Strain identifier
BacDive ID: 4133
Type strain: 
Species: Desulfovibrio oxyclinae
Strain Designation: P1B
Strain history: <- H. Cypionka, Univ. Oldenburg, Germany; P1B <- Y. Cohen, Hebrew Univ. Jerusalem, Israel {1990}
NCBI tax ID(s): 1121459 (strain), 63560 (species)
version 8.1 (current version)
General
@ref: 4389
BacDive-ID: 4133
DSM-Number: 11498
keywords: genome sequence, 16S sequence, Bacteria, anaerobe, mesophilic, motile
description: Desulfovibrio oxyclinae P1B is an anaerobe, mesophilic, motile bacterium that was isolated from hypersaline cyanobacterial mat.
NCBI tax id
| NCBI tax id | Matching level |
|---|---|
| 1121459 | strain |
| 63560 | species |
strain history
- @ref: 4389
- history: <- H. Cypionka, Univ. Oldenburg, Germany; P1B <- Y. Cohen, Hebrew Univ. Jerusalem, Israel {1990}
doi: 10.13145/bacdive4133.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/pseudomonadota
- domain: Bacteria
- phylum: Pseudomonadota
- class: Deltaproteobacteria
- order: Desulfovibrionales
- family: Desulfovibrionaceae
- genus: Desulfovibrio
- species: Desulfovibrio oxyclinae
- full scientific name: Desulfovibrio oxyclinae Krekeler et al. 2000
synonyms
- @ref: 20215
- synonym: Pseudodesulfovibrio oxyclinae
@ref: 4389
domain: Bacteria
phylum: Proteobacteria
class: Deltaproteobacteria
order: Desulfovibrionales
family: Desulfovibrionaceae
genus: Desulfovibrio
species: Desulfovibrio oxyclinae
full scientific name: Desulfovibrio oxyclinae Krekeler et al. 2000
strain designation: P1B
type strain: yes
Morphology
cell morphology
| @ref | motility | confidence | gram stain |
|---|---|---|---|
| 69480 | yes | 94.264 | |
| 69480 | 99.978 | negative |
Culture and growth conditions
culture medium
- @ref: 4389
- name: DESULFOVIBRIO HALOPHILUS MEDIUM (DSMZ Medium 496)
- growth: yes
- link: https://mediadive.dsmz.de/medium/496
- composition: Name: PSEUDODESULFOVIBRIO MEDIUM (DSMZ Medium 496) Composition: NaCl 69.7907 g/l Na2SO4 2.99102 g/l MgCl2 x 6 H2O 2.99102 g/l Na-L-lactate 2.49252 g/l Na2CO3 0.997009 g/l KCl 0.498505 g/l Na2S x 9 H2O 0.398804 g/l NH4Cl 0.299102 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 Sodium resazurin 0.000498505 g/l NaOH 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 (DL)-alpha-Lipoic acid 4.98504e-05 g/l p-Aminobenzoic acid 4.98504e-05 g/l Calcium D-(+)-pantothenate 4.98504e-05 g/l Nicotinic acid 4.98504e-05 g/l Riboflavin 4.98504e-05 g/l Thiamine HCl 4.98504e-05 g/l Na2MoO4 x 2 H2O 3.58923e-05 g/l NiCl2 x 6 H2O 2.39282e-05 g/l Folic acid 1.99402e-05 g/l Biotin 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: 4389
- growth: positive
- type: growth
- temperature: 30
- range: mesophilic
Physiology and metabolism
oxygen tolerance
| @ref | oxygen tolerance | confidence |
|---|---|---|
| 4389 | anaerobe | |
| 69480 | anaerobe | 99.999 |
spore formation
| @ref | spore formation | confidence |
|---|---|---|
| 69481 | no | 100 |
| 69480 | no | 99.821 |
Isolation, sampling and environmental information
isolation
- @ref: 4389
- sample type: hypersaline cyanobacterial mat
- geographic location: Sinai, Solar Lake
- country: Egypt
- origin.country: EGY
- continent: Africa
isolation source categories
| Cat1 | Cat2 | Cat3 |
|---|---|---|
| #Environmental | #Microbial community | #Microbial mat |
| #Host | #Microbial | #Bacteria |
| #Condition | #Saline |
taxonmaps
- @ref: 69479
- File name: preview.99_88008.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_320;96_1791;97_46405;98_60804;99_88008&stattab=map
- Last taxonomy: Desulfovibrio oxyclinae
- 16S sequence: U33316
- Sequence Identity:
- Total samples: 15
- soil counts: 6
- aquatic counts: 8
- animal counts: 1
Safety information
risk assessment
- @ref: 4389
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
- @ref: 4389
- description: Desulfovibrio oxyclinae strain P1B 16S ribosomal RNA gene, partial sequence
- accession: U33316
- length: 1494
- database: ena
- NCBI tax ID: 63560
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Desulfovibrio oxyclinae DSM 11498 | GCA_000375485 | contig | ncbi | 1121459 |
| 66792 | Desulfovibrio oxyclinae DSM 11498 | 1121459.3 | wgs | patric | 1121459 |
| 66792 | Desulfovibrio oxyclinae DSM 11498 | 2515154157 | draft | img | 1121459 |
Genome-based predictions
predictions
| trait | prediction | confidence | training_data |
|---|---|---|---|
| spore-forming | no | 100 | no |
| motile | yes | 91.376 | no |
| flagellated | no | 53 | no |
| gram-positive | no | 98.481 | no |
| anaerobic | yes | 98.952 | yes |
| aerobic | no | 97.739 | no |
| halophile | yes | 50.759 | no |
| spore-forming | no | 95.01 | no |
| thermophile | no | 79.783 | yes |
| glucose-util | no | 60.959 | no |
| glucose-ferment | no | 85.619 | no |
External links
@ref: 4389
culture collection no.: DSM 11498
straininfo link
- @ref: 73636
- straininfo: 49122
literature
- topic: Pathogenicity
- Pubmed-ID: 11207770
- title: Aerotaxis in Desulfovibrio.
- authors: Eschemann A, Kuhl M, Cypionka H
- journal: Environ Microbiol
- DOI: 10.1046/j.1462-2920.1999.00057.x
- year: 1999
- mesh: *Chemotaxis, Desulfovibrio/drug effects/*physiology, Oxygen/pharmacology, *Oxygen Consumption, Water Microbiology
Reference
| @id | authors | catalogue | doi/url | title |
|---|---|---|---|---|
| 4389 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 11498) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-11498 | |
| 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 | |
| 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) | |
| 69479 | João F Matias Rodrigues, Janko Tackmann,Gregor Rot, Thomas SB Schmidt, Lukas Malfertheiner, Mihai Danaila,Marija Dmitrijeva, Daniela Gaio, Nicolas Näpflin and Christian von Mering. University of Zurich. | https://microbeatlas.org/ | MicrobeAtlas 1.0 beta | |
| 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 | |
| 73636 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID49122.1 | StrainInfo: A central database for resolving microbial strain identifiers |