Strain identifier
BacDive ID: 2828
Type strain: 
Species: Clostridium algoriphilum
Strain Designation: 14D1
Strain history: <- V. A. Shcherbakova, Institute of Biochemistry and Physiology of Microorganisms, Russian Academy of Science, Pushchino, Russia; 14D1 <- V. A. Shcherbakova {2000}
NCBI tax ID(s): 198347 (species)
version 8.1 (current version)
General
@ref: 6312
BacDive-ID: 2828
DSM-Number: 16153
keywords: genome sequence, 16S sequence, Bacteria, anaerobe, spore-forming, psychrophilic, motile
description: Clostridium algoriphilum 14D1 is an anaerobe, spore-forming, psychrophilic bacterium that was isolated from water brine in permafrost.
NCBI tax id
- NCBI tax id: 198347
- Matching level: species
strain history
- @ref: 6312
- history: <- V. A. Shcherbakova, Institute of Biochemistry and Physiology of Microorganisms, Russian Academy of Science, Pushchino, Russia; 14D1 <- V. A. Shcherbakova {2000}
doi: 10.13145/bacdive2828.20230509.8.1
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 algoriphilum
- full scientific name: Clostridium algoriphilum Shcherbakova et al. 2010
@ref: 6312
domain: Bacteria
phylum: Firmicutes
class: Clostridia
order: Clostridiales
family: Clostridiaceae
genus: Clostridium
species: Clostridium algoriphilum
full scientific name: Clostridium algoriphilum Shcherbakova et al. 2010
strain designation: 14D1
type strain: yes
Morphology
cell morphology
| @ref | motility | confidence | gram stain |
|---|---|---|---|
| 69480 | yes | 95.319 | |
| 69480 | 100 | positive |
Culture and growth conditions
culture medium
- @ref: 6312
- name: WILKINS-CHALGREN ANAEROBE BROTH (DSMZ Medium 339)
- growth: yes
- link: https://mediadive.dsmz.de/medium/339
- composition: Name: WILKINS-CHALGREN ANAEROBE BROTH (DSMZ Medium 339) Composition: dehydrated Wilkins-Chalgren medium 33.0 g/l L-Cysteine HCl 0.3 g/l Sodium resazurin 0.0005 g/l Distilled water
culture temp
- @ref: 6312
- growth: positive
- type: growth
- temperature: 5
- range: psychrophilic
Physiology and metabolism
oxygen tolerance
| @ref | oxygen tolerance | confidence |
|---|---|---|
| 6312 | anaerobe | |
| 69480 | anaerobe | 99.681 |
spore formation
| @ref | spore formation | confidence |
|---|---|---|
| 69481 | yes | 100 |
| 69480 | yes | 100 |
Isolation, sampling and environmental information
isolation
- @ref: 6312
- sample type: water brine in permafrost
- geographic location: Kolyma Lowland
- country: Russia
- origin.country: RUS
- continent: Asia
isolation source categories
| Cat1 | Cat2 | Cat3 |
|---|---|---|
| #Environmental | #Aquatic | |
| #Environmental | #Terrestrial | #Permafrost |
| #Condition | #Saline |
taxonmaps
- @ref: 69479
- File name: preview.99_154428.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_34;96_327;97_364;98_413;99_154428&stattab=map
- Last taxonomy: Clostridium algoriphilum
- 16S sequence: AY117755
- Sequence Identity:
- Total samples: 7934
- soil counts: 4238
- aquatic counts: 3025
- animal counts: 367
- plant counts: 304
Safety information
risk assessment
- @ref: 6312
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
- @ref: 6312
- description: Clostridium sp. 14D1 16S ribosomal RNA gene, partial sequence
- accession: AY117755
- length: 1481
- database: ena
- NCBI tax ID: 198347
Genome sequences
- @ref: 66792
- description: Clostridium algoriphilum DSM 16153
- accession: GCA_020443705
- assembly level: contig
- database: ncbi
- NCBI tax ID: 198347
GC content
- @ref: 6312
- GC-content: 31.4
- method: thermal denaturation, midpoint method (Tm)
Genome-based predictions
predictions
| trait | prediction | confidence | training_data |
|---|---|---|---|
| spore-forming | yes | 100 | no |
| flagellated | yes | 66.152 | no |
| gram-positive | yes | 71.655 | no |
| anaerobic | yes | 97.171 | yes |
| aerobic | no | 97.716 | yes |
| halophile | no | 95.807 | no |
| spore-forming | yes | 96.482 | no |
| motile | yes | 82.724 | no |
| thermophile | no | 91.07 | yes |
| glucose-util | yes | 93.193 | no |
| glucose-ferment | yes | 56.155 | no |
External links
@ref: 6312
culture collection no.: DSM 16153, VKM B-2271
straininfo link
- @ref: 72352
- straininfo: 297644
literature
- topic: Phylogeny
- Pubmed-ID: 15844014
- title: Novel psychrophilic anaerobic spore-forming bacterium from the overcooled water brine in permafrost: description Clostridium algoriphilum sp. nov.
- authors: Shcherbakova VA, Chuvilskaya NA, Rivkina EM, Pecheritsyna SA, Laurinavichius KS, Suzina NE, Osipov GA, Lysenko AM, Gilichinsky DA, Akimenko VK
- journal: Extremophiles
- DOI: 10.1007/s00792-005-0438-3
- year: 2005
- mesh: Bacteria, Anaerobic/classification/cytology/growth & development/*isolation & purification, Cell Wall/chemistry, Fatty Acids/analysis, Freezing, Hot Temperature, Lipids/analysis, Polysaccharides, Bacterial/isolation & purification, Spores, Bacterial, *Water Microbiology
- topic2: Enzymology
Reference
| @id | authors | catalogue | doi/url | title |
|---|---|---|---|---|
| 6312 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 16153) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-16153 | |
| 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 | |
| 72352 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID297644.1 | StrainInfo: A central database for resolving microbial strain identifiers |