Name: Clostridium drakei SL1
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 2836

Type strain:

Species: Clostridium drakei

Strain Designation: SL1

Culture col. no.: DSM 12750, ATCC BAA-623

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)

SI-ID 49349

DSM 12750, ATCC BAA-623

Other strains from Clostridium drakei

C. drakei FP, DSM 14770

Section

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

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

Information on the name and the taxonomic classification. Name and taxonomic classification

	Last LPSN update	14-12-2023 (DD-MM-YYYY)
	Domain	"Bacteria"
	Phylum	*Bacillota*
	Class	*Clostridia*
	Order	*Eubacteriales*
	Family	*Clostridiaceae*
	Genus	*Clostridium*
	Species	**Clostridium drakei**
	Full Scientific Name (LPSN)	Clostridium drakei Liou et al. 2005

Information on morphological and physiological properties Morphology

[Ref.: #43392]	Gram stain	negative
[Ref.: #69480]	Gram stain	positive Confidence in %99.999

[Ref.: #43392]	Cell length	3-4 µm

[Ref.: #43392]	Cell width	0.6 µm

[Ref.: #43392]	Cell shape	rod-shaped

[Ref.: #43392]	Motility	yes
[Ref.: #69480]	Motility	yes Confidence in %96.373

Information on culture and growth conditions Culture and growth conditions

[Ref.: #4801]

Culture medium

CHOPPED MEAT MEDIUM WITH CARBOHYDRATES (DSMZ Medium 110)

[Ref.: #4801]

Culture medium growth

[Ref.: #4801]

Culture medium link

Medium recipe at MediaDive

[Ref.: #4801]

Culture medium composition

expand / minimize

[Ref.: #4801]

Culture medium

PY + X MEDIUM (DSMZ Medium 104b)

[Ref.: #4801]

Culture medium growth

[Ref.: #4801]

Culture medium link

Medium recipe at MediaDive

[Ref.: #4801]

Culture medium composition

expand / minimize

[Ref.: #43392]

Culture medium

Basal medium

[Ref.: #43392]

Culture medium growth

[Ref.: #43392]

Culture medium composition

expand / minimize

		Temperature
[Ref.: #4801]	growth	30 °C
[Ref.: #43392]	growth	18-42 °C
[Ref.: #43392]	optimum	30-37 °C

[Ref.: #4801]	Temperature range	mesophilic
[Ref.: #43392]	Temperature range	mesophilic

	pH	Kind of pH		pH
[Ref.: #43392]			optimum	5.4-7.5
[Ref.: #43392]			growth	4.6-7.8

Information on physiology and metabolism Physiology and metabolism

[Ref.: #4801]	Oxygen tolerance	anaerobe
[Ref.: #43392]	Oxygen tolerance	obligate anaerobe
[Ref.: #69480]	Oxygen tolerance	anaerobe Confidence in %99.632

[Ref.: #43392]	Ability of spore formation	yes
[Ref.: #69481]	Ability of spore formation	yes Confidence in %100
[Ref.: #69480]	Ability of spore formation	yes Confidence in %100

