Strain identifier
BacDive ID: 2854
Type strain: 
Species: Thermoclostridium caenicola
Strain history: <- K. Ueda, Nihon Univ., College of Bioresource Sci., Fujisawa, Japan; EBR596 <- H. Shiratori {2005}
NCBI tax ID(s): 1121300 (strain), 659425 (species)
version 8.1 (current version)
General
@ref: 7847
BacDive-ID: 2854
DSM-Number: 19027
keywords: genome sequence, 16S sequence, Bacteria, anaerobe, spore-forming, thermophilic, Gram-negative, motile, rod-shaped
description: Thermoclostridium caenicola DSM 19027 is an anaerobe, spore-forming, thermophilic bacterium that was isolated from methanogenic sludge of a cellulose-degrading bioreactor.
NCBI tax id
| NCBI tax id | Matching level |
|---|---|
| 1121300 | strain |
| 659425 | species |
strain history
- @ref: 7847
- history: <- K. Ueda, Nihon Univ., College of Bioresource Sci., Fujisawa, Japan; EBR596 <- H. Shiratori {2005}
doi: 10.13145/bacdive2854.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/bacillota
- domain: Bacteria
- phylum: Bacillota
- class: Clostridia
- order: Eubacteriales
- family: Oscillospiraceae
- genus: Thermoclostridium
- species: Thermoclostridium caenicola
- full scientific name: Thermoclostridium caenicola (Shiratori et al. 2009) Zhang et al. 2018
synonyms
- @ref: 20215
- synonym: Clostridium caenicola
@ref: 7847
domain: Bacteria
phylum: Firmicutes
class: Clostridia
order: Clostridiales
family: Oscillospiraceae
genus: Thermoclostridium
species: Thermoclostridium caenicola
full scientific name: Thermoclostridium caenicola (Shiratori et al. 2009) Zhang et al. 2018
type strain: yes
Morphology
cell morphology
| @ref | gram stain | cell length | cell width | cell shape | motility | confidence |
|---|---|---|---|---|---|---|
| 29002 | negative | 3.1 µm | 0.5 µm | rod-shaped | yes | |
| 69480 | positive | 100 |
pigmentation
- @ref: 29002
- production: no
Culture and growth conditions
culture medium
- @ref: 7847
- name: THERMOCLOSTRIDIUM CAENICOLA MEDIUM (DSMZ Medium 640a)
- growth: yes
- link: https://mediadive.dsmz.de/medium/640a
- composition: Name: THERMOCLOSTRIDIUM CAENICOLA MEDIUM (DSMZ Medium 640a) Composition: NaHCO3 2.0 g/l Trypticase peptone 2.0 g/l K2HPO4 1.5 g/l Cellobiose 1.0 g/l Yeast extract 1.0 g/l NH4Cl 0.9 g/l NaCl 0.9 g/l KH2PO4 0.75 g/l L-Cysteine HCl x H2O 0.5 g/l MgCl2 x 6 H2O 0.4 g/l HCl 0.0025 g/l FeCl3 x 6 H2O 0.0025 g/l FeCl2 x 4 H2O 0.0015 g/l Sodium resazurin 0.0005 g/l CoCl2 x 6 H2O 0.00019 g/l MnCl2 x 4 H2O 0.0001 g/l ZnCl2 7e-05 g/l Na2MoO4 x 2 H2O 3.6e-05 g/l NiCl2 x 6 H2O 2.4e-05 g/l H3BO3 6e-06 g/l CuCl2 x 2 H2O 2e-06 g/l Distilled water
culture temp
| @ref | growth | type | temperature | range | confidence |
|---|---|---|---|---|---|
| 7847 | positive | growth | 55 | thermophilic | |
| 29002 | positive | growth | 50-70 | thermophilic | |
| 29002 | positive | optimum | 60 | thermophilic | |
| 69480 | thermophilic | 97.161 |
culture pH
| @ref | ability | type | pH |
|---|---|---|---|
| 29002 | positive | growth | 6.0-8.0 |
| 29002 | positive | optimum | 6.5 |
Physiology and metabolism
oxygen tolerance
| @ref | oxygen tolerance | confidence |
|---|---|---|
| 7847 | anaerobe | |
| 29002 | anaerobe | |
| 69480 | anaerobe | 100 |
spore formation
| @ref | spore formation | confidence |
|---|---|---|
| 29002 | yes | |
| 69481 | no | 99 |
| 69480 | yes | 99.446 |
halophily
| @ref | salt | growth | tested relation | concentration |
|---|---|---|---|---|
| 29002 | NaCl | positive | growth | 0-1.5 % |
| 29002 | NaCl | positive | optimum | 1 % |
metabolite utilization
| @ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
|---|---|---|---|---|
| 29002 | 22599 | arabinose | + | carbon source |
| 29002 | 17057 | cellobiose | + | carbon source |
| 29002 | 17234 | glucose | + | carbon source |
| 29002 | 17306 | maltose | + | carbon source |
