Strain identifier
BacDive ID: 2573
Type strain: 
Species: Clostridium cochlearium
Strain Designation: 998
Strain history: ATCC 17794 <-- L. S. McClung 998 <-- S. E. Hartsell M-10.
NCBI tax ID(s): 1494 (species)
version 8.1 (current version)
General
@ref: 981
BacDive-ID: 2573
DSM-Number: 2153
keywords: genome sequence, 16S sequence, Bacteria, anaerobe, spore-forming, mesophilic, Gram-positive, human pathogen
description: Clostridium cochlearium 998 is an anaerobe, spore-forming, mesophilic human pathogen of the family Clostridiaceae.
NCBI tax id
- NCBI tax id: 1494
- Matching level: species
strain history
| @ref | history |
|---|---|
| 981 | <- ATCC <- L. S. McClung, University of Wisconsin, Madison, USA; 998 (Clostridium lentoputrescens) |
| 67770 | ATCC 17794 <-- L. S. McClung 998 <-- S. E. Hartsell M-10. |
doi: 10.13145/bacdive2573.20230509.8.1
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 cochlearium
- full scientific name: Clostridium cochlearium (Douglas et al. 1919) Bergey et al. 1923 (Approved Lists 1980)
synonyms
@ref synonym 20215 Clostridium lentoputrescens 20215 Bacillus cochlearius
@ref: 981
domain: Bacteria
phylum: Firmicutes
class: Clostridia
order: Clostridiales
family: Clostridiaceae
genus: Clostridium
species: Clostridium cochlearium
full scientific name: Clostridium cochlearium (Douglas et al. 1919) Bergey et al. 1923
strain designation: 998
type strain: no
Morphology
cell morphology
- @ref: 69480
- gram stain: positive
- confidence: 100
Culture and growth conditions
culture medium
- @ref: 981
- name: CHOPPED MEAT MEDIUM (DSMZ Medium 78)
- growth: yes
- link: https://mediadive.dsmz.de/medium/78
- composition: Name: CHOPPED MEAT MEDIUM (DSMZ Medium 78) Composition: Ground beef 500.0 g/l Casitone 30.0 g/l Agar 15.0 g/l Ethanol 9.5 g/l (optional) K2HPO4 5.0 g/l Yeast extract 5.0 g/l L-Cysteine HCl 0.5 g/l Haemin 0.005 g/l (optional) Resazurin 0.001 g/l Vitamin K3 0.0005 g/l (optional) Vitamin K1 (optional) NaOH (optional) Distilled water
culture temp
| @ref | growth | type | temperature | range |
|---|---|---|---|---|
| 981 | positive | growth | 37 | mesophilic |
| 67770 | positive | growth | 37 | mesophilic |
Physiology and metabolism
oxygen tolerance
| @ref | oxygen tolerance | confidence |
|---|---|---|
| 981 | anaerobe | |
| 69480 | anaerobe | 99.229 |
spore formation
| @ref | spore formation | confidence |
|---|---|---|
| 69481 | yes | 100 |
| 69480 | yes | 100 |
Isolation, sampling and environmental information
taxonmaps
- @ref: 69479
- File name: preview.99_16844.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_34;96_643;97_746;98_865;99_16844&stattab=map
- Last taxonomy: Clostridium cochlearium
- 16S sequence: LC007105
- Sequence Identity:
- Total samples: 3721
- soil counts: 855
- aquatic counts: 733
- animal counts: 1929
- plant counts: 204
Safety information
risk assessment
- @ref: 981
- pathogenicity human: yes, in single cases
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
- @ref: 67770
- description: Clostridium cochlearium gene for 16S ribosomal RNA, partial sequence, strain: JCM 1384
- accession: LC007105
- length: 1474
- database: ena
- NCBI tax ID: 1494
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Clostridium cochlearium strain NCTC13028 | 1494.16 | wgs | patric | 1494 |
| 66792 | Clostridium cochlearium NCTC 13028 | 2808606730 | draft | img | 1494 |
| 67770 | Clostridium cochlearium NCTC13028 | GCA_900446995 | contig | ncbi | 1494 |
GC content
| @ref | GC-content | method |
|---|---|---|
| 981 | 27.0 | |
| 67770 | 27 | thermal denaturation, midpoint method (Tm) |
Genome-based predictions
predictions
| trait | prediction | confidence | training_data |
|---|---|---|---|
| spore-forming | yes | 100 | no |
| motile | yes | 74.915 | no |
| gram-positive | yes | 69.118 | no |
| anaerobic | yes | 99.335 | yes |
| aerobic | no | 96.506 | no |
| halophile | no | 84.535 | no |
| spore-forming | yes | 96.796 | no |
| thermophile | no | 80.734 | yes |
| glucose-util | yes | 85.1 | no |
| flagellated | no | 61.328 | no |
| glucose-ferment | yes | 62.083 | no |
External links
@ref: 981
culture collection no.: DSM 2153, ATCC 17794, NCIMB 10629, JCM 1384, BCRC 14549, NCTC 13028
straininfo link
- @ref: 72106
- straininfo: 36733
Reference
| @id | authors | catalogue | doi/url | title |
|---|---|---|---|---|
| 981 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 2153) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-2153 | |
| 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) | |
| 67770 | Curators of the JCM | https://jcm.brc.riken.jp/en/ | ||
| 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 | |
| 72106 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID36733.1 | StrainInfo: A central database for resolving microbial strain identifiers |