Name: Clostridium purinilyticum DSM 1384
Creator: BacDive
License: https://creativecommons.org/licenses/by/4.0/

Strain identifier

BacDive ID: 2650

Type strain:

Species: Clostridium purinilyticum

Culture col. no.: DSM 1384, ATCC 33906, WA 1

Strain history: <- P. Dürre, Universität Göttingen, Germany; WA1 <- W. Andersch {1977}

NCBI tax ID(s): 1503 (species)

SI-ID 40756

ATCC 33906, DSM 1384, BCRC 14481, CCRC 14481

Special Collections

Section

When using BacDive for research please cite our paper

Clostridium purinilyticum DSM 1384 is an anaerobe, chemoorganotroph, spore-forming bacterium that was isolated from chicken manure contaminated soil.

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

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

	Last LPSN update	09-12-2024 (DD-MM-YYYY)
	Domain	*Bacteria*
	Phylum	*Bacillota*
	Class	*Clostridia*
	Order	*Eubacteriales*
	Family	*Clostridiaceae*
	Genus	*Clostridium*
	Species	Clostridium purinilyticum
	Full Scientific Name (LPSN)	Clostridium purinilyticum corrig. Dürre et al. 1981

	Synonym	Clostridium purinolyticum
	Synonym	**Gottschalkia purinilytica**

Information on morphological and physiological properties Morphology

[Ref.: #43456]	Gram stain	positive

[Ref.: #43456]	Cell length	2.7-9.6 µm

[Ref.: #43456]	Cell width	1.1-1.6 µm

[Ref.: #43456]	Cell shape	rod-shaped

[Ref.: #43456]	Motility	yes

[Ref.: #43456]	Flagellum arrangement	polar

Information on culture and growth conditions Culture and growth conditions

[Ref.: #759]

Culture medium

GOTTSCHALKIA MEDIUM (DSMZ Medium 76)

[Ref.: #759]

Culture medium growth

[Ref.: #759]

Culture medium link

Medium recipe at MediaDive

[Ref.: #759]

Culture medium composition

expand / minimize

	Temperatures	Kind of temperature		Temperature
[Ref.: #759]			growth	35 °C
[Ref.: #43456]			optimum	36 °C

	pH	Kind of pH		pH
[Ref.: #43456]			optimum	7.3-7.8

Information on physiology and metabolism Physiology and metabolism

[Ref.: #759]	Oxygen tolerance	anaerobe
[Ref.: #43456]	Oxygen tolerance	obligate anaerobe
[Ref.: #125439]	Oxygen tolerance	anaerobe Confidence in %96

[Ref.: #43456]

Nutrition type

chemoorganotroph

[Ref.: #43456]	Spore description	spherical terminally located that result in swollen cells
[Ref.: #43456]	Type of spore	endospore
[Ref.: #43456]	Ability of spore formation	yes

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #43456]	adenine ChEBI	+	assimilation
[Ref.: #43456]	adenosine ChEBI	+	assimilation
[Ref.: #43456]	cellobiose ChEBI	-	assimilation
[Ref.: #43456]	D-fructose ChEBI	-	assimilation
[Ref.: #43456]	D-galactose ChEBI	-	assimilation
[Ref.: #43456]	D-glucose ChEBI	-	assimilation
[Ref.: #43456]	D-mannitol ChEBI	-	assimilation
[Ref.: #43456]	D-mannose ChEBI	-	assimilation
[Ref.: #43456]	D-ribose ChEBI	-	assimilation
[Ref.: #43456]	D-sorbitol ChEBI	-	assimilation
[Ref.: #43456]	D-xylose ChEBI	-	assimilation
[Ref.: #43456]	gelatin ChEBI	-	hydrolysis
[Ref.: #43456]	guanine ChEBI	+	assimilation
[Ref.: #43456]	hypoxanthine ChEBI	+	assimilation
[Ref.: #43456]	L-arabinose ChEBI	-	assimilation
[Ref.: #43456]	lactose ChEBI	-	assimilation
[Ref.: #43456]	maltose ChEBI	-	assimilation
[Ref.: #43456]	nitrate ChEBI	-	reduction
[Ref.: #43456]	starch ChEBI	-	hydrolysis
[Ref.: #43456]	sucrose ChEBI	-	assimilation
[Ref.: #43456]	sulfate ChEBI	-	reduction
[Ref.: #43456]	sulfite ChEBI	-	reduction
[Ref.: #43456]	thiosulfate ChEBI	-	reduction
[Ref.: #43456]	uric acid ChEBI	+	assimilation
[Ref.: #43456]	xanthine ChEBI	+	assimilation
	Only first 10 entries are displayed. Click here to see all.

