Strain identifier
BacDive ID: 2692
Type strain: 
Species: Clostridium sp.
Strain Designation: C8
Strain history: IAM 19232 <-- S. Sugama <-- Inst. Pasteur; C8.
NCBI tax ID(s): 1506 (species)
version 9.1 (current version)
General
@ref: 4300
BacDive-ID: 2692
DSM-Number: 11329
keywords: genome sequence, 16S sequence, Bacteria, anaerobe, spore-forming
description: Clostridium sp. C8 is an anaerobe, spore-forming bacterium that was isolated from retting Ramie .
NCBI tax id
- NCBI tax id: 1506
- Matching level: species
strain history
| @ref | history |
|---|---|
| 4300 | <- JCM <- IAM <- S. Sugama <- Institut Pasteur, strain C8, (Clostridium pectinolyticum) |
| 67770 | IAM 19232 <-- S. Sugama <-- Inst. Pasteur; C8. |
doi: 10.13145/bacdive2692.20240916.9.1
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 sp.
- full scientific name: Clostridium Prazmowski 1880 (Approved Lists 1980)
synonyms
@ref synonym 20215 Tyzzerella 20215 Pseudoclostridium 20215 Lachnoclostridium 20215 Anaerobacter 20215 Inflabilis
@ref: 4300
domain: Bacteria
phylum: Firmicutes
class: Clostridia
order: Clostridiales
family: Clostridiaceae
genus: Clostridium
species: Clostridium sp.
full scientific name: Clostridium sp.
strain designation: C8
type strain: no
Culture and growth conditions
culture medium
| @ref | name | growth | link | composition |
|---|---|---|---|---|
| 4300 | 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 |
| 4300 | PY + X MEDIUM (DSMZ Medium 104b) | yes | https://mediadive.dsmz.de/medium/104b | Name: PY + X MEDIUM (DSMZ Medium 104b) Composition: Yeast extract 10.0 g/l D-Glucose 5.0 g/l Trypticase peptone 5.0 g/l Meat peptone 5.0 g/l L-Cysteine HCl x H2O 0.5 g/l NaHCO3 0.4 g/l NaCl 0.08 g/l KH2PO4 0.04 g/l K2HPO4 0.04 g/l MgSO4 x 7 H2O 0.02 g/l CaCl2 x 2 H2O 0.01 g/l Sodium resazurin 0.0005 g/l Distilled water |
culture temp
| @ref | growth | type | temperature |
|---|---|---|---|
| 4300 | positive | growth | 37 |
| 67770 | positive | growth | 37 |
Physiology and metabolism
oxygen tolerance
- @ref: 4300
- oxygen tolerance: anaerobe
Isolation, sampling and environmental information
isolation
- @ref: 4300
- sample type: retting Ramie (Boehmeria nivea)
isolation source categories
- Cat1: #Host
- Cat2: #Plants
- Cat3: #Herbaceous plants (Grass,Crops)
taxonmaps
- @ref: 69479
- File name: preview.99_378.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_34;96_149;97_160;98_179;99_378&stattab=map
- Last taxonomy: Clostridium
- 16S sequence: AB971810
- Sequence Identity:
- Total samples: 10335
- soil counts: 1985
- aquatic counts: 1977
- animal counts: 5931
- plant counts: 442
Sequence information
16S sequences
| @ref | description | accession | length | database | NCBI tax ID |
|---|---|---|---|---|---|
| 20218 | Clostridium beijerinckii gene for 16S rRNA, partial sequence, strain: JCM 7847 | AB020191 | 1404 | nuccore | 1520 |
| 67770 | Clostridium beijerinckii gene for 16S ribosomal RNA, partial sequence, strain: JCM 7847 | AB971810 | 1473 | nuccore | 1520 |
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Clostridium sp. C8 | GCA_001010885 | contig | ncbi | 1667357 |
| 66792 | Clostridium sp. C8 | 1667357.4 | wgs | patric | 1667357 |
| 66792 | Clostridium sp. C8 | 2630968386 | draft | img | 1667357 |
GC content
- @ref: 67770
- GC-content: 31
- method: high performance liquid chromatography (HPLC)
Genome-based predictions
predictions
| @ref | trait | model | description | prediction | confidence | training_data |
|---|---|---|---|---|---|---|
| 69480 | gram-positive | gram-positive | Positive reaction to Gram-staining | yes | 67.312 | no |
| 69480 | anaerobic | anaerobic | Ability to grow under anoxygenic conditions (including facultative anaerobes) | yes | 87.251 | yes |
| 69480 | spore-forming | spore-forming | Ability to form endo- or exospores | yes | 82.224 | no |
| 69480 | aerobic | aerobic | Ability to grow under oxygenic conditions (including facultative aerobes) | no | 97.466 | yes |
| 69480 | thermophilic | thermophile | Ability to grow at temperatures above or equal to 45°C | no | 91.901 | yes |
| 69480 | flagellated | motile2+ | Ability to perform flagellated movement | yes | 81.168 | no |
External links
@ref: 4300
culture collection no.: DSM 11329, IAM 19232, JCM 7847
straininfo link
- @ref: 72220
- straininfo: 49080
Reference
| @id | authors | catalogue | doi/url | title | journal | pubmed |
|---|---|---|---|---|---|---|
| 4300 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 11329) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-11329 | |||
| 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) | |||
| 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) | |||
| 72220 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID49080.1 | StrainInfo: A central database for resolving microbial strain identifiers |