Name: Clostridium paraputrificum DSM 2630
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 2624

Type strain:

Species: Clostridium paraputrificum

Culture col. no.: DSM 2630, ATCC 25780, NCIB 10671, CCUG 32755, NCTC 11833, VPI 1584, JCM 1293, BCRC 14550, NCIMB 10671

Strain history: ATCC 25780 <-- L. DS. Smith VPI 1584.

NCBI tax ID(s): 29363 (species)

SI-ID 265463

ATCC 25780, CCUG 32755, DSM 2630, NCTC 11833, NCIB 10671, JCM 1293, CCRC 14550, NCIMB 10671, BCRC 14550, VTT E-042447

Other strains from Clostridium paraputrificum

Section

Clostridium paraputrificum DSM 2630 is an anaerobe, mesophilic bacterium of the family Clostridiaceae.

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 paraputrificum**
	Full Scientific Name (LPSN)	Clostridium paraputrificum (Bienstock 1906) Snyder 1936 (Approved Lists 1980)

Synonym

"Bacillus paraputrificus"

Information on culture and growth conditions Culture and growth conditions

[Ref.: #1176]

Culture medium

CHOPPED MEAT MEDIUM WITH CARBOHYDRATES (DSMZ Medium 110)

[Ref.: #1176]

Culture medium growth

[Ref.: #1176]

Culture medium link

Medium recipe at MediaDive

[Ref.: #1176]

Culture medium composition

expand / minimize

[Ref.: #1176]

Culture medium

CHOPPED MEAT MEDIUM (DSMZ Medium 78)

[Ref.: #1176]

Culture medium growth

[Ref.: #1176]

Culture medium link

Medium recipe at MediaDive

[Ref.: #1176]

Culture medium composition

expand / minimize

		Temperature
[Ref.: #1176]	growth	37 °C
[Ref.: #51161]	growth	37 °C
[Ref.: #67770]	growth	37 °C

[Ref.: #1176]	Temperature range	mesophilic
[Ref.: #51161]	Temperature range	mesophilic
[Ref.: #67770]	Temperature range	mesophilic