	Metabolite	Production
[Ref.: #43456]	acetate ChEBI	yes
[Ref.: #43456]	ammonia ChEBI	yes
[Ref.: #43456]	butyrate ChEBI	no
[Ref.: #43456]	carbon dioxide ChEBI	yes
[Ref.: #43456]	dihydrogen ChEBI	no
[Ref.: #43456]	formate ChEBI	yes
[Ref.: #43456]	hydrogen sulfide ChEBI	no

	Enzyme	Enzyme activity	EC number
[Ref.: #43456]	catalase	-	1.11.1.6
[Ref.: #43456]	lecithinase	-
[Ref.: #43456]	lipase	-
[Ref.: #43456]	urease	-	3.5.1.5

	Pathway	Enzyme coverage	Annotated reactions
	Pathway annotation	Computationally determined by
[Ref.: #66794]	coenzyme A metabolism	100	4 of 4
[Ref.: #66794]	cardiolipin biosynthesis	100	7 of 7
[Ref.: #66794]	reductive acetyl coenzyme A pathway	100	7 of 7
[Ref.: #66794]	formaldehyde oxidation	100	3 of 3
[Ref.: #66794]	L-lactaldehyde degradation	100	3 of 3
[Ref.: #66794]	CDP-diacylglycerol biosynthesis	100	2 of 2
[Ref.: #66794]	biotin biosynthesis	100	4 of 4
[Ref.: #66794]	UDP-GlcNAc biosynthesis	100	3 of 3
[Ref.: #66794]	lipoate biosynthesis	100	5 of 5
[Ref.: #66794]	folate polyglutamylation	100	1 of 1
[Ref.: #66794]	anapleurotic synthesis of oxalacetate	100	1 of 1
[Ref.: #66794]	palmitate biosynthesis	95.45	21 of 22
[Ref.: #66794]	vitamin B1 metabolism	92.31	12 of 13
[Ref.: #66794]	pyrimidine metabolism	91.11	41 of 45
[Ref.: #66794]	threonine metabolism	90	9 of 10
[Ref.: #66794]	chorismate metabolism	88.89	8 of 9
[Ref.: #66794]	aspartate and asparagine metabolism	88.89	8 of 9
[Ref.: #66794]	heme metabolism	85.71	12 of 14
[Ref.: #66794]	cellulose degradation	80	4 of 5
[Ref.: #66794]	peptidoglycan biosynthesis	80	12 of 15
[Ref.: #66794]	factor 420 biosynthesis	80	4 of 5
[Ref.: #66794]	glycine betaine biosynthesis	80	4 of 5
[Ref.: #66794]	vitamin B12 metabolism	79.41	27 of 34
[Ref.: #66794]	purine metabolism	78.72	74 of 94
[Ref.: #66794]	photosynthesis	78.57	11 of 14
[Ref.: #66794]	tetrahydrofolate metabolism	78.57	11 of 14
[Ref.: #66794]	NAD metabolism	77.78	14 of 18
[Ref.: #66794]	molybdenum cofactor biosynthesis	77.78	7 of 9
[Ref.: #66794]	valine metabolism	77.78	7 of 9
[Ref.: #66794]	phenylalanine metabolism	76.92	10 of 13
[Ref.: #66794]	glycogen biosynthesis	75	3 of 4
[Ref.: #66794]	sulfopterin metabolism	75	3 of 4
[Ref.: #66794]	ppGpp biosynthesis	75	3 of 4
[Ref.: #66794]	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	75	6 of 8
[Ref.: #66794]	flavin biosynthesis	73.33	11 of 15
[Ref.: #66794]	glycolysis	70.59	12 of 17
[Ref.: #66794]	methionine metabolism	69.23	18 of 26
[Ref.: #66794]	alanine metabolism	68.97	20 of 29
[Ref.: #66794]	selenocysteine biosynthesis	66.67	4 of 6
[Ref.: #66794]	acetoin degradation	66.67	2 of 3
[Ref.: #66794]	serine metabolism	66.67	6 of 9
[Ref.: #66794]	glycolate and glyoxylate degradation	66.67	4 of 6
[Ref.: #66794]	enterobactin biosynthesis	66.67	2 of 3
[Ref.: #66794]	cyanate degradation	66.67	2 of 3
[Ref.: #66794]	octane oxidation	66.67	2 of 3
[Ref.: #66794]	oxidative phosphorylation	65.93	60 of 91
[Ref.: #66794]	glutamate and glutamine metabolism	64.29	18 of 28
[Ref.: #66794]	C4 and CAM-carbon fixation	62.5	5 of 8
[Ref.: #66794]	isoleucine metabolism	62.5	5 of 8
[Ref.: #66794]	histidine metabolism	62.07	18 of 29
[Ref.: #66794]	sulfate reduction	61.54	8 of 13
[Ref.: #66794]	urea cycle	61.54	8 of 13
[Ref.: #66794]	cysteine metabolism	61.11	11 of 18
[Ref.: #66794]	methylglyoxal degradation	60	3 of 5
