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

Strain identifier

BacDive ID: 2749

Type strain:

Species: Clostridium thermosuccinogenes

Strain Designation: IC

Culture col. no.: DSM 5807

Strain history: <- J. C. Gottschal, Univ. Groningen, The Netherlands; IC <- W. J. Drent {1989}

NCBI tax ID(s): 1121341 (strain), 84032 (species)

SI-ID 48004

DSM 5807

Other strains from Clostridium thermosuccinogenes

C. thermosuccinogenes ID, DSM 5808
C. thermosuccinogenes IE, DSM 5809
C. thermosuccinogenes IA, DSM 5806

Section

Clostridium thermosuccinogenes IC is an anaerobe, spore-forming, thermophilic bacterium that was isolated from beet pulp, sugar refinery.

Gram-positive
spore-forming
anaerobe
thermophilic
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 thermosuccinogenes**
	Full Scientific Name (LPSN)	Clostridium thermosuccinogenes Drent et al. 1995

Synonym

"Pseudoclostridium thermosuccinogenes"

Information on morphological and physiological properties Morphology

[Ref.: #69480]	Gram stain	positive Confidence in %100

Information on culture and growth conditions Culture and growth conditions

[Ref.: #2191]

Culture medium

THERMOCLOSTRIDIUM (A-GÖ) MEDIUM (DSMZ Medium 326)

[Ref.: #2191]

Culture medium growth

[Ref.: #2191]

Culture medium link

Medium recipe at MediaDive

[Ref.: #2191]

Culture medium composition

expand / minimize

[Ref.: #2191]

Culture medium

PSEUDOCLOSTRIDIUM MEDIUM (DSMZ Medium 502)

[Ref.: #2191]

Culture medium growth

[Ref.: #2191]

Culture medium link

Medium recipe at MediaDive

[Ref.: #2191]

Culture medium composition

expand / minimize

	Temperatures	Kind of temperature		Temperature
[Ref.: #2191]			growth	60 °C

[Ref.: #2191]	Temperature range	thermophilic
[Ref.: #69480]	Temperature range	thermophilic Confidence in %91.872

Information on physiology and metabolism Physiology and metabolism

[Ref.: #2191]	Oxygen tolerance	anaerobe
[Ref.: #69480]	Oxygen tolerance	anaerobe Confidence in %99.998

[Ref.: #69480]

