Strain identifier
BacDive ID: 11349
Type strain: 
Species: Oxalobacter vibrioformis
Strain Designation: WoOx3
Strain history: <- I. Dehning, Universität Tübingen, Lehrstuhl Mikrobiologie, Germany; WoOx3 <- B. Schink, Universität Konstanz, Fakultät für Biologie, Konstanz, Germany {1983}
NCBI tax ID(s): 933080 (species)
General
@ref: 2084
BacDive-ID: 11349
DSM-Number: 5502
keywords: genome sequence, 16S sequence, Bacteria, anaerobe, mesophilic
description: Oxalobacter vibrioformis WoOx3 is an anaerobe, mesophilic bacterium that was isolated from anoxic freshwater sediment.
NCBI tax id
- NCBI tax id: 933080
- Matching level: species
strain history
- @ref: 2084
- history: <- I. Dehning, Universität Tübingen, Lehrstuhl Mikrobiologie, Germany; WoOx3 <- B. Schink, Universität Konstanz, Fakultät für Biologie, Konstanz, Germany {1983}
doi: 10.13145/bacdive11349.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/pseudomonadota
- domain: Bacteria
- phylum: Pseudomonadota
- class: Betaproteobacteria
- order: Burkholderiales
- family: Oxalobacteraceae
- genus: Oxalobacter
- species: Oxalobacter vibrioformis
- full scientific name: Oxalobacter vibrioformis Dehning and Schink 1990
@ref: 2084
domain: Bacteria
phylum: Proteobacteria
class: Betaproteobacteria
order: Burkholderiales
family: Oxalobacteraceae
genus: Oxalobacter
species: Oxalobacter vibrioformis
full scientific name: Oxalobacter vibrioformis Dehning and Schink 1990
strain designation: WoOx3
type strain: yes
Culture and growth conditions
culture medium
- @ref: 2084
- name: OXALOPHAGUS MEDIUM (DSMZ Medium 194b)
- growth: yes
- link: https://www.dsmz.de/microorganisms/medium/pdf/DSMZ_Medium194b.pdf
culture temp
- @ref: 2084
- growth: positive
- type: growth
- temperature: 30
- range: mesophilic
Physiology and metabolism
oxygen tolerance
- @ref: 2084
- oxygen tolerance: anaerobe
Isolation, sampling and environmental information
isolation
- @ref: 2084
- sample type: anoxic freshwater sediment
- geographic location: creek near Konstanz
- country: Germany
- origin.country: DEU
- continent: Europe
isolation source categories
| Cat1 | Cat2 | Cat3 |
|---|---|---|
| #Environmental | #Aquatic | #Freshwater |
| #Environmental | #Aquatic | #Sediment |
| #Condition | #Anoxic (anaerobic) |
taxonmaps
- @ref: 69479
- File name: preview.99_114846.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_12;96_30747;97_54086;98_71498;99_114846&stattab=map
- Last taxonomy: Oxalobacter vibrioformis subclade
- 16S sequence: FR733700
- Sequence Identity:
- Total samples: 352
- soil counts: 72
- aquatic counts: 130
- animal counts: 112
- plant counts: 38
Safety information
risk assessment
- @ref: 2084
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
- @ref: 2084
- description: Oxalobacter vibrioformis partial 16S rRNA gene, type strain DSM5502T
- accession: FR733700
- length: 1524
- database: ena
- NCBI tax ID: 933080
Genome sequences
- @ref: 66792
- description: Oxalobacter vibrioformis WoOx3
- accession: GCA_027118995
- assembly level: complete
- database: ncbi
- NCBI tax ID: 933080
GC content
- @ref: 2084
- GC-content: 51.6
Genome-based predictions
predictions
| trait | prediction | confidence | training_data |
|---|---|---|---|
| motile | yes | 82.749 | no |
| flagellated | no | 67.167 | no |
| gram-positive | no | 98.954 | no |
| anaerobic | yes | 96.382 | yes |
| aerobic | no | 96.32 | no |
| halophile | no | 91.368 | no |
| spore-forming | no | 94.882 | no |
| glucose-ferment | no | 66.936 | no |
| thermophile | no | 94.434 | no |
| glucose-util | no | 71.263 | no |
External links
@ref: 2084
culture collection no.: DSM 5502
straininfo link
- @ref: 80582
- straininfo: 47935
Reference
| @id | authors | catalogue | doi/url | title |
|---|---|---|---|---|
| 2084 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 5502) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-5502 | |
| 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 | |
| 80582 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID47935.1 | StrainInfo: A central database for resolving microbial strain identifiers |