Strain identifier
BacDive ID: 3963
Type strain:
Species: Desulfobacter vibrioformis
Strain Designation: B54
Strain history: <- T. Lien; B54 <- T. Lien {1985}
NCBI tax ID(s): 1121398 (strain), 34031 (species)
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 id | Matching level |
---|---|
34031 | species |
1121398 | strain |
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
@ref | gram stain | cell length | cell width | cell shape | motility | confidence |
---|---|---|---|---|---|---|
23205 | negative | 4.5-8.0 µm | 1.9-2.3 µm | vibrio-shaped | no | |
23205 | yes | |||||
69480 | negative | 99.999 | ||||
69480 | yes | 94.687 |
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
@ref | growth | type | temperature | range |
---|---|---|---|---|
3398 | positive | growth | 30 | mesophilic |
23205 | positive | growth | 5-38 | |
23205 | positive | optimum | 33 | mesophilic |
culture pH
- @ref: 23205
- ability: positive
- type: optimum
- pH: 6.8-7.0
Physiology and metabolism
oxygen tolerance
@ref | oxygen tolerance | confidence |
---|---|---|
3398 | anaerobe | |
69480 | anaerobe | 99.597 |
spore formation
@ref | spore formation | confidence |
---|---|---|
69481 | no | 100 |
69480 | no | 99.857 |
halophily
@ref | salt | growth | tested relation | concentration |
---|---|---|---|---|
23205 | NaCl | positive | growth | 1-5 % |
23205 | MgCl2 | positive | growth | >0.3 % |
metabolite utilization
@ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
---|---|---|---|---|
23205 | 30089 | acetate | + | carbon source |
23205 | 30089 | acetate | + | electron donor |
23205 | 16189 | sulfate | + | reduction |
23205 | 17359 | sulfite | + | reduction |
23205 | 16094 | thiosulfate | + | reduction |
Isolation, sampling and environmental information
isolation
@ref | sample type | geographic location | country | origin.country | continent |
---|---|---|---|---|---|
3398 | water-oil separation system on oil platform | North Sea | Norway | NOR | Europe |
23205 | production water from an oil separation system on a North Sea oil production platform |
isolation source categories
Cat1 | Cat2 | Cat3 |
---|---|---|
#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
@ref | description | accession | assembly level | database | NCBI tax ID |
---|---|---|---|---|---|
66792 | Desulfobacter vibrioformis DSM 8776 | GCA_000745975 | scaffold | ncbi | 1121398 |
66792 | Desulfobacter vibrioformis DSM 8776 | 1121398.3 | wgs | patric | 1121398 |
66792 | Desulfobacter vibrioformis DSM 8776 | 2571042011 | draft | img | 1121398 |
GC content
@ref | GC-content | method |
---|---|---|
3398 | 47.6 | thermal denaturation, midpoint method (Tm) |
23205 | 47.0 | high performance liquid chromatography (HPLC) |
Genome-based predictions
predictions
trait | prediction | confidence | training_data |
---|---|---|---|
spore-forming | no | 100 | no |
motile | yes | 84.384 | no |
flagellated | no | 64.886 | no |
gram-positive | no | 98.589 | no |
anaerobic | yes | 99.274 | no |
aerobic | no | 97.533 | yes |
halophile | no | 77.631 | no |
spore-forming | no | 85.328 | no |
thermophile | no | 98.3 | yes |
glucose-util | yes | 52.601 | no |
glucose-ferment | no | 80.518 | no |
External links
@ref: 3398
culture collection no.: DSM 8776
straininfo link
- @ref: 73472
- straininfo: 48542
Reference
@id | authors | catalogue | doi/url | title | journal | pubmed |
---|---|---|---|---|---|---|
3398 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 8776) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-8776 | |||
20215 | Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M. | 10.1099/ijsem.0.004332 | List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ | |||
23205 | Torleiv Lien, Janiche Beeder | 10.1099/00207713-47-4-1124 | Desulfobacter vibrioformis sp. nov., a Sulfate Reducer from a Water-Oil Separation System | IJSEM 47: 1124-1128 1997 | 9336918 | |
66792 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | https://diaspora-project.de/progress.html#genomes | Automatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) | |||
69480 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | https://diaspora-project.de/progress.html#genomes | Predictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) | |||
69481 | Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch | 10.21203/rs.3.rs-2527258/v1 | Predictions based on the model GenomeNet Sporulation v. 1 | |||
73472 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID48542.1 | StrainInfo: A central database for resolving microbial strain identifiers |