Name: Clostridium celatum GD-1
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 2566

Type strain:

Species: Clostridium celatum

Strain Designation: GD-1, 10039

Culture col. no.: DSM 1785, ATCC 27791, VPI 8759-1, JCM 1394, BCRC 14521, NCTC 10947, NCTC 12746, CIP 104316

Strain history: CIP <- 1994, J.P. Carlier, Inst. Pasteur, Paris, France: strain 10039 <- ATCC <- L.V. Holdeman: strain VPI 8759-1

NCBI tax ID(s): 545697 (strain), 36834 (species)

SI-ID 39177

ATCC 27791, DSM 1785, JCM 1394, CCRC 14521, NCTC 10947, NCTC 12746, BCRC 14521, CIP 104316

Section

Clostridium celatum GD-1 is an anaerobe, spore-forming, mesophilic bacterium that was isolated from human faeces.

Gram-positive
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 celatum**
	Full Scientific Name (LPSN)	Clostridium celatum Hauschild and Holdeman 1974 (Approved Lists 1980)

Information on morphological and physiological properties Morphology

[Ref.: #117229]	Gram stain	positive
[Ref.: #69480]	Gram stain	positive Confidence in %100

[Ref.: #117229]	Cell shape	rod-shaped

[Ref.: #117229]	Motility	no

Information on culture and growth conditions Culture and growth conditions

[Ref.: #652]

Culture medium

CHOPPED MEAT MEDIUM WITH CARBOHYDRATES (DSMZ Medium 110)

[Ref.: #652]

Culture medium growth

[Ref.: #652]

Culture medium link

Medium recipe at MediaDive

[Ref.: #652]

Culture medium composition

expand / minimize

[Ref.: #37172]

Culture medium

MEDIUM 224 - for anaerobic bacteria TGV

[Ref.: #37172]

Culture medium growth

[Ref.: #37172]

Culture medium composition

expand / minimize

[Ref.: #117229]

Culture medium

CIP Medium 20

[Ref.: #117229]

Culture medium growth

[Ref.: #117229]

Culture medium link

Medium recipe provided by DSMZ

		Temperature
[Ref.: #652]	growth	37 °C
[Ref.: #37172]	growth	37 °C
[Ref.: #67770]	growth	37 °C

[Ref.: #652]	Temperature range	mesophilic
[Ref.: #37172]	Temperature range	mesophilic
[Ref.: #67770]	Temperature range	mesophilic

Information on physiology and metabolism Physiology and metabolism

[Ref.: #652]	Oxygen tolerance	anaerobe
[Ref.: #69480]	Oxygen tolerance	anaerobe Confidence in %99.436

[Ref.: #69481]	Ability of spore formation	yes Confidence in %100
[Ref.: #69480]	Ability of spore formation	yes Confidence in %99.999