[Ref.: #66794]	hydrogen production	60	3 of 5
[Ref.: #66794]	starch degradation	60	6 of 10
[Ref.: #66794]	glycogen metabolism	60	3 of 5
[Ref.: #66794]	degradation of aromatic, nitrogen containing compounds	58.33	7 of 12
[Ref.: #66794]	arginine metabolism	58.33	14 of 24
[Ref.: #66794]	tryptophan metabolism	57.89	22 of 38
[Ref.: #66794]	ubiquinone biosynthesis	57.14	4 of 7
[Ref.: #66794]	propanol degradation	57.14	4 of 7
[Ref.: #66794]	citric acid cycle	57.14	8 of 14
[Ref.: #66794]	tyrosine metabolism	57.14	8 of 14
[Ref.: #66794]	pentose phosphate pathway	54.55	6 of 11
[Ref.: #66794]	proline metabolism	54.55	6 of 11
[Ref.: #66794]	d-xylose degradation	54.55	6 of 11
[Ref.: #66794]	leucine metabolism	53.85	7 of 13
[Ref.: #66794]	non-pathway related	52.63	20 of 38
[Ref.: #66794]	polyamine pathway	52.17	12 of 23
[Ref.: #66794]	lysine metabolism	50	21 of 42
[Ref.: #66794]	glutathione metabolism	50	7 of 14
[Ref.: #66794]	CMP-KDO biosynthesis	50	2 of 4
[Ref.: #66794]	gluconeogenesis	50	4 of 8
[Ref.: #66794]	adipate degradation	50	1 of 2
[Ref.: #66794]	dolichol and dolichyl phosphate biosynthesis	50	1 of 2
[Ref.: #66794]	Entner Doudoroff pathway	50	5 of 10
[Ref.: #66794]	cis-vaccenate biosynthesis	50	1 of 2
[Ref.: #66794]	aminopropanol phosphate biosynthesis	50	1 of 2
[Ref.: #66794]	suberin monomers biosynthesis	50	1 of 2
[Ref.: #66794]	pantothenate biosynthesis	50	3 of 6
[Ref.: #66794]	butanoate fermentation	50	2 of 4
[Ref.: #66794]	ketogluconate metabolism	50	4 of 8
[Ref.: #66794]	isoprenoid biosynthesis	50	13 of 26
[Ref.: #66794]	phenylmercury acetate degradation	50	1 of 2
[Ref.: #66794]	vitamin E metabolism	50	2 of 4
[Ref.: #66794]	acetate fermentation	50	2 of 4
[Ref.: #66794]	ethanol fermentation	50	1 of 2
[Ref.: #66794]	glycine metabolism	50	5 of 10
[Ref.: #66794]	d-mannose degradation	44.44	4 of 9
[Ref.: #66794]	nitrate assimilation	44.44	4 of 9
[Ref.: #66794]	CO2 fixation in Crenarchaeota	44.44	4 of 9
[Ref.: #66794]	lipid A biosynthesis	44.44	4 of 9
[Ref.: #66794]	metabolism of amino sugars and derivatives	40	2 of 5
[Ref.: #66794]	propionate fermentation	40	4 of 10
[Ref.: #66794]	metabolism of disaccharids	36.36	4 of 11
[Ref.: #66794]	IAA biosynthesis	33.33	1 of 3
[Ref.: #66794]	acetyl CoA biosynthesis	33.33	1 of 3
[Ref.: #66794]	ascorbate metabolism	31.82	7 of 22
[Ref.: #66794]	phenylpropanoid biosynthesis	30.77	4 of 13
[Ref.: #66794]	phosphatidylethanolamine bioynthesis	30.77	4 of 13
[Ref.: #66794]	phenol degradation	30	6 of 20
[Ref.: #66794]	lipid metabolism	29.03	9 of 31
[Ref.: #66794]	vitamin B6 metabolism	27.27	3 of 11
[Ref.: #66794]	degradation of pentoses	25	7 of 28
[Ref.: #66794]	degradation of sugar alcohols	25	4 of 16
[Ref.: #66794]	lactate fermentation	25	1 of 4
[Ref.: #66794]	cyclohexanol degradation	25	1 of 4
[Ref.: #66794]	toluene degradation	25	1 of 4
[Ref.: #66794]	catecholamine biosynthesis	25	1 of 4
[Ref.: #66794]	degradation of hexoses	22.22	4 of 18
[Ref.: #66794]	4-hydroxymandelate degradation	22.22	2 of 9
		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.: #759]	Sample type/isolated from	chicken manure contaminated soil
[Ref.: #759]	Geographic location (country and/or sea, region)	near Göttingen
[Ref.: #759]	Country	Germany
[Ref.: #759]	Country ISO 3 Code	DEU
[Ref.: #759]	Continent	Europe

