Strain identifier
BacDive ID: 2575
Type strain: 
Species: Thomasclavelia cocleata
Strain Designation: I50
Strain history: C. Kaneuchi I 50 <-- K. Itoh 50.
NCBI tax ID(s): 1121304 (strain), 69824 (species)
version 8.1 (current version)
General
@ref: 818
BacDive-ID: 2575
DSM-Number: 1551
keywords: genome sequence, 16S sequence, Bacteria, anaerobe, mesophilic, Gram-positive, human pathogen
description: Thomasclavelia cocleata I50 is an anaerobe, mesophilic, Gram-positive human pathogen that was isolated from caecal content; wildtype C57BL/6 mouse.
NCBI tax id
| NCBI tax id | Matching level |
|---|---|
| 69824 | species |
| 1121304 | strain |
strain history
| @ref | history |
|---|---|
| 818 | <- C. Kaneuchi, Institute of Physical and Chemical Research, Komagome Branch, Tokyo, Japan; I50 <- C. Kaneuchi {1975} |
| 67770 | C. Kaneuchi I 50 <-- K. Itoh 50. |
doi: 10.13145/bacdive2575.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/bacillota
- domain: Bacteria
- phylum: Bacillota
- class: Erysipelotrichia
- order: Erysipelotrichales
- family: Coprobacillaceae
- genus: Thomasclavelia
- species: Thomasclavelia cocleata
- full scientific name: Thomasclavelia cocleata (Kaneuchi et al. 1979) Lawson et al. 2023
synonyms
- @ref: 20215
- synonym: Clostridium cocleatum
@ref: 818
domain: Bacteria
phylum: Firmicutes
class: Clostridia
order: Clostridiales
family: Clostridiaceae
genus: Clostridium
species: Clostridium cocleatum
full scientific name: Clostridium cocleatum Kaneuchi et al. 1979
strain designation: I50
type strain: yes
Morphology
cell morphology
- @ref: 69480
- gram stain: positive
- confidence: 100
colony morphology
- @ref: 818
- incubation period: 1-2 days
Culture and growth conditions
culture medium
- @ref: 818
- name: CMC MEDIUM (N2/CO2) (DSMZ Medium 110a)
- growth: yes
- link: https://mediadive.dsmz.de/medium/110a
- composition: Name: CMC MEDIUM (N2/CO2) (DSMZ Medium 110a) Composition: Ground beef 500.0 g/l Casitone 30.0 g/l Yeast extract 5.0 g/l K2HPO4 5.0 g/l D-Glucose 4.0 g/l Na2CO3 1.5 g/l Cellobiose 1.0 g/l Maltose 1.0 g/l Starch 1.0 g/l L-Cysteine HCl x H2O 0.5 g/l Sodium resazurin 0.0005 g/l NaOH Distilled water
culture temp
| @ref | growth | type | temperature | range |
|---|---|---|---|---|
| 818 | positive | growth | 37 | mesophilic |
| 57145 | positive | growth | 37 | mesophilic |
| 67770 | positive | growth | 37 | mesophilic |
Physiology and metabolism
oxygen tolerance
| @ref | oxygen tolerance | confidence |
|---|---|---|
| 818 | anaerobe | |
| 57145 | anaerobe | |
| 69480 | anaerobe | 99.999 |
spore formation
- @ref: 69480
- spore formation: no
- confidence: 99.681
Isolation, sampling and environmental information
isolation
| @ref | sample type | geographic location | country | origin.country | continent |
|---|---|---|---|---|---|
| 818 | caecal content; wildtype C57BL/6 mouse | Miyazaki | Japan | JPN | Asia |
| 57145 | Mouse cecum | Japan | JPN | Asia | |
| 67770 | Cecum of mouse |
isolation source categories
| Cat1 | Cat2 | Cat3 |
|---|---|---|
| #Host | #Mammals | #Muridae (Mouse/Rat) |
| #Host Body-Site | #Gastrointestinal tract | #Large intestine |
| #Host Body Product | #Gastrointestinal tract | #Caecal content |
taxonmaps
- @ref: 69479
- File name: preview.99_10040.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_15821;96_590;97_5951;98_7458;99_10040&stattab=map
- Last taxonomy: [Clostridium] cocleatum subclade
- 16S sequence: Y18188
- Sequence Identity:
- Total samples: 63739
- soil counts: 695
- aquatic counts: 565
- animal counts: 62316
- plant counts: 163
Safety information
risk assessment
- @ref: 818
- pathogenicity human: yes, in single cases
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
| @ref | description | accession | length | database | NCBI tax ID |
|---|---|---|---|---|---|
| 20218 | [Clostridium] cocleatum gene for 16S ribosomal RNA, partial sequence | AB910744 | 1488 | ena | 69824 |
| 818 | Clostridium cocleatum 16S rRNA gene, partial, strain DSM 1551 | Y18188 | 1489 | ena | 69824 |
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | [Clostridium] cocleatum strain ATCC 29902 | 69824.4 | wgs | patric | 69824 |
| 66792 | [Clostridium] cocleatum strain DSM 1551 | 69824.3 | wgs | patric | 69824 |
| 66792 | Erysipelatoclostridium cocleatum ATCC 29902 | 2574179769 | draft | img | 69824 |
| 66792 | Clostridium cocleatum DSM 1551 | 2634166354 | draft | img | 1121304 |
| 67770 | Thomasclavelia cocleata DSM 1551 | GCA_900102365 | scaffold | ncbi | 69824 |
| 67770 | Thomasclavelia cocleata ATCC 29902 | GCA_002803405 | scaffold | ncbi | 69824 |
| 66792 | Thomasclavelia cocleata DSM 1551 | GCA_024622895 | contig | ncbi | 69824 |
GC content
- @ref: 818
- GC-content: 27.9
Genome-based predictions
predictions
- trait: spore-forming
- prediction: yes
- confidence: 56
- training_data: no
External links
@ref: 818
culture collection no.: CCUG 46310, CCUG 45854, DSM 1551, ATCC 29902, NCTC 11210, JCM 1397, BCRC 14465, CCM 6166
straininfo link
- @ref: 72108
- straininfo: 39795
Reference
| @id | authors | catalogue | doi/url | title | journal | pubmed |
|---|---|---|---|---|---|---|
| 818 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 1551) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-1551 | |||
| 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 | |
| 57145 | Curators of the CCUG | Culture Collection University of Gothenburg (CCUG) (CCUG 46310) | https://www.ccug.se/strain?id=46310 | |||
| 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 | |
| 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) | |||
| 72108 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID39795.1 | StrainInfo: A central database for resolving microbial strain identifiers |