	Enzymes	Enzyme	EC number
[Ref.: #67770]		urease	3.5.1.5

	Pathway	Enzyme coverage	Annotated reactions
	Pathway annotation	Computationally determined by
[Ref.: #66794]	cellulose degradation	100	5 of 5
[Ref.: #66794]	C4 and CAM-carbon fixation	100	8 of 8
[Ref.: #66794]	gluconeogenesis	100	8 of 8
[Ref.: #66794]	adipate degradation	100	2 of 2
[Ref.: #66794]	ppGpp biosynthesis	100	4 of 4
[Ref.: #66794]	coenzyme A metabolism	100	4 of 4
[Ref.: #66794]	teichoic acid biosynthesis	100	1 of 1
[Ref.: #66794]	CDP-diacylglycerol biosynthesis	100	2 of 2
[Ref.: #66794]	UDP-GlcNAc biosynthesis	100	3 of 3
[Ref.: #66794]	palmitate biosynthesis	100	22 of 22
[Ref.: #66794]	folate polyglutamylation	100	1 of 1
[Ref.: #66794]	suberin monomers biosynthesis	100	2 of 2
[Ref.: #66794]	anapleurotic synthesis of oxalacetate	100	1 of 1
[Ref.: #66794]	L-lactaldehyde degradation	100	3 of 3
[Ref.: #66794]	cis-vaccenate biosynthesis	100	2 of 2
[Ref.: #66794]	starch degradation	90	9 of 10
[Ref.: #66794]	chorismate metabolism	88.89	8 of 9
[Ref.: #66794]	pyrimidine metabolism	88.89	40 of 45
[Ref.: #66794]	serine metabolism	88.89	8 of 9
[Ref.: #66794]	valine metabolism	88.89	8 of 9
[Ref.: #66794]	reductive acetyl coenzyme A pathway	85.71	6 of 7
[Ref.: #66794]	ubiquinone biosynthesis	85.71	6 of 7
[Ref.: #66794]	vitamin B1 metabolism	84.62	11 of 13
[Ref.: #66794]	purine metabolism	84.04	79 of 94
[Ref.: #66794]	hydrogen production	80	4 of 5
[Ref.: #66794]	Entner Doudoroff pathway	80	8 of 10
[Ref.: #66794]	glycogen metabolism	80	4 of 5
[Ref.: #66794]	peptidoglycan biosynthesis	80	12 of 15
[Ref.: #66794]	threonine metabolism	80	8 of 10
[Ref.: #66794]	metabolism of amino sugars and derivatives	80	4 of 5
[Ref.: #66794]	alanine metabolism	79.31	23 of 29
[Ref.: #66794]	photosynthesis	78.57	11 of 14
[Ref.: #66794]	aspartate and asparagine metabolism	77.78	7 of 9
[Ref.: #66794]	phenylalanine metabolism	76.92	10 of 13
[Ref.: #66794]	urea cycle	76.92	10 of 13
[Ref.: #66794]	acetate fermentation	75	3 of 4
[Ref.: #66794]	biotin biosynthesis	75	3 of 4
[Ref.: #66794]	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	75	6 of 8
[Ref.: #66794]	glycogen biosynthesis	75	3 of 4
[Ref.: #66794]	flavin biosynthesis	73.33	11 of 15
[Ref.: #66794]	NAD metabolism	72.22	13 of 18
[Ref.: #66794]	cardiolipin biosynthesis	71.43	5 of 7
[Ref.: #66794]	glutamate and glutamine metabolism	71.43	20 of 28
[Ref.: #66794]	glycolysis	70.59	12 of 17
[Ref.: #66794]	molybdenum cofactor biosynthesis	66.67	6 of 9
[Ref.: #66794]	CO2 fixation in Crenarchaeota	66.67	6 of 9
[Ref.: #66794]	d-mannose degradation	66.67	6 of 9
[Ref.: #66794]	nitrate assimilation	66.67	6 of 9
[Ref.: #66794]	formaldehyde oxidation	66.67	2 of 3
[Ref.: #66794]	enterobactin biosynthesis	66.67	2 of 3
[Ref.: #66794]	acetoin degradation	66.67	2 of 3
[Ref.: #66794]	octane oxidation	66.67	2 of 3
[Ref.: #66794]	methionine metabolism	65.38	17 of 26
[Ref.: #66794]	heme metabolism	64.29	9 of 14
[Ref.: #66794]	tetrahydrofolate metabolism	64.29	9 of 14
[Ref.: #66794]	d-xylose degradation	63.64	7 of 11
[Ref.: #66794]	non-pathway related	63.16	24 of 38
[Ref.: #66794]	oxidative phosphorylation	62.64	57 of 91
[Ref.: #66794]	isoleucine metabolism	62.5	5 of 8
[Ref.: #66794]	histidine metabolism	62.07	18 of 29
[Ref.: #66794]	isoprenoid biosynthesis	61.54	16 of 26
[Ref.: #66794]	degradation of hexoses	61.11	11 of 18
[Ref.: #66794]	factor 420 biosynthesis	60	3 of 5
[Ref.: #66794]	methylglyoxal degradation	60	3 of 5
[Ref.: #66794]	lipid metabolism	58.06	18 of 31
[Ref.: #66794]	citric acid cycle	57.14	8 of 14
[Ref.: #66794]	propanol degradation	57.14	4 of 7
[Ref.: #66794]	degradation of sugar alcohols	56.25	9 of 16
[Ref.: #66794]	metabolism of disaccharids	54.55	6 of 11
[Ref.: #66794]	pentose phosphate pathway	54.55	6 of 11
[Ref.: #66794]	arginine metabolism	54.17	13 of 24
[Ref.: #66794]	leucine metabolism	53.85	7 of 13
[Ref.: #66794]	degradation of sugar acids	52	13 of 25
[Ref.: #66794]	dTDPLrhamnose biosynthesis	50	4 of 8
[Ref.: #66794]	CMP-KDO biosynthesis	50	2 of 4
[Ref.: #66794]	sulfopterin metabolism	50	2 of 4
[Ref.: #66794]	toluene degradation	50	2 of 4
[Ref.: #66794]	selenocysteine biosynthesis	50	3 of 6
[Ref.: #66794]	propionate fermentation	50	5 of 10
[Ref.: #66794]	glycolate and glyoxylate degradation	50	3 of 6
[Ref.: #66794]	ribulose monophosphate pathway	50	1 of 2
[Ref.: #66794]	pantothenate biosynthesis	50	3 of 6
[Ref.: #66794]	glutathione metabolism	50	7 of 14
[Ref.: #66794]	cysteine metabolism	50	9 of 18
[Ref.: #66794]	butanoate fermentation	50	2 of 4
[Ref.: #66794]	ketogluconate metabolism	50	4 of 8
[Ref.: #66794]	lysine metabolism	50	21 of 42
[Ref.: #66794]	phenylmercury acetate degradation	50	1 of 2
[Ref.: #66794]	ethanol fermentation	50	1 of 2
[Ref.: #66794]	aminopropanol phosphate biosynthesis	50	1 of 2
[Ref.: #66794]	degradation of pentoses	46.43	13 of 28
[Ref.: #66794]	sulfate reduction	46.15	6 of 13
[Ref.: #66794]	proline metabolism	45.45	5 of 11
[Ref.: #66794]	vitamin B6 metabolism	45.45	5 of 11
[Ref.: #66794]	tryptophan metabolism	44.74	17 of 38
[Ref.: #66794]	vitamin B12 metabolism	44.12	15 of 34
[Ref.: #66794]	tyrosine metabolism	42.86	6 of 14
[Ref.: #66794]	degradation of aromatic, nitrogen containing compounds	41.67	5 of 12
[Ref.: #66794]	glycine metabolism	40	4 of 10
[Ref.: #66794]	myo-inositol biosynthesis	40	4 of 10
[Ref.: #66794]	arachidonate biosynthesis	40	2 of 5
[Ref.: #66794]	phosphatidylethanolamine bioynthesis	38.46	5 of 13
[Ref.: #66794]	cyanate degradation	33.33	1 of 3
[Ref.: #66794]	methane metabolism	33.33	1 of 3
[Ref.: #66794]	IAA biosynthesis	33.33	1 of 3
[Ref.: #66794]	lipid A biosynthesis	33.33	3 of 9
[Ref.: #66794]	phenylpropanoid biosynthesis	30.77	4 of 13
[Ref.: #66794]	4-hydroxyphenylacetate degradation	30	3 of 10
[Ref.: #66794]	coenzyme M biosynthesis	30	3 of 10
[Ref.: #66794]	benzoyl-CoA degradation	28.57	2 of 7
[Ref.: #66794]	dolichyl-diphosphooligosaccharide biosynthesis	27.27	3 of 11
[Ref.: #66794]	methanogenesis from CO2	25	3 of 12
[Ref.: #66794]	phenol degradation	25	5 of 20
[Ref.: #66794]	cyclohexanol degradation	25	1 of 4
[Ref.: #66794]	lactate fermentation	25	1 of 4
[Ref.: #66794]	ascorbate metabolism	22.73	5 of 22
[Ref.: #66794]	4-hydroxymandelate degradation	22.22	2 of 9
[Ref.: #66794]	polyamine pathway	21.74	5 of 23
		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.: #652]	Sample type/isolated from	human faeces

