Strain identifier

BacDive ID: 2836

Type strain: Yes

Species: Clostridium drakei

Strain Designation: SL1

Strain history: <- K. Küsel, University of Bayreuth, Department of Ecological Microbiology, Bayreuth, Germany; SL1 (Clostridium scatologenes) <- K. Küsel {1996}

NCBI tax ID(s): 332101 (species)

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General

@ref: 4801

BacDive-ID: 2836

DSM-Number: 12750

keywords: genome sequence, 16S sequence, Bacteria, anaerobe, spore-forming, mesophilic, Gram-negative, motile, rod-shaped

description: Clostridium drakei SL1 is an anaerobe, spore-forming, mesophilic bacterium that was isolated from acidic coal mine pond.

NCBI tax id

  • NCBI tax id: 332101
  • Matching level: species

strain history

  • @ref: 4801
  • history: <- K. Küsel, University of Bayreuth, Department of Ecological Microbiology, Bayreuth, Germany; SL1 (Clostridium scatologenes) <- K. Küsel {1996}

doi: 10.13145/bacdive2836.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/bacillota
  • domain: Bacteria
  • phylum: Bacillota
  • class: Clostridia
  • order: Eubacteriales
  • family: Clostridiaceae
  • genus: Clostridium
  • species: Clostridium drakei
  • full scientific name: Clostridium drakei Liou et al. 2005

@ref: 4801

domain: Bacteria

phylum: Firmicutes

class: Clostridia

order: Clostridiales

family: Clostridiaceae

genus: Clostridium

species: Clostridium drakei

full scientific name: Clostridium drakei Liou et al. 2005

strain designation: SL1

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
43392negative3-4 µm0.6 µmrod-shapedyes
69480yes96.373
69480positive99.999

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
4801CHOPPED MEAT MEDIUM WITH CARBOHYDRATES (DSMZ Medium 110)yeshttps://mediadive.dsmz.de/medium/110Name: CHOPPED MEAT MEDIUM WITH CARBOHYDRATES (DSMZ Medium 110) Composition: Ground beef 500.0 g/l Casitone 30.0 g/l Agar 15.0 g/l K2HPO4 5.0 g/l Yeast extract 5.0 g/l D-Glucose 4.0 g/l Starch 1.0 g/l Maltose 1.0 g/l Cellobiose 1.0 g/l L-Cysteine HCl 0.5 g/l Ethanol 0.19 g/l Vitamin K3 0.05 g/l Hemin 0.005 g/l Sodium resazurin 0.0005 g/l Vitamin K1 NaOH Distilled water
4801PY + X MEDIUM (DSMZ Medium 104b)yeshttps://mediadive.dsmz.de/medium/104bName: PY + X MEDIUM (DSMZ Medium 104b) Composition: Yeast extract 10.0 g/l D-Glucose 5.0 g/l Trypticase peptone 5.0 g/l Meat peptone 5.0 g/l L-Cysteine HCl x H2O 0.5 g/l NaHCO3 0.4 g/l NaCl 0.08 g/l KH2PO4 0.04 g/l K2HPO4 0.04 g/l MgSO4 x 7 H2O 0.02 g/l CaCl2 x 2 H2O 0.01 g/l Sodium resazurin 0.0005 g/l Distilled water
43392Basal mediumyes25 ml mineral solution, 10 ml vitamin solution, 10 ml trace metal solution, 1 g yeast extract, 10 g MES, with the pH adjusted to 6.1; and 6 ml cysteine sul?de reducing agent

culture temp

@refgrowthtypetemperaturerange
4801positivegrowth30mesophilic
43392positivegrowth18-42
43392positiveoptimum30-37mesophilic

culture pH

@refabilitytypepH
43392positiveoptimum5.4-7.5
43392positivegrowth4.6-7.8

Physiology and metabolism

oxygen tolerance

@refoxygen toleranceconfidence
4801anaerobe
43392obligate anaerobe
69480anaerobe99.632

spore formation

@refspore formationconfidence
43392yes
69481yes100
69480yes100

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
4339216449alanine+growth
4339227613amygdalin-growth
4339229016arginine+growth
4339222653asparagine+growth
4339235391aspartate+growth
4339217750betaine+growth
4339228885butanol+growth
4339216526carbon dioxide+growth
4339217245carbon monoxide+growth
43392casamino acids+growth
4339217057cellobiose+growth
4339262968cellulose+growth
4339215354choline+growth
4339216947citrate+growth
4339217108D-arabinose-growth
4339218276dihydrogen+growth
4339224996lactate+growth
4339225115malate+growth
433924853esculin-hydrolysis
4339216236ethanol+growth
4339229749ferulate+assimilation
4339228757fructose+growth
4339233984fucose+growth
4339229806fumarate+growth
4339228260galactose+growth
433925291gelatin-hydrolysis
4339224265gluconate+growth
4339217234glucose+growth
4339217234glucose+fermentation
4339217754glycerol+growth
4339227570histidine+growth
4339217268myo-inositol+growth
4339230849L-arabinose+growth
4339229985L-glutamate+growth
4339217716lactose-growth
4339217306maltose-growth
4339229864mannitol+growth
4339237684mannose+growth
433926731melezitose+growth
4339228053melibiose-growth
4339217790methanol-growth
4339217632nitrate-reduction
4339217309pectin-growth
4339228831propanol+growth
4339216634raffinose-growth
4339226546rhamnose+growth
4339233942ribose+growth
4339217822serine+growth
4339230911sorbitol-growth
4339228017starch+growth
4339230031succinate-growth
4339217992sucrose+growth
43392132111syringate+growth
4339227082trehalose-growth
4339216632vanillate+assimilation
4339218222xylose+growth