[Ref.: #43456]	Sample type/isolated from	farm soil containing chicken manure
[Ref.: #43456]	Geographic location (country and/or sea, region)	Bovenden-Eddigehausen
[Ref.: #43456]	Country	Germany
[Ref.: #43456]	Country ISO 3 Code	DEU
[Ref.: #43456]	Continent	Europe
* marker position based on {}

Isolation sources categories

#Engineered	#Contamination	-
#Engineered	#Agriculture	#Livestock (Husbandry)
#Environmental	#Terrestrial	#Soil
#Host	#Birds	#Chicken
#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.: #759]

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.: #759]	Clostridium purinilyticum partial 16S rRNA gene, type strain DSM 1384T	FR749894	1517	GenBank ENA	1503 tax ID
[Ref.: #20218]	Clostridium purinilyticum strain ATCC 33906 16S ribosomal RNA gene, partial sequence	M60491	1510	GenBank ENA	1503 tax ID	*

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Gottschalkia purinilytica DSM 1384	GCA_001190785	contig	GenBank ENA	1503 tax ID	*
[Ref.: #66792]	Gottschalkia purinilytica strain DSM 1384	1503.6	wgs	PATRIC	1503 tax ID	*
[Ref.: #66792]	Gottschalkia purinilytica DSM 1384	2645727973	draft	JGI IMG/M	1503 tax ID	*

