Strain identifier
BacDive ID: 1324
Type strain:
Species: Caldibacillus debilis
Strain Designation: Tf
Strain history: <- I. M. Banat <- R. Marchant and I. M. Banat; Tf
NCBI tax ID(s): 1121917 (strain), 301148 (species)
General
@ref: 6154
BacDive-ID: 1324
DSM-Number: 16016
keywords: genome sequence, 16S sequence, Bacteria, aerobe, spore-forming, thermophilic, Gram-negative, motile, rod-shaped
description: Caldibacillus debilis Tf is an aerobe, spore-forming, thermophilic bacterium that was isolated from soil.
NCBI tax id
NCBI tax id | Matching level |
---|---|
1121917 | strain |
301148 | species |
strain history
- @ref: 6154
- history: <- I. M. Banat <- R. Marchant and I. M. Banat; Tf
doi: 10.13145/bacdive1324.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/bacillota
- domain: Bacteria
- phylum: Bacillota
- class: Bacilli
- order: Caryophanales
- family: Bacillaceae
- genus: Caldibacillus
- species: Caldibacillus debilis
- full scientific name: Caldibacillus debilis (Banat et al. 2004) Coorevits et al. 2012
synonyms
- @ref: 20215
- synonym: Geobacillus debilis
@ref: 6154
domain: Bacteria
phylum: Firmicutes
class: Bacilli
order: Bacillales
family: Bacillaceae
genus: Caldibacillus
species: Caldibacillus debilis
full scientific name: Caldibacillus debilis (Banat et al. 2004) Coorevits et al. 2012
strain designation: Tf
type strain: yes
Morphology
cell morphology
@ref | gram stain | cell length | cell width | cell shape | motility | confidence |
---|---|---|---|---|---|---|
31293 | negative | 6 µm | 0.5 µm | rod-shaped | yes | |
69480 | yes | 92.503 | ||||
69480 | positive | 100 |
pigmentation
- @ref: 31293
- production: yes
Culture and growth conditions
culture medium
- @ref: 6154
- name: CASO AGAR (MERCK 105458) (DSMZ Medium 220)
- growth: yes
- link: https://mediadive.dsmz.de/medium/220
- composition: Name: CASO AGAR (Merck 105458) (DSMZ Medium 220) Composition: Agar 15.0 g/l Casein peptone 15.0 g/l NaCl 5.0 g/l Soy peptone 5.0 g/l Distilled water
culture temp
@ref | growth | type | temperature | range | confidence |
---|---|---|---|---|---|
6154 | positive | growth | 55 | thermophilic | |
31293 | positive | growth | 50-70 | thermophilic | |
69480 | thermophilic | 98.373 |
Physiology and metabolism
oxygen tolerance
- @ref: 31293
- oxygen tolerance: aerobe
spore formation
@ref | spore formation | confidence |
---|---|---|
31293 | yes | |
69481 | yes | 100 |
69480 | yes | 100 |
metabolite utilization
@ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
---|---|---|---|---|
31293 | 22599 | arabinose | + | carbon source |
31293 | 16634 | raffinose | + | carbon source |
31293 | 26546 | rhamnose | + | carbon source |
31293 | 33942 | ribose | + | carbon source |
31293 | 30911 | sorbitol | + | carbon source |
31293 | 27082 | trehalose | + | carbon source |
31293 | 18222 | xylose | + | carbon source |
enzymes
- @ref: 31293
- value: gelatinase
- activity: +
Isolation, sampling and environmental information
isolation
- @ref: 6154
- sample type: soil
- geographic location: Aghadowey
- continent: Europe
isolation source categories
- Cat1: #Environmental
- Cat2: #Terrestrial
- Cat3: #Soil
taxonmaps
- @ref: 69479
- File name: preview.99_6372.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_79;96_3024;97_3715;98_4709;99_6372&stattab=map
- Last taxonomy: Bacillaceae
- 16S sequence: FN428699
- Sequence Identity:
- Total samples: 4021
- soil counts: 1441
- aquatic counts: 564
- animal counts: 1602
- plant counts: 414
Safety information
risk assessment
- @ref: 6154
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
@ref | description | accession | length | database | NCBI tax ID |
---|---|---|---|---|---|