metabolite production

@refChebi-IDmetaboliteproduction
4339230089acetateyes
4339228885butanolyes
4339217968butyrateyes
4339216236ethanolyes
4339215688acetoinno
4339235581indoleno

metabolite tests

@refChebi-IDmetabolitemethylred-testvoges-proskauer-test
4339217234glucose+
4339215688acetoin-

Isolation, sampling and environmental information

isolation

@refsample typecountryorigin.countrycontinentgeographic location
4801acidic coal mine pondGermanyDEUEurope
43392sediment collected from an acidic coal-mine pondGermanyDEUEuropeEast-central Germany

isolation source categories

Cat1Cat2Cat3
#Engineered#Other#Mine
#Environmental#Aquatic#Pond (small)
#Condition#Acidic
#Environmental#Aquatic#Sediment

taxonmaps

  • @ref: 69479
  • File name: preview.99_3450.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_34;96_1801;97_2159;98_2649;99_3450&stattab=map
  • Last taxonomy: Clostridium
  • 16S sequence: Y18813
  • Sequence Identity:
  • Total samples: 12042
  • soil counts: 5169
  • aquatic counts: 4051
  • animal counts: 2029
  • plant counts: 793

Safety information

risk assessment

  • @ref: 4801
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 4801
  • description: Clostridium drakei partial 16S rRNA gene, type strain SL1T
  • accession: Y18813
  • length: 1491
  • database: ena
  • NCBI tax ID: 332101

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Clostridium drakei SL1GCA_003096175completencbi332101
66792Clostridium drakei SL1GCA_000633595scaffoldncbi332101
66792Clostridium drakei SL12574180002draftimg332101

GC content

@refGC-contentmethod
480130.3high performance liquid chromatography (HPLC)
4339230-32high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingyes100no
flagellatedno58.254no
gram-positiveno66.464yes
anaerobicyes97.842no
halophileno96.501no
spore-formingyes94.844no
glucose-utilyes90.037yes
aerobicno97.805yes
thermophileno97.07yes
motileyes83.354no
glucose-fermentyes64.412yes

External links

@ref: 4801

culture collection no.: DSM 12750, ATCC BAA 623

straininfo link

  • @ref: 72360
  • straininfo: 49349

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny16166714Clostridium carboxidivorans sp. nov., a solvent-producing clostridium isolated from an agricultural settling lagoon, and reclassification of the acetogen Clostridium scatologenes strain SL1 as Clostridium drakei sp. nov.Liou JS, Balkwill DL, Drake GR, Tanner RSInt J Syst Evol Microbiol10.1099/ijs.0.63482-02005Acetic Acid/*metabolism, *Agriculture, Bacterial Typing Techniques, Carbon Monoxide/*metabolism, Clostridium/*classification/genetics/growth & development/isolation & purification, DNA, Bacterial/analysis, DNA, Ribosomal/analysis, Genes, rRNA, Geologic Sediments/*microbiology, Molecular Sequence Data, Nucleic Acid Hybridization, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Solvents/*metabolism, *Water MicrobiologyMetabolism
Phylogeny35353674Clostridium muellerianum sp. nov., a carbon monoxide-oxidizing acetogen isolated from old hay.Doyle DA, Smith PR, Lawson PA, Tanner RSInt J Syst Evol Microbiol10.1099/ijsem.0.0052972022Bacterial Typing Techniques, Base Composition, *Carbon Monoxide, Clostridium, DNA, Bacterial/genetics, *Fatty Acids/chemistry, Oxidation-Reduction, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNATranscriptome

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
4801Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 12750)https://www.dsmz.de/collection/catalogue/details/culture/DSM-12750
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
43392Jack S.-C. Liou, David L. Balkwill, Gwendolyn R. Drake, Ralph S. Tanner10.1099/ijs.0.63482-0Clostridium carboxidivorans sp. nov., a solvent-producing clostridium isolated from an agricultural settling lagoon, and reclassification of the acetogen Clostridium scatologenes strain SL1 as Clostridium drakei sp. nov.IJSEM 55: 2085-2091 200516166714
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)
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
72360Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID49349.1StrainInfo: A central database for resolving microbial strain identifiers