

doi: 10.13145/bacdive5578.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/bacteroidota
  • domain: Bacteria
  • phylum: Bacteroidota
  • class: Flavobacteriia
  • order: Flavobacteriales
  • family: Flavobacteriaceae
  • genus: Flavobacterium
  • species: Flavobacterium swingsii
  • full scientific name: Flavobacterium swingsii Ali et al. 2009

@ref: 15952

domain: Bacteria

phylum: Bacteroidetes

class: Flavobacteriia

order: Flavobacteriales

family: Flavobacteriaceae

genus: Flavobacterium

species: Flavobacterium swingsii

full scientific name: Flavobacterium swingsii Ali et al. 2009

strain designation: WB2.3-68

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
29215negative5.25 µm0.3 µmrod-shapedno
69480negative100
123396negativerod-shapedno

pigmentation

  • @ref: 29215
  • production: yes

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
15952CY-AGAR (DSMZ Medium 67)yeshttps://mediadive.dsmz.de/medium/67Name: CY-AGAR (DSMZ Medium 67) Composition: Agar 15.0 g/l Casitone 3.0 g/l CaCl2 x 2 H2O 1.36 g/l Yeast extract 1.0 g/l Distilled water
15952R2A 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
34226MEDIUM 34 - for Flavobacterium branchiophilum and Flavobacterium columnareyesDistilled water make up to (1000.000 ml);Agar (10.000 g);Yeast extract (0.500 g);Sodium acetate (0.200 g);Tryptone (0.500 g);Beef extract (0.200 g)
123396CIP Medium 566yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=566

culture temp

@refgrowthtypetemperaturerange
15952positivegrowth24psychrophilic
29215positivegrowth03-26
29215positiveoptimum24-26
34226positivegrowth25mesophilic

culture pH

  • @ref: 29215
  • ability: positive
  • type: growth
  • pH: 7

Physiology and metabolism

oxygen tolerance

  • @ref: 29215
  • oxygen tolerance: aerobe

spore formation

@refspore formationconfidence
69481no100
69480no99.997

halophily

  • @ref: 29215
  • salt: NaCl
  • growth: positive
  • tested relation: growth
  • concentration: 0 %

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
2921553423tween 40+carbon source
2921517632nitrate+reduction
12339617632nitrate+reduction
12339616301nitrite-reduction

metabolite production

  • @ref: 29215
  • Chebi-ID: 16136
  • metabolite: hydrogen sulfide
  • production: yes

enzymes

@refvalueactivityec
29215catalase+1.11.1.6
29215cytochrome oxidase+1.9.3.1
68382alpha-fucosidase-3.2.1.51
68382alpha-mannosidase-3.2.1.24
68382N-acetyl-beta-glucosaminidase-3.2.1.52
68382beta-glucosidase-3.2.1.21
68382alpha-glucosidase-3.2.1.20
68382beta-glucuronidase-3.2.1.31
68382beta-galactosidase-3.2.1.23
68382alpha-galactosidase-3.2.1.22
68382naphthol-AS-BI-phosphohydrolase+
68382acid phosphatase+3.1.3.2
68382alpha-chymotrypsin+3.4.21.1
68382trypsin-3.4.21.4
68382cystine arylamidase-3.4.11.3
68382valine arylamidase+
68382leucine arylamidase+3.4.11.1
68382lipase (C 14)-
68382esterase lipase (C 8)+
68382esterase (C 4)-
68382alkaline phosphatase+3.1.3.1
123396oxidase+
123396catalase+1.11.1.6
123396urease-3.5.1.5

API zym

@refControlAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
123396-+-+-++--+++--------

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
15952water of a hardwater creekHarz Mountains, Westerhöfer Bach, Westerhof, 40 km north of GöttingenGermanyDEUEurope
123396Environment, Hard water, riverWesterhöfer Bach, Harz mountainsGermanyDEUEurope

isolation source categories

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

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
159521Risk group (German classification)
1233961Risk group (French classification)

Sequence information

16S sequences

  • @ref: 15952
  • description: Flavobacterium swingsii partial 16S rRNA gene, type strain WB2.3-68T
  • accession: AM934651
  • length: 1484
  • database: ena
  • NCBI tax ID: 498292

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Flavobacterium swingsii DSM 21789GCA_900111965contigncbi498292
66792Flavobacterium swingsii strain DSM 21789498292.3wgspatric498292
66792Flavobacterium swingsii DSM 217892599185297draftimg498292

GC content

@refGC-contentmethod
1595233.3high performance liquid chromatography (HPLC)
2921533.3

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
gram-positiveno99.124yes
anaerobicno98.749yes
halophileno93.909no
spore-formingno95.433no
glucose-utilyes73.502no
aerobicyes89.015yes
thermophileno98.617yes
motileno92.481yes
flagellatedno97.416yes
glucose-fermentno92.896no

External links

@ref: 15952

culture collection no.: DSM 21789, CIP 109868, WB 2.3-68

straininfo link

  • @ref: 75060
  • straininfo: 363445

literature

  • topic: Phylogeny
  • Pubmed-ID: 19622646
  • title: Flavobacterium rivuli sp. nov., Flavobacterium subsaxonicum sp. nov., Flavobacterium swingsii sp. nov. and Flavobacterium reichenbachii sp. nov., isolated from a hard water rivulet.
  • authors: Ali Z, Cousin S, Fruhling A, Brambilla E, Schumann P, Yang Y, Stackebrandt E
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijs.0.008771-0
  • year: 2009
  • mesh: DNA, Bacterial/genetics, DNA, Ribosomal/genetics, Fatty Acids/chemistry/metabolism, Flavobacterium/chemistry/classification/genetics/*isolation & purification, Fresh Water/*microbiology, Molecular Sequence Data, Phylogeny, RNA, Ribosomal, 16S/genetics
  • topic2: Genetics

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmed
15952Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 21789)https://www.dsmz.de/collection/catalogue/details/culture/DSM-21789
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
29215Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2563628776041
34226Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/7661
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)
68382Automatically annotated from API zym
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
75060Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID363445.1StrainInfo: A central database for resolving microbial strain identifiers
123396Curators of the CIPCollection of Institut Pasteur (CIP 109868)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20109868