Strain identifier
BacDive ID: 2822
Type strain: 
Species: Clostridium frigoris
Strain Designation: D-1/D-an/II, H8
Strain history: <- H. Hippe, Leibniz-Institut DSMZ GmbH, Braunschweig, Germany; D-1/D-an/II <- H. Hippe {1999}
NCBI tax ID(s): 205327 (species)
version 8.1 (current version)
General
@ref: 5247
BacDive-ID: 2822
DSM-Number: 14204
keywords: genome sequence, 16S sequence, Bacteria, anaerobe, spore-forming, psychrophilic, Gram-positive
description: Clostridium frigoris D-1/D-an/II is an anaerobe, spore-forming, psychrophilic bacterium that was isolated from microbial mat sample.
NCBI tax id
- NCBI tax id: 205327
- Matching level: species
strain history
- @ref: 5247
- history: <- H. Hippe, Leibniz-Institut DSMZ GmbH, Braunschweig, Germany; D-1/D-an/II <- H. Hippe {1999}
doi: 10.13145/bacdive2822.20230509.8.1
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 frigoris
- full scientific name: Clostridium frigoris Spring et al. 2003
@ref: 5247
domain: Bacteria
phylum: Firmicutes
class: Clostridia
order: Clostridiales
family: Clostridiaceae
genus: Clostridium
species: Clostridium frigoris
full scientific name: Clostridium frigoris Spring et al. 2003
strain designation: D-1/D-an/II, H8
type strain: yes
Morphology
cell morphology
- @ref: 69480
- gram stain: positive
- confidence: 99.257
colony morphology
- @ref: 5247
- incubation period: 8-14 days
Culture and growth conditions
culture medium
- @ref: 5247
- 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; with strain-specific modifications) Composition: dehydrated Wilkins-Chalgren medium 33.0 g/l D-Glucose 5.0 g/l NaHCO3 2.0 g/l L-Cysteine HCl 0.3 g/l Sodium resazurin 0.0005 g/l Distilled water
culture temp
- @ref: 5247
- growth: positive
- type: growth
- temperature: 6
- range: psychrophilic
Physiology and metabolism
oxygen tolerance
| @ref | oxygen tolerance | confidence |
|---|---|---|
| 5247 | anaerobe | |
| 69480 | anaerobe | 99.465 |
spore formation
| @ref | spore formation | confidence |
|---|---|---|
| 69481 | yes | 99 |
| 69480 | yes | 99.998 |
Isolation, sampling and environmental information
isolation
- @ref: 5247
- sample type: microbial mat sample
- geographic location: McMurdo Dry Valley Region, Lake Fryxell
- country: Antarctica
- origin.country: ATA
- continent: Australia and Oceania
isolation source categories
- Cat1: #Environmental
- Cat2: #Microbial community
- Cat3: #Microbial mat
taxonmaps
- @ref: 69479
- File name: preview.99_505.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_34;96_327;97_364;98_413;99_505&stattab=map
- Last taxonomy: Clostridium
- 16S sequence: AJ506117
- Sequence Identity:
- Total samples: 18467
- soil counts: 9246
- aquatic counts: 5428
- animal counts: 1548
- plant counts: 2245
Safety information
risk assessment
- @ref: 5247
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
| @ref | description | accession | length | database | NCBI tax ID |
|---|---|---|---|---|---|
| 5247 | Clostridium frigoris 16S rRNA gene, type strain DSM 14204, clone 5 | AJ506116 | 1477 | ena | 205327 |
| 5247 | Clostridium frigoris 16S rRNA gene, type strain DSM 14204, clone 10 | AJ506117 | 1477 | ena | 205327 |
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Clostridium frigoris DSM 14204 | GCA_018861865 | contig | ncbi | 205327 |
| 66792 | Clostridium frigoris strain DSM 14204 | 205327.3 | wgs | patric | 205327 |
GC content
- @ref: 5247
- GC-content: 31.9
- method: high performance liquid chromatography (HPLC)
Genome-based predictions
predictions
| trait | prediction | confidence | training_data |
|---|---|---|---|
| spore-forming | yes | 99 | no |
| motile | yes | 85.731 | no |
| gram-positive | yes | 72.027 | no |
| anaerobic | yes | 98.505 | yes |
| aerobic | no | 98.253 | yes |
| halophile | no | 96.553 | no |
| spore-forming | yes | 95.954 | no |
| glucose-util | yes | 89.554 | no |
| flagellated | yes | 71.621 | no |
| thermophile | no | 96.339 | no |
| glucose-ferment | yes | 59.779 | no |
External links
@ref: 5247
culture collection no.: DSM 14204, ATCC BAA 579
straininfo link
- @ref: 72346
- straininfo: 87995
literature
- topic: Phylogeny
- Pubmed-ID: 12892121
- title: Characterization of novel psychrophilic clostridia from an Antarctic microbial mat: description of Clostridium frigoris sp. nov., Clostridium lacusfryxellense sp. nov., Clostridium bowmanii sp. nov. and Clostridium psychrophilum sp. nov. and reclassification of Clostridium laramiense as Clostridium estertheticum subsp. laramiense subsp. nov.
- authors: Spring S, Merkhoffer B, Weiss N, Kroppenstedt RM, Hippe H, Stackebrandt E
- journal: Int J Syst Evol Microbiol
- DOI: 10.1099/ijs.0.02554-0
- year: 2003
- mesh: Antarctic Regions, Clostridium/*classification/genetics/isolation & purification/metabolism, DNA, Bacterial/genetics, DNA, Ribosomal/genetics, Fresh Water/microbiology, Genotype, Molecular Sequence Data, Phenotype, Phylogeny, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Species Specificity, Terminology as Topic
- topic2: Genetics
Reference
| @id | authors | catalogue | doi/url | title |
|---|---|---|---|---|
| 5247 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 14204) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-14204 | |
| 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 | |
| 72346 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID87995.1 | StrainInfo: A central database for resolving microbial strain identifiers |