Strain identifier
BacDive ID: 2505
Type strain: 
Species: Oxobacter pfennigii
Strain Designation: V5-2
Strain history: <- M.P. Bryant, V5-2
NCBI tax ID(s): 36849 (species)
version 8.1 (current version)
General
@ref: 1318
BacDive-ID: 2505
DSM-Number: 3222
keywords: genome sequence, 16S sequence, Bacteria, anaerobe, spore-forming, mesophilic, Gram-positive
description: Oxobacter pfennigii V5-2 is an anaerobe, spore-forming, mesophilic bacterium that was isolated from rumen of cattle.
NCBI tax id
- NCBI tax id: 36849
- Matching level: species
strain history
- @ref: 1318
- history: <- M.P. Bryant, V5-2
doi: 10.13145/bacdive2505.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/bacillota
- domain: Bacteria
- phylum: Bacillota
- class: Clostridia
- order: Eubacteriales
- family: Clostridiaceae
- genus: Oxobacter
- species: Oxobacter pfennigii
- full scientific name: Oxobacter pfennigii (Krumholz and Bryant 1985) Collins et al. 1994
synonyms
- @ref: 20215
- synonym: Clostridium pfennigii
@ref: 1318
domain: Bacteria
phylum: Firmicutes
class: Clostridia
order: Clostridiales
family: Clostridiaceae
genus: Oxobacter
species: Oxobacter pfennigii
full scientific name: Oxobacter pfennigii (Krumholz and Bryant 1985) Collins et al. 1994
strain designation: V5-2
type strain: yes
Morphology
cell morphology
- @ref: 69480
- gram stain: positive
- confidence: 100
colony morphology
- @ref: 1318
- incubation period: 2-3 days
Culture and growth conditions
culture medium
- @ref: 1318
- name: OXOBACTER PFENNIGII MEDIUM (DSMZ Medium 336)
- growth: yes
- link: https://mediadive.dsmz.de/medium/336
- composition: Name: OXOBACTER PFENNIGII MEDIUM (DSMZ Medium 336) Composition: Na-vanillate 1.9685 g/l Yeast extract 1.9685 g/l Na2CO3 1.47638 g/l KH2PO4 0.492126 g/l NH4Cl 0.393701 g/l NaCl 0.393701 g/l MgCl2 x 6 H2O 0.324803 g/l L-Cysteine HCl x H2O 0.295276 g/l Na2S x 9 H2O 0.0885827 g/l CaCl2 x 2 H2O 0.0492126 g/l HCl 0.00246063 g/l FeCl2 x 4 H2O 0.00147638 g/l Sodium resazurin 0.000478346 g/l Pyridoxine hydrochloride 0.000295276 g/l Thiamine-HCl x 2 H2O 0.00019685 g/l Nicotinic acid 0.00019685 g/l CoCl2 x 6 H2O 0.000187008 g/l MnCl2 x 4 H2O 9.84252e-05 g/l Vitamin B12 9.84252e-05 g/l Calcium pantothenate 9.84252e-05 g/l p-Aminobenzoic acid 7.87402e-05 g/l ZnCl2 6.88976e-05 g/l Na2MoO4 x 2 H2O 3.54331e-05 g/l NiCl2 x 6 H2O 2.3622e-05 g/l D-(+)-biotin 1.9685e-05 g/l H3BO3 5.90551e-06 g/l CuCl2 x 2 H2O 1.9685e-06 g/l Rumen fluid Distilled water
culture temp
- @ref: 1318
- growth: positive
- type: growth
- temperature: 37
- range: mesophilic
Physiology and metabolism
oxygen tolerance
| @ref | oxygen tolerance | confidence |
|---|---|---|
| 1318 | anaerobe | |
| 69480 | anaerobe | 100 |
spore formation
| @ref | spore formation | confidence |
|---|---|---|
| 69481 | yes | 91 |
| 69480 | yes | 99.48 |
Isolation, sampling and environmental information
isolation
- @ref: 1318
- sample type: rumen of cattle
- country: USA
- origin.country: USA
- continent: North America
isolation source categories
| Cat1 | Cat2 | Cat3 |
|---|---|---|
| #Host | #Mammals | #Bovinae (Cow, Cattle) |
| #Host Body-Site | #Organ | #Rumen |
Safety information
risk assessment
- @ref: 1318
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
| @ref | description | accession | length | database | NCBI tax ID |
|---|---|---|---|---|---|
| 20218 | Oxobacter pfennigii 16S rRNA gene, strain DSM 3222 | X77838 | 1496 | ena | 36849 |
| 1318 | Oxobacter pfennigii partial 16S rRNA gene, type strain DSM 3222T, clone 3 | HF546397 | 1500 | ena | 36849 |
| 1318 | Oxobacter pfennigii partial 16S rRNA gene, type strain DSM 3222T, clone 6 | HF546398 | 1500 | ena | 36849 |
| 1318 | Oxobacter pfennigii partial 16S rRNA gene, type strain DSM 3222T, clone 32 | HF546399 | 1518 | ena | 36849 |
| 1318 | Oxobacter pfennigii partial 16S rRNA gene, type strain DSM 3222T, clone 36 | HF546400 | 1499 | ena | 36849 |
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Oxobacter pfennigii DSM 3222 | GCA_001317355 | contig | ncbi | 36849 |
| 66792 | Oxobacter pfennigii strain DSM 3222 | 36849.5 | wgs | patric | 36849 |
| 66792 | Oxobacter pfennigii DSM 3222 | 2713896874 | draft | img | 36849 |
GC content
- @ref: 1318
- GC-content: 37.9
Genome-based predictions
predictions
| trait | prediction | confidence | training_data |
|---|---|---|---|
| spore-forming | yes | 91 | no |
| gram-positive | yes | 59.485 | no |
| anaerobic | yes | 98.852 | yes |
| halophile | no | 94.106 | no |
| spore-forming | yes | 95.314 | no |
| glucose-util | yes | 73.73 | no |
| aerobic | no | 95.551 | yes |
| motile | yes | 88.355 | no |
| flagellated | no | 61.205 | no |
| thermophile | no | 96.665 | yes |
| glucose-ferment | no | 64.186 | no |
External links
@ref: 1318
culture collection no.: DSM 3222
straininfo link
- @ref: 72041
- straininfo: 41923
literature
- topic: Genetics
- Pubmed-ID: 26634756
- title: Genome Sequence of the Acetogenic Bacterium Oxobacter pfennigii DSM 3222T.
- authors: Bengelsdorf FR, Poehlein A, Schiel-Bengelsdorf B, Daniel R, Durre P
- journal: Genome Announc
- DOI: 10.1128/genomeA.01408-15
- year: 2015
Reference
| @id | authors | catalogue | doi/url | title | journal | pubmed |
|---|---|---|---|---|---|---|
| 1318 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 3222) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-3222 | |||
| 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 | |||
| 20218 | Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P. | 10.1016/j.syapm.2013.11.002 | StrainInfo introduces electronic passports for microorganisms. | Syst Appl Microbiol. 37: 42-50 2014 | 24321274 | |
| 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) | |||
| 66794 | Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg | 10.1093/nar/gkaa1025 | BRENDA, the ELIXIR core data resource in 2021: new developments and updates | Nucleic Acids Res. 49: D498-D508 2020 | 33211880 | |
| 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 | |||
| 72041 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID41923.1 | StrainInfo: A central database for resolving microbial strain identifiers |