Strain identifier
BacDive ID: 2813
Type strain: 
Species: Clostridium algidicarnis
Strain Designation: Dainty C
Strain history: <- NCIMB <- NCFB <- R. H. Dainty, Agricultural and Food Research Council, Institute of Food Research, Bristol, UK; Dainty C
NCBI tax ID(s): 1121295 (strain), 37659 (species)
version 8.1 (current version)
General
@ref: 5711
BacDive-ID: 2813
DSM-Number: 15099
keywords: genome sequence, 16S sequence, Bacteria, anaerobe, spore-forming, psychrophilic, motile
description: Clostridium algidicarnis Dainty C is an anaerobe, spore-forming, psychrophilic bacterium that was isolated from vacuum-packed refrigerated pork.
NCBI tax id
| NCBI tax id | Matching level |
|---|---|
| 37659 | species |
| 1121295 | strain |
strain history
- @ref: 5711
- history: <- NCIMB <- NCFB <- R. H. Dainty, Agricultural and Food Research Council, Institute of Food Research, Bristol, UK; Dainty C
doi: 10.13145/bacdive2813.20230509.8.1
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 algidicarnis
- full scientific name: Clostridium algidicarnis Lawson et al. 1995
@ref: 5711
domain: Bacteria
phylum: Firmicutes
class: Clostridia
order: Clostridiales
family: Clostridiaceae
genus: Clostridium
species: Clostridium algidicarnis
full scientific name: Clostridium algidicarnis Lawson et al. 1995
strain designation: Dainty C
type strain: yes
Morphology
cell morphology
| @ref | motility | confidence | gram stain |
|---|---|---|---|
| 69480 | yes | 92.817 | |
| 69480 | 100 | positive |
Culture and growth conditions
culture medium
- @ref: 5711
- name: CHOPPED MEAT MEDIUM WITH CARBOHYDRATES (DSMZ Medium 110)
- growth: yes
- link: https://mediadive.dsmz.de/medium/110
- composition: 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: 5711
- growth: positive
- type: growth
- temperature: 22
- range: psychrophilic
Physiology and metabolism
oxygen tolerance
| @ref | oxygen tolerance | confidence |
|---|---|---|
| 5711 | anaerobe | |
| 69480 | anaerobe | 99.998 |
spore formation
| @ref | spore formation | confidence |
|---|---|---|
| 69481 | yes | 100 |
| 69480 | yes | 99.667 |
Isolation, sampling and environmental information
isolation
- @ref: 5711
- sample type: vacuum-packed refrigerated pork
isolation source categories
| Cat1 | Cat2 | Cat3 |
|---|---|---|
| #Engineered | #Food production | #Bottled, canned, packed food |
| #Engineered | #Food production | #Meat |
taxonmaps
- @ref: 69479
- File name: preview.99_2592.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_34;96_899;97_1048;98_2008;99_2592&stattab=map
- Last taxonomy: Clostridium
- 16S sequence: AF127023
- Sequence Identity:
- Total samples: 19709
- soil counts: 4363
- aquatic counts: 3822
- animal counts: 10663
- plant counts: 861
Safety information
risk assessment
- @ref: 5711
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
| @ref | description | accession | length | database | NCBI tax ID |
|---|---|---|---|---|---|
| 20218 | Clostridium algidicarnis 16S ribosomal RNA gene, partial sequence | AF127023 | 1481 | ena | 37659 |
| 5711 | Clostridium algidicarnis 16S rRNA gene, strain NCFB 2931 | X77676 | 1511 | ena | 37659 |
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Clostridium algidicarnis DSM 15099 | GCA_002934235 | scaffold | ncbi | 1121295 |
| 66792 | Clostridium algidicarnis DSM 15099 | 1121295.3 | wgs | patric | 1121295 |
| 66792 | Clostridium algidicarnis DSM 15099 | 2695420939 | draft | img | 1121295 |
Genome-based predictions
predictions
| trait | prediction | confidence | training_data |
|---|---|---|---|
| spore-forming | yes | 100 | no |
| flagellated | yes | 61.628 | no |
| gram-positive | yes | 88.995 | no |
| anaerobic | yes | 98.129 | yes |
| aerobic | no | 95.674 | yes |
| halophile | no | 80.529 | no |
| spore-forming | yes | 97.198 | no |
| glucose-util | yes | 90.051 | no |
| thermophile | no | 99.351 | yes |
| motile | yes | 85.825 | no |
| glucose-ferment | yes | 66.524 | no |
External links
@ref: 5711
culture collection no.: DSM 15099, NCFB 2931, NCIMB 702931
straininfo link
- @ref: 72339
- straininfo: 62026
literature
- topic: Phylogeny
- Pubmed-ID: 9562877
- title: Efficacy of heat and ethanol spore treatments for the isolation of psychrotrophic Clostridium spp. associated with the spoilage of chilled vacuum-packed meats.
- authors: Broda DM, De Lacy KM, Bell RG
- journal: Int J Food Microbiol
- DOI: 10.1016/s0168-1605(97)00119-0
- year: 1998
- mesh: Animals, Cattle, Clostridium/drug effects/growth & development/*isolation & purification, Ethanol/*pharmacology, Food Microbiology, *Food Packaging, *Hot Temperature, Meat/*microbiology, Sheep, Spores, Bacterial/drug effects/growth & development/*isolation & purification, Time Factors
- topic2: Enzymology
Reference
| @id | authors | catalogue | doi/url | title | journal | pubmed |
|---|---|---|---|---|---|---|
| 5711 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 15099) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-15099 | |||
| 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 | |||
| 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 | |||
| 72339 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID62026.1 | StrainInfo: A central database for resolving microbial strain identifiers |