| 29002 | 29864 | mannitol | + | carbon source |
| 29002 | 17814 | salicin | + | carbon source |
| 29002 | 4853 | esculin | + | hydrolysis |
Isolation, sampling and environmental information
isolation
- @ref: 7847
- sample type: methanogenic sludge of a cellulose-degrading bioreactor
- country: Japan
- origin.country: JPN
- continent: Asia
isolation source categories
| Cat1 | Cat2 | Cat3 |
|---|---|---|
| #Engineered | #Biodegradation | |
| #Engineered | #Bioreactor | |
| #Environmental | #Terrestrial | #Mud (Sludge) |
| #Condition | #Anoxic (anaerobic) |
taxonmaps
- @ref: 69479
- File name: preview.99_16815.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_246;96_8626;97_10374;98_12724;99_16815&stattab=map
- Last taxonomy: Thermoclostridium caenicola subclade
- 16S sequence: AB221372
- Sequence Identity:
- Total samples: 1486
- soil counts: 549
- aquatic counts: 428
- animal counts: 256
- plant counts: 253
Safety information
risk assessment
- @ref: 7847
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
- @ref: 7847
- description: Clostridium caenicola gene for 16S rRNA, partial sequence
- accession: AB221372
- length: 1565
- database: ena
- NCBI tax ID: 659425
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Thermoclostridium caenicola DSM 19027 | GCA_900142095 | scaffold | ncbi | 659425 |
| 66792 | Thermoclostridium caenicola strain DSM 19027 | 659425.3 | wgs | patric | 659425 |
| 66792 | Thermoclostridium caenicola DSM 19027 | 2700988698 | draft | img | 659425 |
GC content
- @ref: 7847
- GC-content: 51.1
Genome-based predictions
predictions
| trait | prediction | confidence | training_data |
|---|---|---|---|
| spore-forming | no | 99 | no |
| motile | yes | 84.217 | yes |
| flagellated | no | 70.697 | no |
| gram-positive | yes | 76.396 | no |
| anaerobic | yes | 99.66 | yes |
| aerobic | no | 98.858 | no |
| halophile | no | 93.88 | yes |
| spore-forming | yes | 94.28 | yes |
| thermophile | yes | 99.289 | yes |
| glucose-util | yes | 88.076 | yes |
| glucose-ferment | yes | 57.096 | no |
External links
@ref: 7847
culture collection no.: DSM 19027, NBRC 102590, EBR 596
straininfo link
- @ref: 72378
- straininfo: 408015
literature
- topic: Phylogeny
- Pubmed-ID: 19542130
- title: Clostridium clariflavum sp. nov. and Clostridium caenicola sp. nov., moderately thermophilic, cellulose-/cellobiose-digesting bacteria isolated from methanogenic sludge.
- authors: Shiratori H, Sasaya K, Ohiwa H, Ikeno H, Ayame S, Kataoka N, Miya A, Beppu T, Ueda K
- journal: Int J Syst Evol Microbiol
- DOI: 10.1099/ijs.0.003483-0
- year: 2009
- mesh: Bacterial Typing Techniques, Base Composition, Cellobiose/*metabolism, Cellulose/*metabolism, Clostridium/*classification/genetics/isolation & purification/physiology, DNA, Bacterial/analysis, Fatty Acids/analysis, Genes, rRNA, Genotype, *Hot Temperature, Methane/*metabolism, Molecular Sequence Data, Nucleic Acid Hybridization, Phenotype, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sewage/*microbiology, Species Specificity
- topic2: Genetics
Reference
| @id | authors | catalogue | doi/url | title | ID_cross_reference | pubmed |
|---|---|---|---|---|---|---|
| 7847 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 19027) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-19027 | |||
| 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 | |||
| 29002 | Barberan A, Caceres Velazquez H, Jones S, Fierer N. | 10.1128/mSphere.00237-17 | Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information | 25435 | 28776041 | |
| 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) | |||
| 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 | |||
| 72378 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID408015.1 | StrainInfo: A central database for resolving microbial strain identifiers |