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Strain identifier

BacDive ID: 2854

Type strain: Yes

Species: Thermoclostridium caenicola

Strain history: <- K. Ueda, Nihon Univ., College of Bioresource Sci., Fujisawa, Japan; EBR596 <- H. Shiratori {2005}

For citation purpose refer to the digital object identifier (doi) of the current version.
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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 idMatching level
1121300strain
659425species

strain history: <- K. Ueda, Nihon Univ., College of Bioresource Sci., Fujisawa, Japan; EBR596 <- H. Shiratori {2005}

doi: 10.13145/bacdive2854.20221219.7.1

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

@refgram staincell lengthcell widthcell shapemotilityconfidence
29002negative3.1 µm0.5 µmrod-shapedyes
69480positive86.148

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

@refgrowthtypetemperaturerangeconfidence
7847positivegrowth55thermophilic
29002positivegrowth50-70thermophilic
29002positiveoptimum60thermophilic
69480thermophilic98.578

culture pH

@refabilitytypepH
29002positivegrowth6.0-8.0
29002positiveoptimum6.5

Physiology and metabolism

oxygen tolerance

@refoxygen toleranceconfidence
7847anaerobe
29002anaerobe
69480anaerobe99.999

spore formation

@refspore formationconfidence
29002yes
69480yes91.376

halophily

@refsaltgrowthtested relationconcentrationhalophily levelconfidence
29002NaClpositivegrowth0-1.5 %
29002NaClpositiveoptimum1 %
69480non-halophilic99.413

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
2900222599arabinose+carbon source
2900217057cellobiose+carbon source
2900217234glucose+carbon source
2900217306maltose+carbon source
2900229864mannitol+carbon source
2900217814salicin+carbon source
290024853esculin+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

Cat1Cat2Cat3
#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

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Thermoclostridium caenicola DSM 19027GCA_900142095scaffoldncbi659425
66792Thermoclostridium caenicola strain DSM 19027659425.3wgspatric659425
66792Thermoclostridium caenicola DSM 190272700988698draftimg659425

GC content

  • @ref: 7847
  • GC-content: 51.1

External links

@ref: 7847

culture collection no.: DSM 19027, NBRC 102590, EBR 596

straininfo link

@refpassport
20218http://www.straininfo.net/strains/843207
20218http://www.straininfo.net/strains/843208

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

@idauthorscataloguedoi/urltitlejournalpubmedID_cross_reference
7847Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 19027)https://www.dsmz.de/collection/catalogue/details/culture/DSM-19027
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
2543510.1099/ijs.0.003483-019542130
29002Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2877604125435
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)
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)