Strain identifier

BacDive ID: 2773

Type strain: Yes

Species: Thermoclostridium stercorarium

Strain history: <- ATCC <- NCIMB <- R. H. Madden

NCBI tax ID(s): 1121335 (strain), 1510 (species)

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General

@ref: 3229

BacDive-ID: 2773

DSM-Number: 8532

keywords: genome sequence, 16S sequence, Bacteria, anaerobe, thermophilic, Gram-positive

description: Thermoclostridium stercorarium DSM 8532 is an anaerobe, thermophilic, Gram-positive bacterium that was isolated from compost heap.

NCBI tax id

NCBI tax idMatching level
1121335strain
1510species

strain history

  • @ref: 3229
  • history: <- ATCC <- NCIMB <- R. H. Madden

doi: 10.13145/bacdive2773.20230509.8.1

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 stercorarium
  • full scientific name: Thermoclostridium stercorarium (Madden 1983) Zhang et al. 2018

  • synonyms

    • @ref: 20215
    • synonym: Clostridium stercorarium

@ref: 3229

domain: Bacteria

phylum: Firmicutes

class: Clostridia

order: Clostridiales

family: Oscillospiraceae

genus: Thermoclostridium

species: Thermoclostridium stercorarium subsp. stercorarium

full scientific name: Thermoclostridium stercorarium subsp. stercorarium (Madden 1983) Zhang et al. 2018

type strain: yes

Morphology

cell morphology

  • @ref: 69480
  • gram stain: positive
  • confidence: 99.999

Culture and growth conditions

culture medium

  • @ref: 3229
  • name: CLOSTRIDIUM (GS) MEDIUM (DSMZ Medium 255)
  • growth: yes
  • link: https://mediadive.dsmz.de/medium/255
  • composition: Name: CLOSTRIDIUM (GS) MEDIUM (DSMZ Medium 255) Composition: Morpholinopropane sulfonic acid 9.98004 g/l Yeast extract 5.98802 g/l Cellobiose 4.99002 g/l Urea 1.99601 g/l L-Cysteine HCl x H2O 0.998004 g/l K2HPO4 x 3 H2O 0.998004 g/l KH2PO4 0.499002 g/l MgCl2 x 6 H2O 0.499002 g/l CaCl2 x 2 H2O 0.0499002 g/l FeSO4 x 7 H2O 0.0012475 g/l Sodium resazurin 0.000499002 g/l Distilled water

culture temp

@refgrowthtypetemperaturerangeconfidence
3229positivegrowth60thermophilic
69480thermophilic98.977

Physiology and metabolism

oxygen tolerance

@refoxygen toleranceconfidence
3229anaerobe
69480anaerobe99.747

compound production

@refcompound
3229xylanase
3229exogluconase
3229endoglucanase

Isolation, sampling and environmental information

isolation

  • @ref: 3229
  • sample type: compost heap
  • geographic location: Aberdeenshire
  • country: United Kingdom
  • origin.country: GBR
  • continent: Europe

isolation source categories

  • Cat1: #Engineered
  • Cat2: #Biodegradation
  • Cat3: #Composting

taxonmaps

  • @ref: 69479
  • File name: preview.99_1650.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_246;96_941;97_1095;98_1306;99_1650&stattab=map
  • Last taxonomy: Thermoclostridium stercorarium subclade
  • 16S sequence: AJ310082
  • Sequence Identity:
  • Total samples: 6000
  • soil counts: 1258
  • aquatic counts: 584
  • animal counts: 3737
  • plant counts: 421

Safety information

risk assessment

  • @ref: 3229
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Clostridium stercorarium subsp. leptospartum 16S ribosomal RNA gene, partial sequenceAF2664611518ena160385
20218Clostridium stercorarium (NCIMB 11754) 16S ribosomal RNA (16S rRNA) geneL091741519ena1510
3229Clostridium stercorarium 16S rRNA gene, strain DSM 8532TAJ3100821500ena1510

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Thermoclostridium stercorarium subsp. stercorarium DSM 8532GCA_000331995completencbi1121335
66792Thermoclostridium stercorarium subsp. stercorarium DSM 8532GCA_000349885completencbi1121335
66792[Clostridium] stercorarium subsp. stercorarium DSM 85321121335.11completepatric1121335
66792Clostridium stercorarium subsp. stercorarium DSM 85321121335.3completepatric1121335
66792Thermoclostridium stercorarium stercorarium DSM 85322522125167completeimg1121335
66792Thermoclostridium stercorarium stercorarium DSM 85322540341047completeimg1121335

GC content

@refGC-contentmethod
322939thermal denaturation, midpoint method (Tm)
322942.2sequence analysis

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno56no
motileyes71.555no
flagellatedno81.107no
gram-positiveyes69.234no
anaerobicyes98.96yes
aerobicno98.42no
halophileno93.968no
spore-formingyes86.501no
thermophileyes99.69no
glucose-utilyes88.893no
glucose-fermentno51.094no

External links

@ref: 3229

culture collection no.: DSM 8532, ATCC 35414, NCIMB 11754

straininfo link

  • @ref: 72303
  • straininfo: 41063

literature

  • topic: Enzymology
  • Pubmed-ID: 31685873
  • title: Biochemical characterisation of four rhamnosidases from thermophilic bacteria of the genera Thermotoga, Caldicellulosiruptor and Thermoclostridium.
  • authors: Baudrexl M, Schwarz WH, Zverlov VV, Liebl W
  • journal: Sci Rep
  • DOI: 10.1038/s41598-019-52251-0
  • year: 2019
  • mesh: Bacterial Proteins/chemistry/*metabolism, Caldicellulosiruptor, Cloning, Molecular, Clostridiales/*enzymology, Cobalt/chemistry/metabolism, Edetic Acid/chemistry/metabolism, Firmicutes/*enzymology, Flavanones/metabolism, Glycoside Hydrolases/chemistry/*metabolism, Hydrogen-Ion Concentration, Inhibitory Concentration 50, Kinetics, Recombinant Proteins/biosynthesis/chemistry/isolation & purification, Rhamnose/metabolism, Substrate Specificity, Temperature, Thermotoga maritima/*enzymology, Thermotoga neapolitana/*enzymology
  • topic2: Metabolism

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
3229Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 8532)https://www.dsmz.de/collection/catalogue/details/culture/DSM-8532
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
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)
72303Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID41063.1StrainInfo: A central database for resolving microbial strain identifiers