Strain identifier

BacDive ID: 3963

Type strain: Yes

Species: Desulfobacter vibrioformis

Strain Designation: B54

Strain history: <- T. Lien; B54 <- T. Lien {1985}

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General

@ref: 3398

BacDive-ID: 3963

DSM-Number: 8776

keywords: genome sequence, 16S sequence, Bacteria, anaerobe, mesophilic, Gram-negative, vibrio-shaped

description: Desulfobacter vibrioformis B54 is an anaerobe, mesophilic, Gram-negative bacterium that was isolated from water-oil separation system on oil platform.

NCBI tax id

NCBI tax idMatching level
34031species
1121398strain

strain history

  • @ref: 3398
  • history: <- T. Lien; B54 <- T. Lien {1985}

doi: 10.13145/bacdive3963.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Deltaproteobacteria
  • order: Desulfobacterales
  • family: Desulfobacteraceae
  • genus: Desulfobacter
  • species: Desulfobacter vibrioformis
  • full scientific name: Desulfobacter vibrioformis Lien and Beeder 1997

@ref: 3398

domain: Bacteria

phylum: Proteobacteria

class: Deltaproteobacteria

order: Desulfobacterales

family: Desulfobacteraceae

genus: Desulfobacter

species: Desulfobacter vibrioformis

full scientific name: Desulfobacter vibrioformis Lien and Beeder 1997

strain designation: B54

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
23205negative4.5-8.0 µm1.9-2.3 µmvibrio-shapedno
23205yes
69480negative99.999
69480yes94.687

Culture and growth conditions

culture medium

  • @ref: 3398
  • name: DESULFOBACTER MEDIUM (DSMZ Medium 195)
  • growth: yes
  • link: https://mediadive.dsmz.de/medium/195
  • composition: Name: DESULFOBACTER MEDIUM (DSMZ Medium 195) Composition: NaCl 20.9372 g/l Na2SO4 2.99103 g/l MgCl2 x 6 H2O 2.99103 g/l Na-acetate x 3 H2O 2.49252 g/l Na2CO3 1.49551 g/l KCl 0.498504 g/l Na2S x 9 H2O 0.398804 g/l NH4Cl 0.299103 g/l KH2PO4 0.199402 g/l CaCl2 x 2 H2O 0.149551 g/l HCl 0.00249252 g/l FeCl2 x 4 H2O 0.00149551 g/l NaOH 0.000498504 g/l Sodium resazurin 0.000498504 g/l CoCl2 x 6 H2O 0.000189432 g/l Pyridoxine hydrochloride 9.97009e-05 g/l MnCl2 x 4 H2O 9.97009e-05 g/l ZnCl2 6.97906e-05 g/l p-Aminobenzoic acid 4.98504e-05 g/l (DL)-alpha-Lipoic acid 4.98504e-05 g/l Thiamine HCl 4.98504e-05 g/l Calcium D-(+)-pantothenate 4.98504e-05 g/l Riboflavin 4.98504e-05 g/l Nicotinic acid 4.98504e-05 g/l Na2MoO4 x 2 H2O 3.58923e-05 g/l NiCl2 x 6 H2O 2.39282e-05 g/l Biotin 1.99402e-05 g/l Folic acid 1.99402e-05 g/l H3BO3 5.98205e-06 g/l Na2WO4 x 2 H2O 3.98804e-06 g/l Na2SeO3 x 5 H2O 2.99103e-06 g/l CuCl2 x 2 H2O 1.99402e-06 g/l Vitamin B12 9.97009e-07 g/l Distilled water

culture temp

@refgrowthtypetemperaturerange
3398positivegrowth30mesophilic
23205positivegrowth5-38
23205positiveoptimum33mesophilic

culture pH

  • @ref: 23205
  • ability: positive
  • type: optimum
  • pH: 6.8-7.0

Physiology and metabolism

oxygen tolerance

@refoxygen toleranceconfidence
3398anaerobe
69480anaerobe99.597

spore formation

@refspore formationconfidence
69481no100
69480no99.857

halophily

@refsaltgrowthtested relationconcentration
23205NaClpositivegrowth1-5 %
23205MgCl2positivegrowth>0.3 %

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
2320530089acetate+carbon source
2320530089acetate+electron donor
2320516189sulfate+reduction
2320517359sulfite+reduction
2320516094thiosulfate+reduction

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
3398water-oil separation system on oil platformNorth SeaNorwayNOREurope
23205production water from an oil separation system on a North Sea oil production platform

isolation source categories

Cat1Cat2Cat3
#Engineered#Industrial#Oil reservoir
#Environmental#Aquatic

Safety information

risk assessment

  • @ref: 3398
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 3398
  • description: Desulfobacter vibrioforme B54 16S ribosomal RNA gene, complete sequence
  • accession: U12254
  • length: 1516
  • database: ena
  • NCBI tax ID: 34031

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Desulfobacter vibrioformis DSM 8776GCA_000745975scaffoldncbi1121398
66792Desulfobacter vibrioformis DSM 87761121398.3wgspatric1121398
66792Desulfobacter vibrioformis DSM 87762571042011draftimg1121398

GC content

@refGC-contentmethod
339847.6thermal denaturation, midpoint method (Tm)
2320547.0high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileyes84.384no
flagellatedno64.886no
gram-positiveno98.589no
anaerobicyes99.274no
aerobicno97.533yes
halophileno77.631no
spore-formingno85.328no
thermophileno98.3yes
glucose-utilyes52.601no
glucose-fermentno80.518no

External links

@ref: 3398

culture collection no.: DSM 8776

straininfo link

  • @ref: 73472
  • straininfo: 48542

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
3398Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 8776)https://www.dsmz.de/collection/catalogue/details/culture/DSM-8776
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
23205Torleiv Lien, Janiche Beeder10.1099/00207713-47-4-1124Desulfobacter vibrioformis sp. nov., a Sulfate Reducer from a Water-Oil Separation SystemIJSEM 47: 1124-1128 19979336918
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)
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
73472Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID48542.1StrainInfo: A central database for resolving microbial strain identifiers