Information on physiology and metabolism Physiology and metabolism

[Ref.: #1176]	Oxygen tolerance	anaerobe
[Ref.: #51161]	Oxygen tolerance	anaerobe

	Pathway	Enzyme coverage	Annotated reactions
	Pathway annotation	Computationally determined by
[Ref.: #66794]	cis-vaccenate biosynthesis	100	2 of 2
[Ref.: #66794]	ppGpp biosynthesis	100	4 of 4
[Ref.: #66794]	formaldehyde oxidation	100	3 of 3
[Ref.: #66794]	coenzyme A metabolism	100	4 of 4
[Ref.: #66794]	starch degradation	100	10 of 10
[Ref.: #66794]	CDP-diacylglycerol biosynthesis	100	2 of 2
[Ref.: #66794]	L-lactaldehyde degradation	100	3 of 3
[Ref.: #66794]	UDP-GlcNAc biosynthesis	100	3 of 3
[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]	adipate degradation	100	2 of 2
[Ref.: #66794]	vitamin B1 metabolism	92.31	12 of 13
[Ref.: #66794]	palmitate biosynthesis	90.91	20 of 22
[Ref.: #66794]	chorismate metabolism	88.89	8 of 9
[Ref.: #66794]	peptidoglycan biosynthesis	86.67	13 of 15
[Ref.: #66794]	reductive acetyl coenzyme A pathway	85.71	6 of 7
[Ref.: #66794]	hydrogen production	80	4 of 5
[Ref.: #66794]	pyrimidine metabolism	80	36 of 45
[Ref.: #66794]	cellulose degradation	80	4 of 5
[Ref.: #66794]	glycogen metabolism	80	4 of 5
[Ref.: #66794]	glycine betaine biosynthesis	80	4 of 5
[Ref.: #66794]	Entner Doudoroff pathway	80	8 of 10
[Ref.: #66794]	threonine metabolism	80	8 of 10
[Ref.: #66794]	purine metabolism	79.79	75 of 94
[Ref.: #66794]	serine metabolism	77.78	7 of 9
[Ref.: #66794]	valine metabolism	77.78	7 of 9
[Ref.: #66794]	d-mannose degradation	77.78	7 of 9
[Ref.: #66794]	glycolysis	76.47	13 of 17
[Ref.: #66794]	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	75	6 of 8
[Ref.: #66794]	acetate fermentation	75	3 of 4
[Ref.: #66794]	sulfopterin metabolism	75	3 of 4
[Ref.: #66794]	glycogen biosynthesis	75	3 of 4
[Ref.: #66794]	C4 and CAM-carbon fixation	75	6 of 8
[Ref.: #66794]	NAD metabolism	72.22	13 of 18
[Ref.: #66794]	cardiolipin biosynthesis	71.43	5 of 7
[Ref.: #66794]	photosynthesis	71.43	10 of 14
[Ref.: #66794]	non-pathway related	71.05	27 of 38
[Ref.: #66794]	phenylalanine metabolism	69.23	9 of 13
[Ref.: #66794]	alanine metabolism	68.97	20 of 29
[Ref.: #66794]	aspartate and asparagine metabolism	66.67	6 of 9
[Ref.: #66794]	degradation of hexoses	66.67	12 of 18
[Ref.: #66794]	molybdenum cofactor biosynthesis	66.67	6 of 9
[Ref.: #66794]	acetoin degradation	66.67	2 of 3
[Ref.: #66794]	nitrate assimilation	66.67	6 of 9
[Ref.: #66794]	CO2 fixation in Crenarchaeota	66.67	6 of 9
[Ref.: #66794]	octane oxidation	66.67	2 of 3
[Ref.: #66794]	histidine metabolism	65.52	19 of 29
[Ref.: #66794]	methionine metabolism	65.38	17 of 26
[Ref.: #66794]	glutathione metabolism	64.29	9 of 14
[Ref.: #66794]	tetrahydrofolate metabolism	64.29	9 of 14
[Ref.: #66794]	heme metabolism	64.29	9 of 14
[Ref.: #66794]	pentose phosphate pathway	63.64	7 of 11
[Ref.: #66794]	d-xylose degradation	63.64	7 of 11
[Ref.: #66794]	isoleucine metabolism	62.5	5 of 8
[Ref.: #66794]	gluconeogenesis	62.5	5 of 8
[Ref.: #66794]	arginine metabolism	62.5	15 of 24
[Ref.: #66794]	isoprenoid biosynthesis	61.54	16 of 26
[Ref.: #66794]	leucine metabolism	61.54	8 of 13
[Ref.: #66794]	glutamate and glutamine metabolism	60.71	17 of 28
[Ref.: #66794]	oxidative phosphorylation	60.44	55 of 91
[Ref.: #66794]	methylglyoxal degradation	60	3 of 5
[Ref.: #66794]	lipoate biosynthesis	60	3 of 5
[Ref.: #66794]	metabolism of amino sugars and derivatives	60	3 of 5
[Ref.: #66794]	factor 420 biosynthesis	60	3 of 5
[Ref.: #66794]	propanol degradation	57.14	4 of 7
[Ref.: #66794]	cysteine metabolism	55.56	10 of 18
[Ref.: #66794]	tryptophan metabolism	55.26	21 of 38
[Ref.: #66794]	lipid metabolism	54.84	17 of 31
[Ref.: #66794]	metabolism of disaccharids	54.55	6 of 11
[Ref.: #66794]	urea cycle	53.85	7 of 13
[Ref.: #66794]	toluene degradation	50	2 of 4
[Ref.: #66794]	ethanol fermentation	50	1 of 2
[Ref.: #66794]	ribulose monophosphate pathway	50	1 of 2
[Ref.: #66794]	glycolate and glyoxylate degradation	50	3 of 6
[Ref.: #66794]	CMP-KDO biosynthesis	50	2 of 4
[Ref.: #66794]	aminopropanol phosphate biosynthesis	50	1 of 2
[Ref.: #66794]	biotin biosynthesis	50	2 of 4
[Ref.: #66794]	selenocysteine biosynthesis	50	3 of 6
[Ref.: #66794]	butanoate fermentation	50	2 of 4
[Ref.: #66794]	citric acid cycle	50	7 of 14
[Ref.: #66794]	degradation of aromatic, nitrogen containing compounds	50	6 of 12
[Ref.: #66794]	ketogluconate metabolism	50	4 of 8
[Ref.: #66794]	phenylmercury acetate degradation	50	1 of 2
[Ref.: #66794]	proline metabolism	45.45	5 of 11
[Ref.: #66794]	lysine metabolism	45.24	19 of 42
[Ref.: #66794]	ubiquinone biosynthesis	42.86	3 of 7
[Ref.: #66794]	propionate fermentation	40	4 of 10
[Ref.: #66794]	arachidonate biosynthesis	40	2 of 5
[Ref.: #66794]	glycine metabolism	40	4 of 10
[Ref.: #66794]	flavin biosynthesis	40	6 of 15
[Ref.: #66794]	coenzyme M biosynthesis	40	4 of 10
[Ref.: #66794]	degradation of pentoses	39.29	11 of 28
[Ref.: #66794]	arachidonic acid metabolism	38.89	7 of 18
[Ref.: #66794]	phenylpropanoid biosynthesis	38.46	5 of 13
[Ref.: #66794]	sulfate reduction	38.46	5 of 13
[Ref.: #66794]	vitamin B12 metabolism	38.24	13 of 34
[Ref.: #66794]	tyrosine metabolism	35.71	5 of 14
[Ref.: #66794]	enterobactin biosynthesis	33.33	1 of 3
[Ref.: #66794]	cyanate degradation	33.33	1 of 3
[Ref.: #66794]	lipid A biosynthesis	33.33	3 of 9
[Ref.: #66794]	sphingosine metabolism	33.33	2 of 6
[Ref.: #66794]	pantothenate biosynthesis	33.33	2 of 6
[Ref.: #66794]	IAA biosynthesis	33.33	1 of 3
[Ref.: #66794]	phosphatidylethanolamine bioynthesis	30.77	4 of 13
[Ref.: #66794]	polyamine pathway	30.43	7 of 23
[Ref.: #66794]	4-hydroxyphenylacetate degradation	30	3 of 10
[Ref.: #66794]	myo-inositol biosynthesis	30	3 of 10
[Ref.: #66794]	benzoyl-CoA degradation	28.57	2 of 7
[Ref.: #66794]	ascorbate metabolism	27.27	6 of 22
[Ref.: #66794]	vitamin B6 metabolism	27.27	3 of 11
[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]	dTDPLrhamnose biosynthesis	25	2 of 8
[Ref.: #66794]	carnitine metabolism	25	2 of 8
[Ref.: #66794]	androgen and estrogen metabolism	25	4 of 16
[Ref.: #66794]	degradation of sugar acids	24	6 of 25
[Ref.: #66794]	allantoin 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.: #69479]

