Strain identifier

BacDive ID: 1324

Type strain: Yes

Species: Caldibacillus debilis

Strain Designation: Tf

Strain history: <- I. M. Banat <- R. Marchant and I. M. Banat; Tf

For citation purpose refer to the digital object identifier (doi) of the current version.
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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 idMatching level
1121917strain
301148species

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

@refgram staincell lengthcell widthcell shapemotilityconfidence
31293negative6 µm0.5 µmrod-shapedyes
69480yes92.503
69480positive100

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

@refgrowthtypetemperaturerangeconfidence
6154positivegrowth55thermophilic
31293positivegrowth50-70thermophilic
69480thermophilic98.373

Physiology and metabolism

oxygen tolerance

  • @ref: 31293
  • oxygen tolerance: aerobe

spore formation

@refspore formationconfidence
31293yes
69481yes100
69480yes100

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3129322599arabinose+carbon source
3129316634raffinose+carbon source
3129326546rhamnose+carbon source
3129333942ribose+carbon source
3129330911sorbitol+carbon source
3129327082trehalose+carbon source
3129318222xylose+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

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Geobacillus debilis partial 16S rRNA gene, strain R-35653FN4286991512ena301148
31293Geobacillus debilis partial 16S rRNA gene, type strain TfTAJ5646161525nuccore301148

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Caldibacillus debilis DSM 16016GCA_000383875scaffoldncbi1121917
66792Caldibacillus debilis DSM 160161121917.3wgspatric1121917
66792Caldibacillus debilis DSM 160162515154121draftimg1121917

GC content

  • @ref: 31293
  • GC-content: 49.9

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingyes100no
motileyes89.855yes
flagellatedyes79.189no
gram-positiveyes90.505no
anaerobicno95.839yes
aerobicyes82.887yes
halophileyes52.594no
spore-formingyes94.369yes
thermophileyes99.661yes
glucose-utilyes88.21no
glucose-fermentno79.439no

External links

@ref: 6154

culture collection no.: DSM 16016

straininfo link

  • @ref: 70974
  • straininfo: 134422

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny15545458Geobacillus 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 TJInt J Syst Evol Microbiol10.1099/ijs.0.63231-02004Aerobiosis, 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, TemperatureEnzymology
Phylogeny21856988Taxonomic 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 NAInt J Syst Evol Microbiol10.1099/ijs.0.030346-02011Aerobiosis, 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/cytologyGenetics

Reference

@idauthorscataloguedoi/urltitlejournalpubmedID_cross_reference
6154Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 16016)https://www.dsmz.de/collection/catalogue/details/culture/DSM-16016
20215Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M.10.1099/ijsem.0.004332List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ
20218Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P.10.1016/j.syapm.2013.11.002StrainInfo introduces electronic passports for microorganisms.Syst Appl Microbiol. 37: 42-50 201424321274
31293Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2877604127612
66792Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmannhttps://diaspora-project.de/progress.html#genomesAutomatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)
66794Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg10.1093/nar/gkaa1025BRENDA, the ELIXIR core data resource in 2021: new developments and updatesNucleic Acids Res. 49: D498-D508 202033211880
69479João 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
69480Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmannhttps://diaspora-project.de/progress.html#genomesPredictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)
69481Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch10.21203/rs.3.rs-2527258/v1Predictions based on the model GenomeNet Sporulation v. 1
70974Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID134422.1StrainInfo: A central database for resolving microbial strain identifiers