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #43392]	alanine ChEBI	+	growth
[Ref.: #43392]	amygdalin ChEBI	-	growth
[Ref.: #43392]	arginine ChEBI	+	growth
[Ref.: #43392]	asparagine ChEBI	+	growth
[Ref.: #43392]	aspartate ChEBI	+	growth
[Ref.: #43392]	betaine ChEBI	+	growth
[Ref.: #43392]	butanol ChEBI	+	growth
[Ref.: #43392]	carbon dioxide ChEBI	+	growth
[Ref.: #43392]	carbon monoxide ChEBI	+	growth
[Ref.: #43392]	casamino acids	+	growth
[Ref.: #43392]	cellobiose ChEBI	+	growth
[Ref.: #43392]	cellulose ChEBI	+	growth
[Ref.: #43392]	choline ChEBI	+	growth
[Ref.: #43392]	citrate ChEBI	+	growth
[Ref.: #43392]	D-arabinose ChEBI	-	growth
[Ref.: #43392]	dihydrogen ChEBI	+	growth
[Ref.: #43392]	esculin ChEBI	-	hydrolysis
[Ref.: #43392]	ethanol ChEBI	+	growth
[Ref.: #43392]	ferulate ChEBI	+	assimilation
[Ref.: #43392]	fructose ChEBI	+	growth
[Ref.: #43392]	fucose ChEBI	+	growth
[Ref.: #43392]	fumarate ChEBI	+	growth
[Ref.: #43392]	galactose ChEBI	+	growth
[Ref.: #43392]	gelatin ChEBI	-	hydrolysis
[Ref.: #43392]	gluconate ChEBI	+	growth
[Ref.: #43392]	glucose ChEBI	+	growth
[Ref.: #43392]	glucose ChEBI	+	fermentation
[Ref.: #43392]	glycerol ChEBI	+	growth
[Ref.: #43392]	histidine ChEBI	+	growth
[Ref.: #43392]	L-arabinose ChEBI	+	growth
[Ref.: #43392]	L-glutamate ChEBI	+	growth
[Ref.: #43392]	lactate ChEBI	+	growth
[Ref.: #43392]	lactose ChEBI	-	growth
[Ref.: #43392]	malate ChEBI	+	growth
[Ref.: #43392]	maltose ChEBI	-	growth
[Ref.: #43392]	mannitol ChEBI	+	growth
[Ref.: #43392]	mannose ChEBI	+	growth
[Ref.: #43392]	melezitose ChEBI	+	growth
[Ref.: #43392]	melibiose ChEBI	-	growth
[Ref.: #43392]	methanol ChEBI	-	growth
[Ref.: #43392]	myo-inositol ChEBI	+	growth
[Ref.: #43392]	nitrate ChEBI	-	reduction
[Ref.: #43392]	pectin ChEBI	-	growth
[Ref.: #43392]	propanol ChEBI	+	growth
[Ref.: #43392]	raffinose ChEBI	-	growth
[Ref.: #43392]	rhamnose ChEBI	+	growth
[Ref.: #43392]	ribose ChEBI	+	growth
[Ref.: #43392]	serine ChEBI	+	growth
[Ref.: #43392]	sorbitol ChEBI	-	growth
[Ref.: #43392]	starch ChEBI	+	growth
[Ref.: #43392]	succinate ChEBI	-	growth
[Ref.: #43392]	sucrose ChEBI	+	growth
[Ref.: #43392]	syringate ChEBI	+	growth
[Ref.: #43392]	trehalose ChEBI	-	growth
[Ref.: #43392]	vanillate ChEBI	+	assimilation
[Ref.: #43392]	xylose ChEBI	+	growth
	Only first 10 entries are displayed. Click here to see all.

	Metabolite	Production
[Ref.: #43392]	acetate ChEBI	yes
[Ref.: #43392]	acetoin ChEBI	no
[Ref.: #43392]	butanol ChEBI	yes
[Ref.: #43392]	butyrate ChEBI	yes
[Ref.: #43392]	ethanol ChEBI	yes
[Ref.: #43392]	indole ChEBI	no

	Physiological tests	Metabolite	Voges-Proskauer-test	Methylred-test
[Ref.: #43392]		acetoin ChEBI	-
[Ref.: #43392]		glucose ChEBI		+

Information on isolation source, the sampling and environmental conditions Isolation, sampling and environmental information

[Ref.: #4801]	Sample type/isolated from	acidic coal mine pond
[Ref.: #4801]	Country	Germany
[Ref.: #4801]	Country ISO 3 Code	DEU
[Ref.: #4801]	Continent	Europe

[Ref.: #43392]	Sample type/isolated from	sediment collected from an acidic coal-mine pond
[Ref.: #43392]	Geographic location (country and/or sea, region)	East-central Germany
[Ref.: #43392]	Country	Germany
[Ref.: #43392]	Country ISO 3 Code	DEU
[Ref.: #43392]	Continent	Europe
* marker position based on {}

Isolation sources categories

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

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence Y18813 (>99% sequence identity) for Clostridium from Microbeatlas