Ability of spore formation

yes Confidence in %99.521

	Pathway	Enzyme coverage	Annotated reactions
	Pathway annotation	Computationally determined by
[Ref.: #66794]	anapleurotic synthesis of oxalacetate	100	1 of 1
[Ref.: #66794]	coenzyme A metabolism	100	4 of 4
[Ref.: #66794]	UDP-GlcNAc biosynthesis	100	3 of 3
[Ref.: #66794]	cis-vaccenate biosynthesis	100	2 of 2
[Ref.: #66794]	palmitate biosynthesis	100	22 of 22
[Ref.: #66794]	folate polyglutamylation	100	1 of 1
[Ref.: #66794]	L-lactaldehyde degradation	100	3 of 3
[Ref.: #66794]	formaldehyde oxidation	100	3 of 3
[Ref.: #66794]	glycine betaine biosynthesis	100	5 of 5
[Ref.: #66794]	CDP-diacylglycerol biosynthesis	100	2 of 2
[Ref.: #66794]	pentose phosphate pathway	90.91	10 of 11
[Ref.: #66794]	starch degradation	90	9 of 10
[Ref.: #66794]	threonine metabolism	90	9 of 10
[Ref.: #66794]	aspartate and asparagine metabolism	88.89	8 of 9
[Ref.: #66794]	d-mannose degradation	88.89	8 of 9
[Ref.: #66794]	vitamin B1 metabolism	84.62	11 of 13
[Ref.: #66794]	peptidoglycan biosynthesis	80	12 of 15
[Ref.: #66794]	methylglyoxal degradation	80	4 of 5
[Ref.: #66794]	cellulose degradation	80	4 of 5
[Ref.: #66794]	photosynthesis	78.57	11 of 14
[Ref.: #66794]	valine metabolism	77.78	7 of 9
[Ref.: #66794]	NAD metabolism	77.78	14 of 18
[Ref.: #66794]	chorismate metabolism	77.78	7 of 9
[Ref.: #66794]	degradation of hexoses	77.78	14 of 18
[Ref.: #66794]	acetate fermentation	75	3 of 4
[Ref.: #66794]	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	75	6 of 8
[Ref.: #66794]	C4 and CAM-carbon fixation	75	6 of 8
[Ref.: #66794]	ppGpp biosynthesis	75	3 of 4
[Ref.: #66794]	cardiolipin biosynthesis	71.43	5 of 7
[Ref.: #66794]	glycolysis	70.59	12 of 17
[Ref.: #66794]	Entner Doudoroff pathway	70	7 of 10
[Ref.: #66794]	methionine metabolism	69.23	18 of 26
[Ref.: #66794]	phenylalanine metabolism	69.23	9 of 13
[Ref.: #66794]	degradation of sugar alcohols	68.75	11 of 16
[Ref.: #66794]	glutamate and glutamine metabolism	67.86	19 of 28
[Ref.: #66794]	acetoin degradation	66.67	2 of 3
[Ref.: #66794]	pyrimidine metabolism	66.67	30 of 45
[Ref.: #66794]	serine metabolism	66.67	6 of 9
[Ref.: #66794]	octane oxidation	66.67	2 of 3
[Ref.: #66794]	selenocysteine biosynthesis	66.67	4 of 6
[Ref.: #66794]	purine metabolism	64.89	61 of 94
[Ref.: #66794]	tetrahydrofolate metabolism	64.29	9 of 14
[Ref.: #66794]	d-xylose degradation	63.64	7 of 11
[Ref.: #66794]	gluconeogenesis	62.5	5 of 8
[Ref.: #66794]	ketogluconate metabolism	62.5	5 of 8
[Ref.: #66794]	isoleucine metabolism	62.5	5 of 8
[Ref.: #66794]	oxidative phosphorylation	61.54	56 of 91
[Ref.: #66794]	degradation of pentoses	60.71	17 of 28
[Ref.: #66794]	metabolism of amino sugars and derivatives	60	3 of 5
[Ref.: #66794]	glycogen metabolism	60	3 of 5
[Ref.: #66794]	hydrogen production	60	3 of 5
[Ref.: #66794]	myo-inositol biosynthesis	60	6 of 10
[Ref.: #66794]	isoprenoid biosynthesis	57.69	15 of 26
[Ref.: #66794]	reductive acetyl coenzyme A pathway	57.14	4 of 7
[Ref.: #66794]	citric acid cycle	57.14	8 of 14
[Ref.: #66794]	propanol degradation	57.14	4 of 7
[Ref.: #66794]	ubiquinone biosynthesis	57.14	4 of 7
[Ref.: #66794]	lipid A biosynthesis	55.56	5 of 9
[Ref.: #66794]	histidine metabolism	55.17	16 of 29
[Ref.: #66794]	alanine metabolism	55.17	16 of 29
[Ref.: #66794]	arginine metabolism	54.17	13 of 24
[Ref.: #66794]	tryptophan metabolism	52.63	20 of 38
[Ref.: #66794]	non-pathway related	52.63	20 of 38
[Ref.: #66794]	dTDPLrhamnose biosynthesis	50	4 of 8
[Ref.: #66794]	suberin monomers biosynthesis	50	1 of 2
[Ref.: #66794]	ethanol fermentation	50	1 of 2
[Ref.: #66794]	adipate degradation	50	1 of 2
[Ref.: #66794]	butanoate fermentation	50	2 of 4
[Ref.: #66794]	lactate fermentation	50	2 of 4
[Ref.: #66794]	CMP-KDO biosynthesis	50	2 of 4
[Ref.: #66794]	toluene degradation	50	2 of 4
[Ref.: #66794]	kanosamine biosynthesis II	50	1 of 2
[Ref.: #66794]	glycolate and glyoxylate degradation	50	3 of 6
[Ref.: #66794]	sulfopterin metabolism	50	2 of 4
[Ref.: #66794]	ribulose monophosphate pathway	50	1 of 2
[Ref.: #66794]	propionate fermentation	50	5 of 10
[Ref.: #66794]	quinate degradation	50	1 of 2
[Ref.: #66794]	glycine metabolism	50	5 of 10
[Ref.: #66794]	glutathione metabolism	50	7 of 14
[Ref.: #66794]	phenylmercury acetate degradation	50	1 of 2
[Ref.: #66794]	biotin biosynthesis	50	2 of 4
[Ref.: #66794]	glycogen biosynthesis	50	2 of 4
[Ref.: #66794]	polyamine pathway	47.83	11 of 23
[Ref.: #66794]	leucine metabolism	46.15	6 of 13
[Ref.: #66794]	metabolism of disaccharids	45.45	5 of 11
[Ref.: #66794]	vitamin B6 metabolism	45.45	5 of 11
[Ref.: #66794]	proline metabolism	45.45	5 of 11
[Ref.: #66794]	lipid metabolism	45.16	14 of 31
[Ref.: #66794]	CO2 fixation in Crenarchaeota	44.44	4 of 9
[Ref.: #66794]	cysteine metabolism	44.44	8 of 18
[Ref.: #66794]	degradation of sugar acids	44	11 of 25
[Ref.: #66794]	lysine metabolism	42.86	18 of 42
[Ref.: #66794]	4-hydroxyphenylacetate degradation	40	4 of 10
[Ref.: #66794]	lipoate biosynthesis	40	2 of 5
[Ref.: #66794]	arachidonate biosynthesis	40	2 of 5
[Ref.: #66794]	flavin biosynthesis	40	6 of 15
[Ref.: #66794]	urea cycle	38.46	5 of 13
[Ref.: #66794]	tyrosine metabolism	35.71	5 of 14
[Ref.: #66794]	acetyl CoA biosynthesis	33.33	1 of 3
[Ref.: #66794]	IAA biosynthesis	33.33	1 of 3
[Ref.: #66794]	nitrate assimilation	33.33	3 of 9
[Ref.: #66794]	molybdenum cofactor biosynthesis	33.33	3 of 9
[Ref.: #66794]	degradation of aromatic, nitrogen containing compounds	33.33	4 of 12
[Ref.: #66794]	aclacinomycin biosynthesis	28.57	2 of 7
[Ref.: #66794]	cholesterol biosynthesis	27.27	3 of 11
[Ref.: #66794]	dolichyl-diphosphooligosaccharide biosynthesis	27.27	3 of 11
[Ref.: #66794]	ascorbate metabolism	27.27	6 of 22
[Ref.: #66794]	cyclohexanol degradation	25	1 of 4
[Ref.: #66794]	androgen and estrogen metabolism	25	4 of 16
[Ref.: #66794]	vitamin B12 metabolism	23.53	8 of 34
[Ref.: #66794]	sulfate reduction	23.08	3 of 13
[Ref.: #66794]	phosphatidylethanolamine bioynthesis	23.08	3 of 13
[Ref.: #66794]	phenylpropanoid biosynthesis	23.08	3 of 13
[Ref.: #66794]	heme metabolism	21.43	3 of 14
		Only first 10 entries are displayed. Click here to see all.