[Ref.: #759]	GC-content	29.0 mol%
[Ref.: #43456]	GC-content	28.8 mol%
[Ref.: #759]	GC-content	28.8 mol%	sequence analysis

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

	Model	Trait	Prediction	Confidence in %	In training data
	Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Gottschalkia purinilytica strain DSM 1384 PATRIC: 1503.6
[Ref.: #125438]	gram-positive	gram-positiveⓘ	yes	70.292	no
[Ref.: #125438]	anaerobic	anaerobicⓘ	yes	87.368	no
[Ref.: #125438]	spore-forming	spore-formingⓘ	yes	83.463	yes
[Ref.: #125438]	aerobic	aerobicⓘ	no	94.513	yes
[Ref.: #125438]	thermophile	thermophilicⓘ	no	78.082	no
[Ref.: #125438]	motile2+	flagellatedⓘ	yes	85.789	yes

	Model	Trait	Prediction	Confidence in %
	Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Gottschalkia purinilytica DSM 1384 NCBI: GCA_001190785
[Ref.: #125439]	BacteriaNet	spore_formationⓘ	yes	51
[Ref.: #125439]	BacteriaNet	motilityⓘ	yes	69
[Ref.: #125439]	BacteriaNet	gram_stainⓘ	positive	88.3
[Ref.: #125439]	BacteriaNet	oxygen_toleranceⓘ	anaerobe	96

Availability in culture collections External links

[Ref.: #759]

Culture collection no.

DSM 1384, ATCC 33906, WA 1

[Ref.: #72181]

SI-ID 40756

Literature:

Topic	Title	Authors	Journal	DOI	Year
Genetics	Draft Genome Sequence of Purine-Degrading Gottschalkia purinilyticum (Formerly Clostridium purinilyticum) WA1 (DSM 1384).	Poehlein A, Bengelsdorf FR, Schiel-Bengelsdorf B, Daniel R, Durre P	Genome Announc	10.1128/genomeA.01088-15	2015	*

References

#759	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 1384

#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 )

#20218

Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P.: StrainInfo introduces electronic passports for microorganisms.. Syst Appl Microbiol. 37: 42 - 50 2014 ( DOI 10.1016/j.syapm.2013.11.002 , PubMed 24321274 )

#43456

Anja Poehlein, Natalya Yutin, Rolf Daniel, Michael Y. Galperin: Proposal for the reclassification of obligately purine-fermenting bacteria Clostridium acidurici (Barker 1938) and Clostridium purinilyticum (Dürre et al. 1981) as Gottschalkia acidurici gen. nov. comb. nov. and Gottschalkia purinilytica comb. nov. and of Eubacterium angustum (Beuscher and Andreesen 1985) as Andreesenia angusta gen. nov. comb. nov. in the family Gottschalkiaceae fam. nov.. IJSEM 67: 2711 - 2719 2017 ( DOI 10.1099/ijsem.0.002008 , PubMed 28853681 )

#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 )

#72181

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-ID40756.1 )

#125438

Julia Koblitz, Lorenz Christian Reimer, Rüdiger Pukall, Jörg Overmann: Predicting bacterial phenotypic traits through improved machine learning using high-quality, curated datasets. 2024 ( DOI 10.1101/2024.08.12.607695 )

#125439

Philipp Münch, René Mreches, Martin Binder, Hüseyin Anil Gündüz, Xiao-Yin To, Alice McHardy: deepG: Deep Learning for Genome Sequence Data. R package version 0.3.1 .

* 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 Gottschalkia purinilytica in external resources:
SILVA
BRENDA
PANGAEA
GBIF

Gottschalkia purinilytica strain DSM 1384

Gottschalkia purinilytica DSM 1384

Change proposal

Change proposal