Aquatic Samples	4051
Soil Samples	5169
Animal Samples	2029
Plant Samples	793
Total Samples	12042

Information on possible application of the strain and its possible interaction with e.g. potential hosts Safety information

[Ref.: #4801]

Biosafety level

Risk group (German classification)
According to TRBA 466

Information on genomic background e.g. entries in nucleic sequence databass Sequence information

16S Sequence information:

	Sequence accession description	Seq. accession number	Sequence length (bp)	Sequence database	Associated NCBI tax ID
[Ref.: #4801]	Clostridium drakei partial 16S rRNA gene, type strain SL1T	Y18813	1491	ENA	332101 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Clostridium drakei SL1	GCA_003096175	complete	GenBank	332101 tax ID	*
[Ref.: #66792]	Clostridium drakei SL1	GCA_000633595	scaffold	GenBank	332101 tax ID	*
[Ref.: #66792]	Clostridium drakei SL1	2574180002	draft	JGI IMG/M	332101 tax ID	*

[Ref.: #4801]	GC-content	30.3 mol%	high performance liquid chromatography (HPLC)
[Ref.: #43392]	GC-content	30-32 mol%	high performance liquid chromatography (HPLC)

Data predicted using genome information as a basis Genome-based predictions

	Trait	Prediction	Confidence in %	In training data
	Predictions from GenomeNet Sporulation v. 1 based on: Clostridium drakei SL1 NCBI: GCA_003096175.1
[Ref.: #69481]	spore-forming	yes	100	no

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Clostridium drakei SL1 NCBI: GCA_003096175.1
[Ref.: #69480]	flagellated	no	58.254	no
[Ref.: #69480]	gram-positive	no	66.464	yes
[Ref.: #69480]	anaerobic	yes	97.842	no
[Ref.: #69480]	halophile	no	96.501	no
[Ref.: #69480]	spore-forming	yes	94.844	no
[Ref.: #69480]	glucose-util	yes	90.037	yes
[Ref.: #69480]	aerobic	no	97.805	yes
[Ref.: #69480]	thermophile	no	97.07	yes
[Ref.: #69480]	motile	yes	83.354	no
[Ref.: #69480]	glucose-ferment	yes	64.412	yes

Availability in culture collections External links

[Ref.: #4801]

Culture collection no.

DSM 12750, ATCC BAA-623

[Ref.: #72360]

SI-ID 49349

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Clostridium muellerianum sp. nov., a carbon monoxide-oxidizing acetogen isolated from old hay.	Doyle DA, Smith PR, Lawson PA, Tanner RS	Int J Syst Evol Microbiol	10.1099/ijsem.0.005297	2022	*
Phylogeny	Clostridium 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 RS	Int J Syst Evol Microbiol	10.1099/ijs.0.63482-0	2005	*

References

#4801

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 12750

#20215

Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M.: List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ. IJSEM ( DOI 10.1099/ijsem.0.004332 )

#43392

Jack S.-C. Liou, David L. Balkwill, Gwendolyn R. Drake, Ralph S. Tanner: Clostridium 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 2005 ( DOI 10.1099/ijs.0.63482-0 , PubMed 16166714 )

#66792

Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann: Automatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) .

#69479

João 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.: MicrobeAtlas 1.0 beta .

#69480

Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann: Predictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) .

#69481

Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch: Predictions based on the model GenomeNet Sporulation v. 1 . ( DOI 10.21203/rs.3.rs-2527258/v1 )

#72360

Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.: StrainInfo: A central database for resolving microbial strain identifiers . ( DOI 10.60712/SI-ID49349.1 )

* These data were automatically processed and therefore are not curated

Change proposal

You found an error in BacDive? Please tell us about it!

Note that changes will be reviewed and judged. If your changes are legitimate, changes will occur within the next BacDive update. Only proposed changes supported by the according reference will be reviewed. The BacDive team reserves the right to reject proposed changes.

Search for species Clostridium drakei in external resources:
SILVA
BRENDA
PANGAEA
StrainInfo
GBIF