Strain identifier
BacDive ID: 2749
Type strain: 
Species: Clostridium thermosuccinogenes
Strain Designation: IC
Strain history: <- J. C. Gottschal, Univ. Groningen, The Netherlands; IC <- W. J. Drent {1989}
NCBI tax ID(s): 1121341 (strain), 84032 (species)
version 8.1 (current version)
General
@ref: 2191
BacDive-ID: 2749
DSM-Number: 5807
keywords: genome sequence, 16S sequence, Bacteria, anaerobe, spore-forming, thermophilic, Gram-positive
description: Clostridium thermosuccinogenes IC is an anaerobe, spore-forming, thermophilic bacterium that was isolated from beet pulp, sugar refinery.
NCBI tax id
| NCBI tax id | Matching level |
|---|---|
| 84032 | species |
| 1121341 | strain |
strain history
- @ref: 2191
- history: <- J. C. Gottschal, Univ. Groningen, The Netherlands; IC <- W. J. Drent {1989}
doi: 10.13145/bacdive2749.20230509.8.1
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 thermosuccinogenes
- full scientific name: Clostridium thermosuccinogenes Drent et al. 1995
synonyms
- @ref: 20215
- synonym: Pseudoclostridium thermosuccinogenes
@ref: 2191
domain: Bacteria
phylum: Firmicutes
class: Clostridia
order: Clostridiales
family: Clostridiaceae
genus: Clostridium
species: Clostridium thermosuccinogenes
full scientific name: Clostridium thermosuccinogenes Drent et al. 1995
strain designation: IC
type strain: yes
Morphology
cell morphology
- @ref: 69480
- gram stain: positive
- confidence: 100
Culture and growth conditions
culture medium
| @ref | name | growth | link | composition |
|---|---|---|---|---|
| 2191 | THERMOCLOSTRIDIUM (A-GÖ) MEDIUM (DSMZ Medium 326) | yes | https://mediadive.dsmz.de/medium/326 | Name: THERMOCLOSTRIDIUM (A-GÖ) MEDIUM (DSMZ Medium 326) Composition: Sucrose 4.99002 g/l KH2PO4 3.29341 g/l Yeast extract 1.99601 g/l Trypticase peptone 1.99601 g/l Na2CO3 0.998004 g/l Na2S x 9 H2O 0.299401 g/l L-Cysteine HCl x H2O 0.299401 g/l MgCl2 x 6 H2O 0.159681 g/l HCl 0.00249501 g/l FeCl2 x 4 H2O 0.00149701 g/l Sodium resazurin 0.000499002 g/l CoCl2 x 6 H2O 0.000189621 g/l Pyridoxine hydrochloride 9.98004e-05 g/l MnCl2 x 4 H2O 9.98004e-05 g/l ZnCl2 6.98603e-05 g/l Nicotinic acid 4.99002e-05 g/l (DL)-alpha-Lipoic acid 4.99002e-05 g/l Calcium D-(+)-pantothenate 4.99002e-05 g/l Thiamine HCl 4.99002e-05 g/l Riboflavin 4.99002e-05 g/l p-Aminobenzoic acid 4.99002e-05 g/l Na2MoO4 x 2 H2O 3.59281e-05 g/l NiCl2 x 6 H2O 2.39521e-05 g/l Biotin 1.99601e-05 g/l Folic acid 1.99601e-05 g/l H3BO3 5.98802e-06 g/l CuCl2 x 2 H2O 1.99601e-06 g/l Vitamin B12 9.98004e-07 g/l Distilled water |
| 2191 | PSEUDOCLOSTRIDIUM MEDIUM (DSMZ Medium 502) | yes | https://mediadive.dsmz.de/medium/502 | Name: PSEUDOCLOSTRIDIUM MEDIUM (DSMZ Medium 502) Composition: Inulin 4.99002 g/l Na2HPO4 2.65469 g/l Na2CO3 1.49701 g/l NaCl 1.1976 g/l MgCl2 x 6 H2O 0.399202 g/l KCl 0.299401 g/l NH4Cl 0.269461 g/l KH2PO4 0.209581 g/l Na2S x 9 H2O 0.149701 g/l CaCl2 x 2 H2O 0.149701 g/l Na2SO4 0.0998004 g/l Casamino acids 0.0299401 g/l Yeast extract 0.0299401 g/l HCl 0.00249501 g/l FeCl2 x 4 H2O 0.00149701 g/l Sodium resazurin 0.000499002 g/l CoCl2 x 6 H2O 0.000189621 g/l Pyridoxine hydrochloride 9.98004e-05 g/l MnCl2 x 4 H2O 9.98004e-05 g/l ZnCl2 6.98603e-05 g/l Riboflavin 4.99002e-05 g/l Nicotinic acid 4.99002e-05 g/l Calcium D-(+)-pantothenate 4.99002e-05 g/l p-Aminobenzoic acid 4.99002e-05 g/l (DL)-alpha-Lipoic acid 4.99002e-05 g/l Thiamine HCl 4.99002e-05 g/l Na2MoO4 x 2 H2O 3.59281e-05 g/l NiCl2 x 6 H2O 2.39521e-05 g/l Folic acid 1.99601e-05 g/l Biotin 1.99601e-05 g/l H3BO3 5.98802e-06 g/l CuCl2 x 2 H2O 1.99601e-06 g/l Vitamin B12 9.98004e-07 g/l Distilled water |