[Ref.: #67770]	Sample type/isolated from	Human feces

[Ref.: #117229]	Sample type/isolated from	Human, (feces)
* marker position based on {}

Isolation sources categories

#Host	#Human	-
#Host Body Product	#Gastrointestinal tract	#Feces (Stool)

What are isolation sources categories?

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

[Ref.: #652]	Biosafety level	1	Risk group (German classification) According to TRBA 466
[Ref.: #117229]	Biosafety level	2	Risk group (French classification)

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.: #652]	Clostridium celatum 16S rRNA gene, strain DSM 1785	X77844	1326	ENA	36834 tax ID
[Ref.: #67770]	Clostridium celatum gene for 16S ribosomal RNA, partial sequence, strain: JCM 1394	AB971795	1477	ENA	36834 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #67770]	Clostridium celatum DSM 1785	GCA_000320405	scaffold	GenBank	545697 tax ID
[Ref.: #66792]	Clostridium celatum DSM 1785	545697.3	wgs	PATRIC	545697 tax ID	*
[Ref.: #66792]	Clostridium celatum DSM 1785	2524023202	draft	JGI IMG/M	545697 tax ID	*

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 celatum DSM 1785 PATRIC: 545697.3
[Ref.: #69481]	spore-forming	yes	100	no

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Clostridium celatum DSM 1785 PATRIC: 545697.3
[Ref.: #69480]	gram-positive	yes	88.511	no
[Ref.: #69480]	anaerobic	yes	97.731	yes
[Ref.: #69480]	halophile	no	71.745	no
[Ref.: #69480]	spore-forming	yes	74.614	no
[Ref.: #69480]	glucose-util	yes	89.787	no
[Ref.: #69480]	thermophile	no	96.168	yes
[Ref.: #69480]	aerobic	no	97.407	no
[Ref.: #69480]	motile	no	86.727	no
[Ref.: #69480]	flagellated	no	90.249	no
[Ref.: #69480]	glucose-ferment	yes	62.264	no

Availability in culture collections External links

[Ref.: #652]

Culture collection no.

DSM 1785, ATCC 27791, VPI 8759-1, JCM 1394, BCRC 14521, NCTC 10947, NCTC 12746, CIP 104316

[Ref.: #72099]

SI-ID 39177

References

#652	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 1785

#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 )

#37172 ; Curators of the CIP;

#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 )

#67770 Japan Collection of Microorganism (JCM) ; Curators of the JCM;

#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 )

#72099

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-ID39177.1 )

#117229 Collection of Institut Pasteur ; Curators of the CIP; CIP 104316
* These data were automatically processed and therefore are not curated

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Clostridium celatum DSM 1785

Clostridium celatum DSM 1785

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