Strain identifier
BacDive ID: 2615
Type strain: 
Species: Clostridium magnum
Strain Designation: WoBdP1
Strain history: <- B. Schink, WoBdP1
NCBI tax ID(s): 1121326 (strain), 33954 (species)
version 8.1 (current version)
General
@ref: 1214
BacDive-ID: 2615
DSM-Number: 2767
keywords: genome sequence, 16S sequence, Bacteria, anaerobe, mesophilic
description: Clostridium magnum WoBdP1 is an anaerobe, mesophilic bacterium that was isolated from freshwater mud.
NCBI tax id
| NCBI tax id | Matching level |
|---|---|
| 1121326 | strain |
| 33954 | species |
strain history
- @ref: 1214
- history: <- B. Schink, WoBdP1
doi: 10.13145/bacdive2615.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/bacillota
- domain: Bacteria
- phylum: Bacillota
- class: Clostridia
- order: Eubacteriales
- family: Clostridiaceae
- genus: Clostridium
- species: Clostridium magnum
- full scientific name: Clostridium magnum Schink 1984
@ref: 1214
domain: Bacteria
phylum: Firmicutes
class: Clostridia
order: Clostridiales
family: Clostridiaceae
genus: Clostridium
species: Clostridium magnum
full scientific name: Clostridium magnum Schink 1984
strain designation: WoBdP1
type strain: yes
Culture and growth conditions
culture medium
- @ref: 1214
- name: PY + X MEDIUM (DSMZ Medium 104b)
- growth: yes
- link: https://mediadive.dsmz.de/medium/104b
- composition: Name: PY + X MEDIUM (DSMZ Medium 104b) Composition: Yeast extract 10.0 g/l D-Glucose 5.0 g/l Trypticase peptone 5.0 g/l Meat peptone 5.0 g/l L-Cysteine HCl x H2O 0.5 g/l NaHCO3 0.4 g/l NaCl 0.08 g/l KH2PO4 0.04 g/l K2HPO4 0.04 g/l MgSO4 x 7 H2O 0.02 g/l CaCl2 x 2 H2O 0.01 g/l Sodium resazurin 0.0005 g/l Distilled water
culture temp
- @ref: 1214
- growth: positive
- type: growth
- temperature: 30
- range: mesophilic
Physiology and metabolism
oxygen tolerance
- @ref: 1214
- oxygen tolerance: anaerobe
Isolation, sampling and environmental information
isolation
- @ref: 1214
- sample type: freshwater mud
- geographic location: Konstanz
- country: Germany
- origin.country: DEU
- continent: Europe
isolation source categories
| Cat1 | Cat2 | Cat3 |
|---|---|---|
| #Environmental | #Aquatic | #Freshwater |
| #Environmental | #Terrestrial | #Mud (Sludge) |
taxonmaps
- @ref: 69479
- File name: preview.99_91935.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_34;96_495;97_564;98_649;99_91935&stattab=map
- Last taxonomy: Clostridium magnum subclade
- 16S sequence: X77835
- Sequence Identity:
- Total samples: 245
- soil counts: 137
- aquatic counts: 70
- animal counts: 28
- plant counts: 10
Safety information
risk assessment
- @ref: 1214
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
| @ref | description | accession | length | database | NCBI tax ID |
|---|---|---|---|---|---|
| 20218 | Clostridium magnum strain DSM 2767 16S ribosomal RNA gene, partial sequence | DQ911269 | 320 | ena | 33954 |
| 1214 | Clostridium magnum 16S rRNA gene, strain DSM 2767 | X77835 | 1387 | ena | 1121326 |
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Clostridium magnum DSM 2767 | GCA_900129955 | scaffold | ncbi | 1121326 |
| 66792 | Clostridium magnum DSM 2767 | GCA_001623875 | contig | ncbi | 1121326 |
| 66792 | Clostridium magnum DSM 2767 | 1121326.3 | wgs | patric | 1121326 |
| 66792 | Clostridium magnum DSM 2767 strain DSM 2767 | 1121326.7 | wgs | patric | 1121326 |
| 66792 | Clostridium magnum DSM 2767 | 2744054832 | draft | img | 1121326 |
| 66792 | Clostridium magnum DSM 2767 | 2585428069 | draft | img | 1121326 |
| 66792 | Clostridium magnum WoBdP1, DSM 2767 | 2639762517 | draft | img | 1121326 |
GC content
- @ref: 1214
- GC-content: 29.1
Genome-based predictions
predictions
| trait | prediction | confidence | training_data |
|---|---|---|---|
| motile | yes | 88.259 | no |
| flagellated | yes | 69.381 | no |
| gram-positive | no | 52.475 | no |
| anaerobic | yes | 98.217 | yes |
| aerobic | no | 97.6 | yes |
| halophile | no | 96.193 | no |
| spore-forming | yes | 94.955 | no |
| thermophile | no | 96.288 | yes |
| glucose-util | yes | 90.753 | no |
| glucose-ferment | yes | 55.269 | no |
External links
@ref: 1214
culture collection no.: DSM 2767, ATCC 49199, KCTC 15177
straininfo link
- @ref: 72146
- straininfo: 42349
literature
| topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
|---|---|---|---|---|---|---|---|---|
| Metabolism | 26899448 | Clostridium kogasensis sp. nov., a novel member of the genus Clostridium, isolated from soil under a corroded gas pipeline. | Shin Y, Kang SS, Paek J, Jin TE, Song HS, Kim H, Park HM, Chang YH | Anaerobe | 10.1016/j.anaerobe.2016.02.006 | 2016 | Acetic Acid/metabolism, Anaerobiosis, Base Composition, Butyrates/metabolism, Cardiolipins/metabolism, Cell Wall/*chemistry/metabolism, Clostridium/classification/drug effects/*isolation & purification/metabolism, Corrosion, Diaminopimelic Acid/metabolism, Fatty Acids/metabolism, Fermentation, Flagella/*chemistry/metabolism, Glucose/metabolism/pharmacology, Iron/chemistry, Peptidoglycan/metabolism, Phosphatidylethanolamines/metabolism, *Phylogeny, RNA, Ribosomal, 16S/genetics, *Soil Microbiology, Spores, Bacterial/*chemistry/metabolism | Phylogeny |
| Genetics | 27284147 | Genome Sequence of the Autotrophic Acetogen Clostridium magnum DSM 2767. | Uhlig R, Poehlein A, Fischer RJ, Daniel R, Bahl H | Genome Announc | 10.1128/genomeA.00464-16 | 2016 |
Reference
| @id | authors | catalogue | doi/url | title | journal | pubmed |
|---|---|---|---|---|---|---|
| 1214 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 2767) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-2767 | |||
| 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 | |
| 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 | |||
| 72146 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID42349.1 | StrainInfo: A central database for resolving microbial strain identifiers |