Strain identifier
BacDive ID: 2799
Type strain: 
Species: Clostridium akagii
Strain Designation: CK-58
Strain history: <- C. Matthies, University of Bayreuth, Department of Ecological Microbiology, Bayreuth, Germany; CK-58 <- C. H. Kuhner {1994}
NCBI tax ID(s): 1121293 (strain), 91623 (species)
version 8.1 (current version)
General
@ref: 4762
BacDive-ID: 2799
DSM-Number: 12554
keywords: genome sequence, 16S sequence, Bacteria, anaerobe, spore-forming, psychrophilic, motile
description: Clostridium akagii CK-58 is an anaerobe, spore-forming, psychrophilic bacterium that was isolated from beech litter.
NCBI tax id
| NCBI tax id | Matching level |
|---|---|
| 91623 | species |
| 1121293 | strain |
strain history
- @ref: 4762
- history: <- C. Matthies, University of Bayreuth, Department of Ecological Microbiology, Bayreuth, Germany; CK-58 <- C. H. Kuhner {1994}
doi: 10.13145/bacdive2799.20230509.8.1
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 akagii
- full scientific name: Clostridium akagii Kuhner et al. 2000
@ref: 4762
domain: Bacteria
phylum: Firmicutes
class: Clostridia
order: Clostridiales
family: Clostridiaceae
genus: Clostridium
species: Clostridium akagii
full scientific name: Clostridium akagii Kuhner et al. 2000
strain designation: CK-58
type strain: yes
Morphology
cell morphology
| @ref | motility | confidence | gram stain |
|---|---|---|---|
| 69480 | yes | 90.765 | |
| 69480 | 99.52 | positive |
Culture and growth conditions
culture medium
- @ref: 4762
- name: ANAEROBIC TRYPTIC SOY BROTH MEDIUM (DSMZ Medium 869)
- growth: yes
- link: https://mediadive.dsmz.de/medium/869
- composition: Name: ANAEROBIC TRYPTIC SOY BROTH MEDIUM (DSMZ Medium 869) Composition: Trypticase soy broth 5.5 g/l D-Glucose 2.0 g/l Resazurin 0.0005 g/l Distilled water
culture temp
- @ref: 4762
- growth: positive
- type: growth
- temperature: 20
- range: psychrophilic
Physiology and metabolism
oxygen tolerance
| @ref | oxygen tolerance | confidence |
|---|---|---|
| 4762 | anaerobe | |
| 69480 | anaerobe | 100 |
spore formation
| @ref | spore formation | confidence |
|---|---|---|
| 69481 | yes | 100 |
| 69480 | yes | 100 |
Isolation, sampling and environmental information
isolation
- @ref: 4762
- sample type: beech litter
- geographic location: Fichtelgebirge
- country: Germany
- origin.country: DEU
- continent: Europe
isolation source categories
| Cat1 | Cat2 | Cat3 |
|---|---|---|
| #Host | #Plants | #Decomposing plant |
| #Host | #Plants | #Tree |
Safety information
risk assessment
- @ref: 4762
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
- @ref: 4762
- description: Clostridium akagii 16S rRNA gene, strain CK58
- accession: AJ237755
- length: 1492
- database: ena
- NCBI tax ID: 91623
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Clostridium akagii DSM 12554 | GCA_000686725 | scaffold | ncbi | 1121293 |
| 66792 | Clostridium akagii DSM 12554 | 1121293.3 | wgs | patric | 1121293 |
| 66792 | Clostridium akagii DSM 12554 | 2563366732 | draft | img | 1121293 |
GC content
- @ref: 4762
- GC-content: 31.4
- method: high performance liquid chromatography (HPLC)
Genome-based predictions
predictions
| trait | prediction | confidence | training_data |
|---|---|---|---|
| spore-forming | yes | 100 | no |
| motile | yes | 87.061 | no |
| flagellated | yes | 68.532 | no |
| gram-positive | yes | 83.182 | no |
| anaerobic | yes | 95 | no |
| halophile | no | 96.407 | no |
| spore-forming | yes | 96.492 | no |
| glucose-util | yes | 90.266 | no |
| aerobic | no | 94.978 | yes |
| thermophile | no | 98.761 | yes |
| glucose-ferment | yes | 70.661 | no |
External links
@ref: 4762
culture collection no.: DSM 12554, ATCC BAA 166
straininfo link
- @ref: 72325
- straininfo: 46989
literature
- topic: Phylogeny
- Pubmed-ID: 10758899
- title: Clostridium akagii sp. nov. and Clostridium acidisoli sp. nov.: acid-tolerant, N2-fixing clostridia isolated from acidic forest soil and litter.
- authors: Kuhner CH, Matthies C, Acker G, Schmittroth M, Gossner AS, Drake HL
- journal: Int J Syst Evol Microbiol
- DOI: 10.1099/00207713-50-2-873
- year: 2000
- mesh: Anaerobiosis, Clostridium/*classification/isolation & purification/*physiology/ultrastructure, DNA, Bacterial/genetics, DNA, Ribosomal/genetics, Genes, rRNA, Hydrogen-Ion Concentration, Microscopy, Electron, Molecular Sequence Data, *Nitrogen Fixation, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Trees
- topic2: Genetics
Reference
| @id | authors | catalogue | doi/url | title |
|---|---|---|---|---|
| 4762 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 12554) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-12554 | |
| 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) | |
| 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 | |
| 72325 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID46989.1 | StrainInfo: A central database for resolving microbial strain identifiers |