20218 | Geobacillus debilis partial 16S rRNA gene, strain R-35653 | FN428699 | 1512 | ena | 301148 |
31293 | Geobacillus debilis partial 16S rRNA gene, type strain TfT | AJ564616 | 1525 | nuccore | 301148 |
Genome sequences
@ref | description | accession | assembly level | database | NCBI tax ID |
---|---|---|---|---|---|
66792 | Caldibacillus debilis DSM 16016 | GCA_000383875 | scaffold | ncbi | 1121917 |
66792 | Caldibacillus debilis DSM 16016 | 1121917.3 | wgs | patric | 1121917 |
66792 | Caldibacillus debilis DSM 16016 | 2515154121 | draft | img | 1121917 |
GC content
- @ref: 31293
- GC-content: 49.9
Genome-based predictions
predictions
trait | prediction | confidence | training_data |
---|---|---|---|
spore-forming | yes | 100 | no |
motile | yes | 89.855 | yes |
flagellated | yes | 79.189 | no |
gram-positive | yes | 90.505 | no |
anaerobic | no | 95.839 | yes |
aerobic | yes | 82.887 | yes |
halophile | yes | 52.594 | no |
spore-forming | yes | 94.369 | yes |
thermophile | yes | 99.661 | yes |
glucose-util | yes | 88.21 | no |
glucose-ferment | no | 79.439 | no |
External links
@ref: 6154
culture collection no.: DSM 16016
straininfo link
- @ref: 70974
- straininfo: 134422
literature
topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
---|---|---|---|---|---|---|---|---|
Phylogeny | 15545458 | Geobacillus debilis sp. nov., a novel obligately thermophilic bacterium isolated from a cool soil environment, and reassignment of Bacillus pallidus to Geobacillus pallidus comb. nov. | Banat IM, Marchant R, Rahman TJ | Int J Syst Evol Microbiol | 10.1099/ijs.0.63231-0 | 2004 | Aerobiosis, Bacillaceae/*classification/cytology/*isolation & purification/physiology, Bacterial Typing Techniques, DNA, Bacterial/chemistry/isolation & purification, DNA, Ribosomal/chemistry/isolation & purification, Genes, rRNA, Gentian Violet, Hot Temperature, Molecular Sequence Data, Movement, Northern Ireland, Phenazines, Phylogeny, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Spores, Bacterial/cytology, Temperature | Enzymology |
Phylogeny | 21856988 | Taxonomic revision of the genus Geobacillus: emendation of Geobacillus, G. stearothermophilus, G. jurassicus, G. toebii, G. thermodenitrificans and G. thermoglucosidans (nom. corrig., formerly 'thermoglucosidasius'); transfer of Bacillus thermantarcticus to the genus as G. thermantarcticus comb. nov.; proposal of Caldibacillus debilis gen. nov., comb. nov.; transfer of G. tepidamans to Anoxybacillus as A. tepidamans comb. nov.; and proposal of Anoxybacillus caldiproteolyticus sp. nov. | Coorevits A, Dinsdale AE, Halket G, Lebbe L, De Vos P, Van Landschoot A, Logan NA | Int J Syst Evol Microbiol | 10.1099/ijs.0.030346-0 | 2011 | Aerobiosis, Bacillales/*classification/genetics/physiology, Bacterial Typing Techniques, Cluster Analysis, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis, Molecular Sequence Data, Nucleic Acid Hybridization, Phospholipids/analysis, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Spores, Bacterial/cytology | Genetics |
Reference
@id | authors | catalogue | doi/url | title | journal | pubmed | ID_cross_reference |
---|---|---|---|---|---|---|---|
6154 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 16016) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-16016 | ||||
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 | ||
31293 | 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 | 28776041 | 27612 | ||
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) | ||||
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 | ||||
70974 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID134422.1 | StrainInfo: A central database for resolving microbial strain identifiers |