Strain identifier

BacDive ID: 2734

Type strain: No

Species: Thermoclostridium stercorarium subsp. thermolacticum

Strain history: E. Uematsu <-- ATCC 43738 <-- DSM 2911 <-- P. Le Ruyet TC21.

NCBI tax ID(s): 1291049 (strain), 29351 (subspecies)

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General

@ref: 1244

BacDive-ID: 2734

DSM-Number: 2911

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

description: Thermoclostridium stercorarium subsp. thermolacticum DSM 2911 is an anaerobe, spore-forming, thermophilic bacterium that was isolated from composted cattle manure.

NCBI tax id

NCBI tax idMatching level
1291049strain
29351subspecies

strain history

@refhistory
1244<- P. Le Ruyet and H.C. Dubourguier, TC21
67770E. Uematsu <-- ATCC 43738 <-- DSM 2911 <-- P. Le Ruyet TC21.

doi: 10.13145/bacdive2734.20230509.8.1

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 subsp. thermolacticum
  • full scientific name: Thermoclostridium stercorarium subsp. thermolacticum (Le Ruyet et al. 1988) Zhang et al. 2018

  • synonyms

    @refsynonym
    20215Clostridium stercorarium subsp. thermolacticum
    20215Clostridium thermolacticum

@ref: 1244

domain: Bacteria

phylum: Firmicutes

class: Clostridia

order: Clostridiales

family: Oscillospiraceae

genus: Thermoclostridium

species: Thermoclostridium stercorarium subsp. thermolacticum

full scientific name: Thermoclostridium stercorarium subsp. thermolacticum (Le Ruyet et al. 1988) Zhang et al. 2018

type strain: no

Morphology

cell morphology

  • @ref: 69480
  • gram stain: positive
  • confidence: 99.998

Culture and growth conditions

culture medium

  • @ref: 1244
  • name: THERMOCLOSTRIDIUM (A-GÖ) MEDIUM (DSMZ Medium 326)
  • growth: yes
  • link: https://mediadive.dsmz.de/medium/326
  • composition: Name: THERMOCLOSTRIDIUM (A-GÖ) MEDIUM (DSMZ Medium 326) Composition: Sucrose 4.99002 g/l KH2PO4 3.29341 g/l Yeast extract 1.99601 g/l Trypticase peptone 1.99601 g/l Na2CO3 0.998004 g/l Na2S x 9 H2O 0.299401 g/l L-Cysteine HCl x H2O 0.299401 g/l MgCl2 x 6 H2O 0.159681 g/l HCl 0.00249501 g/l FeCl2 x 4 H2O 0.00149701 g/l Sodium resazurin 0.000499002 g/l CoCl2 x 6 H2O 0.000189621 g/l Pyridoxine hydrochloride 9.98004e-05 g/l MnCl2 x 4 H2O 9.98004e-05 g/l ZnCl2 6.98603e-05 g/l Nicotinic acid 4.99002e-05 g/l (DL)-alpha-Lipoic acid 4.99002e-05 g/l Calcium D-(+)-pantothenate 4.99002e-05 g/l Thiamine HCl 4.99002e-05 g/l Riboflavin 4.99002e-05 g/l p-Aminobenzoic acid 4.99002e-05 g/l Na2MoO4 x 2 H2O 3.59281e-05 g/l NiCl2 x 6 H2O 2.39521e-05 g/l Biotin 1.99601e-05 g/l Folic acid 1.99601e-05 g/l H3BO3 5.98802e-06 g/l CuCl2 x 2 H2O 1.99601e-06 g/l Vitamin B12 9.98004e-07 g/l Distilled water

culture temp

@refgrowthtypetemperaturerangeconfidence
1244positivegrowth60thermophilic
67770positivegrowth60thermophilic
69480thermophilic99.326

Physiology and metabolism

oxygen tolerance

@refoxygen toleranceconfidence
1244anaerobe
69480anaerobe99.748

spore formation

  • @ref: 69481
  • spore formation: yes
  • confidence: 90

observation

  • @ref: 67770
  • observation: Production of Lactate from glucose and xylose

metabolite production

  • @ref: 67770
  • Chebi-ID: 24996
  • metabolite: lactate
  • production: yes

Isolation, sampling and environmental information

isolation

  • @ref: 1244
  • sample type: composted cattle manure
  • country: France
  • origin.country: FRA
  • continent: Europe

isolation source categories

Cat1Cat2Cat3
#Engineered#Biodegradation#Composting
#Host#Mammals#Bovinae (Cow, Cattle)
#Host Body Product#Gastrointestinal tract#Feces (Stool)

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: LC037223
  • Sequence Identity:
  • Total samples: 6000
  • soil counts: 1258
  • aquatic counts: 584
  • animal counts: 3737
  • plant counts: 421

Safety information

risk assessment

  • @ref: 1244
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
1244Clostridium stercorarium subsp. thermolacticum 16S ribosomal RNA gene, complete sequenceL091761519ena29351
67770[Clostridium] stercorarium subsp. thermolacticum gene for 16S ribosomal RNA, partial sequence, strain: JCM 9324LC0372231456ena1291049

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Thermoclostridium stercorarium subsp. thermolacticum JCM 9324GCA_001310995contigncbi1291049
66792[Clostridium] stercorarium subsp. thermolacticum JCM 93241291049.3wgspatric1291049
66792Thermoclostridium stercorarium thermolacticum JCM 93242728369666draftimg1291049

GC content

@refGC-contentmethod
124442.3
6777042.3thermal denaturation, midpoint method (Tm)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingyes90no
motileyes71.205no
gram-positiveyes64.244no
anaerobicyes98.918yes
aerobicno98.432yes
halophileno93.713no
spore-formingyes84.873no
glucose-utilyes88.589no
flagellatedno80.359no
thermophileyes99.501no
glucose-fermentno51.892no

External links

@ref: 1244

culture collection no.: DSM 2911, TC 21, JCM 9324, ATCC 43738

straininfo link

  • @ref: 72263
  • straininfo: 47025

literature

  • topic: Metabolism
  • Pubmed-ID: 16454492
  • title: Screening of thermophilic anaerobic bacteria for solid substrate cultivation on lignocellulosic substrates.
  • authors: Chinn MS, Nokes SE, Strobel HJ
  • journal: Biotechnol Prog
  • DOI: 10.1021/bp050163x
  • year: 2006
  • mesh: Acetic Acid/analysis/metabolism, Bacteria, Anaerobic/growth & development/*metabolism, *Bioreactors, Biotechnology/methods, Cellulose/*metabolism, Clostridium/growth & development/metabolism, Clostridium thermocellum/growth & development/metabolism, Ethanol/analysis/metabolism, Hot Temperature, Lactic Acid/analysis/biosynthesis, Lignin/*metabolism, Thermoanaerobacter/growth & development/metabolism, Thermotoga neapolitana/growth & development/metabolism
  • topic2: Stress

Reference

@idauthorscataloguedoi/urltitle
1244Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 2911)https://www.dsmz.de/collection/catalogue/details/culture/DSM-2911
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
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)
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
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
72263Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID47025.1StrainInfo: A central database for resolving microbial strain identifiers