Strain identifier
BacDive ID: 2807
Type strain:
Species: Clostridium laramiense
Strain Designation: NK1
Strain history: <- ATCC <- B. Ray, University of Wyoming, Laramie, USA; NK1 <- N. Kalchayanand {1989}
NCBI tax ID(s): 205326 (subspecies)
General
@ref: 5584
BacDive-ID: 2807
DSM-Number: 14864
keywords: genome sequence, 16S sequence, Bacteria, anaerobe, spore-forming, psychrophilic, motile
description: Clostridium laramiense NK1 is an anaerobe, spore-forming, psychrophilic bacterium that was isolated from spoiled umcooked beef.
NCBI tax id
- NCBI tax id: 205326
- Matching level: subspecies
strain history
- @ref: 5584
- history: <- ATCC <- B. Ray, University of Wyoming, Laramie, USA; NK1 <- N. Kalchayanand {1989}
doi: 10.13145/bacdive2807.20230509.8.1
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 laramiense
- full scientific name: Clostridium laramiense corrig. Kalchayanand et al. 1993
synonyms
@ref synonym 20215 Clostridium laramie 20215 Clostridium estertheticum subsp. laramiense
@ref: 5584
domain: Bacteria
phylum: Firmicutes
class: Clostridia
order: Clostridiales
family: Clostridiaceae
genus: Clostridium
species: Clostridium estertheticum subsp. laramiense
full scientific name: Clostridium estertheticum subsp. laramiense (Kalchayanand et al. 1993) Spring et al. 2003
strain designation: NK1
type strain: yes
Morphology
cell morphology
@ref | motility | confidence | gram stain |
---|---|---|---|
69480 | yes | 93.092 | |
69480 | 100 | positive |
colony morphology
- @ref: 5584
- incubation period: >14 days
Culture and growth conditions
culture medium
@ref | name | growth | link | composition |
---|---|---|---|---|
5584 | WILKINS-CHALGREN ANAEROBE BROTH (DSMZ Medium 339) | yes | https://mediadive.dsmz.de/medium/339 | 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 |
5584 | CHOPPED MEAT MEDIUM WITH CARBOHYDRATES (DSMZ Medium 110) | yes | https://mediadive.dsmz.de/medium/110 | Name: CHOPPED MEAT MEDIUM WITH CARBOHYDRATES (DSMZ Medium 110) Composition: Ground beef 500.0 g/l Casitone 30.0 g/l Agar 15.0 g/l K2HPO4 5.0 g/l Yeast extract 5.0 g/l D-Glucose 4.0 g/l Starch 1.0 g/l Maltose 1.0 g/l Cellobiose 1.0 g/l L-Cysteine HCl 0.5 g/l Ethanol 0.19 g/l Vitamin K3 0.05 g/l Hemin 0.005 g/l Sodium resazurin 0.0005 g/l Vitamin K1 NaOH Distilled water |
culture temp
- @ref: 5584
- growth: positive
- type: growth
- temperature: 10
- range: psychrophilic
Physiology and metabolism
oxygen tolerance
@ref | oxygen tolerance | confidence |
---|---|---|
5584 | anaerobe | |
69480 | anaerobe | 99.491 |
spore formation
@ref | spore formation | confidence |
---|---|---|
69481 | yes | 100 |
69480 | yes | 100 |
Isolation, sampling and environmental information
isolation
- @ref: 5584
- sample type: spoiled umcooked beef
- country: USA
- origin.country: USA
- continent: North America
isolation source categories
Cat1 | Cat2 | Cat3 |
---|---|---|
#Engineered | #Food production | #Meat |
#Host | #Other | #Decomposing animal |
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: AJ506115
- Sequence Identity:
- Total samples: 18467
- soil counts: 9246
- aquatic counts: 5428
- animal counts: 1548
- plant counts: 2245
Safety information
risk assessment
- @ref: 5584
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
@ref | description | accession | length | database | NCBI tax ID |
---|---|---|---|---|---|
20218 | Clostridium estertheticum subsp. laramiense strain DSM 14864 16S ribosomal RNA gene, partial sequence | DQ911251 | 327 | ena | 205326 |
5584 | Clostridium estertheticum subsp. laramiense 16S rRNA gene, strain DSM 14864 | AJ506115 | 1473 | ena | 205326 |
Genome sequences
@ref | description | accession | assembly level | database | NCBI tax ID |
---|---|---|---|---|---|
66792 | Clostridium estertheticum subsp. laramiense DSM 14864 | GCA_008933175 | contig | ncbi | 205326 |
66792 | Clostridium estertheticum subsp. laramiense strain DSM 14864 | 205326.4 | wgs | patric | 205326 |
66792 | Clostridium estertheticum laramiense DSM 14864 | 2860493848 | draft | img | 205326 |
GC content
@ref | GC-content | method |
---|---|---|
5584 | 32 | high performance liquid chromatography (HPLC) |
5584 | 26 | thermal denaturation, midpoint method (Tm) |
Genome-based predictions
predictions
trait | prediction | confidence | training_data |
---|---|---|---|
spore-forming | yes | 100 | no |
motile | yes | 81.979 | no |
gram-positive | yes | 69.701 | no |
anaerobic | yes | 95.946 | no |
aerobic | no | 96.585 | yes |
halophile | no | 96.821 | no |
spore-forming | yes | 94.251 | no |
glucose-util | yes | 91.943 | no |
flagellated | yes | 58.507 | no |
thermophile | no | 98.847 | yes |
glucose-ferment | yes | 66.958 | no |
External links
@ref: 5584
culture collection no.: DSM 14864, ATCC 51254
straininfo link
- @ref: 72333
- straininfo: 265711
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 | journal | pubmed |
---|---|---|---|---|---|---|
5584 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 14864) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-14864 | |||
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) | |||
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 | |||
72333 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID265711.1 | StrainInfo: A central database for resolving microbial strain identifiers |