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

[Ref.: #2191]	Sample type/isolated from	beet pulp, sugar refinery
[Ref.: #2191]	Country	Netherlands
[Ref.: #2191]	Country ISO 3 Code	NLD
[Ref.: #2191]	Continent	Europe
* marker position based on {}

Isolation sources categories

#Host Body-Site

#Plant

#Fruit (Seed)

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence Y18180 (>99% sequence identity) for Pseudoclostridium thermosuccinogenes subclade from Microbeatlas

Aquatic Samples	513
Soil Samples	1800
Animal Samples	446
Plant Samples	638
Total Samples	3397

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

[Ref.: #2191]

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.: #2191]	Clostridium thermosuccinogenes 16S rRNA gene, partial, strain DSM 5807	Y18180	1640	ENA	84032 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Pseudoclostridium thermosuccinogenes DSM 5807	GCA_002896855	complete	GenBank	84032 tax ID	*
[Ref.: #66792]	[Clostridium] thermosuccinogenes strain DSM 5807	84032.3	complete	PATRIC	84032 tax ID	*
[Ref.: #66792]	Pseudoclostridium thermosuccinogenes DSM 5807	2795385491	complete	JGI IMG/M	84032 tax ID	*

[Ref.: #2191]

GC-content

35.9 mol%

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: Pseudoclostridium thermosuccinogenes DSM 5807 NCBI: GCA_002896855.1
[Ref.: #69481]	spore-forming	yes	61	no

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Pseudoclostridium thermosuccinogenes DSM 5807 NCBI: GCA_002896855.1
[Ref.: #69480]	flagellated	no	72.075	no
[Ref.: #69480]	gram-positive	yes	66.417	no
[Ref.: #69480]	anaerobic	yes	99.51	yes
[Ref.: #69480]	halophile	no	94.628	no
[Ref.: #69480]	spore-forming	yes	82.36	no
[Ref.: #69480]	glucose-util	yes	84.663	no
[Ref.: #69480]	aerobic	no	99.222	yes
[Ref.: #69480]	thermophile	yes	99.56	yes
[Ref.: #69480]	motile	yes	73.416	no
[Ref.: #69480]	glucose-ferment	yes	60.102	no

Availability in culture collections External links

[Ref.: #2191]

Culture collection no.

DSM 5807

[Ref.: #72279]

SI-ID 48004

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Gracilibacter thermotolerans gen. nov., sp. nov., an anaerobic, thermotolerant bacterium from a constructed wetland receiving acid sulfate water.	Lee YJ, Romanek CS, Mills GL, Davis RC, Whitman WB, Wiegel J	Int J Syst Evol Microbiol	10.1099/ijs.0.64040-0	2006	*

References

#2191

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 5807

#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 )

#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) .

#66794

Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg: BRENDA, the ELIXIR core data resource in 2021: new developments and updates. Nucleic Acids Res. 49: D498 - D508 2020 ( DOI 10.1093/nar/gkaa1025 , PubMed 33211880 )

#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 )

#72279

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-ID48004.1 )

* These data were automatically processed and therefore are not curated

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Pseudoclostridium thermosuccinogenes DSM 5807

Pseudoclostridium thermosuccinogenes DSM 5807

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