culture temp
| @ref | growth | type | temperature | range | confidence |
|---|---|---|---|---|---|
| 2191 | positive | growth | 60 | thermophilic | |
| 69480 | thermophilic | 91.872 |
Physiology and metabolism
oxygen tolerance
| @ref | oxygen tolerance | confidence |
|---|---|---|
| 2191 | anaerobe | |
| 69480 | anaerobe | 99.998 |
spore formation
- @ref: 69480
- spore formation: yes
- confidence: 99.521
Isolation, sampling and environmental information
isolation
- @ref: 2191
- sample type: beet pulp, sugar refinery
- country: Netherlands
- origin.country: NLD
- continent: Europe
isolation source categories
- Cat1: #Host Body-Site
- Cat2: #Plant
- Cat3: #Fruit (Seed)
taxonmaps
- @ref: 69479
- File name: preview.99_31786.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_196;96_13782;97_18927;98_23599;99_31786&stattab=map
- Last taxonomy: Pseudoclostridium thermosuccinogenes subclade
- 16S sequence: Y18180
- Sequence Identity:
- Total samples: 3397
- soil counts: 1800
- aquatic counts: 513
- animal counts: 446
- plant counts: 638
Safety information
risk assessment
- @ref: 2191
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
- @ref: 2191
- description: Clostridium thermosuccinogenes 16S rRNA gene, partial, strain DSM 5807
- accession: Y18180
- length: 1640
- database: ena
- NCBI tax ID: 84032
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Pseudoclostridium thermosuccinogenes DSM 5807 | GCA_002896855 | complete | ncbi | 84032 |
| 66792 | [Clostridium] thermosuccinogenes strain DSM 5807 | 84032.3 | complete | patric | 84032 |
| 66792 | Pseudoclostridium thermosuccinogenes DSM 5807 | 2795385491 | complete | img | 84032 |
GC content
- @ref: 2191
- GC-content: 35.9
Genome-based predictions
predictions
| trait | prediction | confidence | training_data |
|---|---|---|---|
| spore-forming | yes | 61 | no |
| flagellated | no | 72.075 | no |
| gram-positive | yes | 66.417 | no |
| anaerobic | yes | 99.51 | yes |
| halophile | no | 94.628 | no |
| spore-forming | yes | 82.36 | no |
| glucose-util | yes | 84.663 | no |
| aerobic | no | 99.222 | yes |
| thermophile | yes | 99.56 | yes |
| motile | yes | 73.416 | no |
| glucose-ferment | yes | 60.102 | no |
External links
@ref: 2191
culture collection no.: DSM 5807
straininfo link
- @ref: 72279
- straininfo: 48004
literature
- topic: Phylogeny
- Pubmed-ID: 16957104
- title: Gracilibacter thermotolerans gen. nov., sp. nov., an anaerobic, thermotolerant bacterium from a constructed wetland receiving acid sulfate water.
- authors: Lee YJ, Romanek CS, Mills GL, Davis RC, Whitman WB, Wiegel J
- journal: Int J Syst Evol Microbiol
- DOI: 10.1099/ijs.0.64040-0
- year: 2006
- mesh: Bacteria, Anaerobic/classification/metabolism, Clostridium/classification/genetics/*isolation & purification/metabolism, Molecular Sequence Data, RNA, Ribosomal, 16S/analysis/genetics, Sulfates/*metabolism, Water Microbiology
- topic2: Metabolism
Reference
| @id | authors | catalogue | doi/url | title | journal | pubmed |
|---|---|---|---|---|---|---|
| 2191 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 5807) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-5807 | |||
| 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) | |||
| 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) | |||
| 72279 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID48004.1 | StrainInfo: A central database for resolving microbial strain identifiers |