Global distribution of 16S sequence AB536771 (>99% sequence identity) for Clostridium paraputrificum subclade from Microbeatlas

Aquatic Samples	4616
Soil Samples	2219
Animal Samples	54761
Plant Samples	345
Total Samples	61941

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

[Ref.: #1176]

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.: #1176]	C.paraputrificum 16S rRNA gene	X75907	1467	ENA	29363 tax ID
[Ref.: #20218]	Clostridium paraputrificum strain DSM 2630 16S ribosomal RNA gene, partial sequence	HM245948	836	ENA	29363 tax ID	*
[Ref.: #20218]	Clostridium paraputrificum 16S rRNA gene, strain DSM 2630	X73445	1511	ENA	29363 tax ID	*
[Ref.: #20218]	Clostridium paraputrificum gene for 16S ribosomal RNA, partial sequence, strain: JCM 1293	AB536771	1476	ENA	29363 tax ID	*

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #67770]	Clostridium paraputrificum NCTC11833	GCA_900447045	contig	GenBank	29363 tax ID
[Ref.: #66792]	Clostridium paraputrificum strain NCTC11833	29363.20	wgs	PATRIC	29363 tax ID	*

[Ref.: #1176]	GC-content	27.0 mol%
[Ref.: #67770]	GC-content	27 mol%	thermal denaturation, midpoint method (Tm)

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

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Clostridium paraputrificum strain NCTC11833 PATRIC: 29363.20
[Ref.: #69480]	gram-positive	yes	81.675	no
[Ref.: #69480]	anaerobic	yes	98.399	yes
[Ref.: #69480]	halophile	no	84.564	no
[Ref.: #69480]	spore-forming	yes	93.606	no
[Ref.: #69480]	glucose-util	yes	88.506	no
[Ref.: #69480]	motile	yes	81.069	no
[Ref.: #69480]	flagellated	yes	60.005	no
[Ref.: #69480]	aerobic	no	98.435	yes
[Ref.: #69480]	thermophile	no	95.024	no
[Ref.: #69480]	glucose-ferment	yes	63.563	no

Availability in culture collections External links

[Ref.: #1176]

Culture collection no.

DSM 2630, ATCC 25780, NCIB 10671, CCUG 32755, NCTC 11833, VPI 1584, JCM 1293, BCRC 14550, NCIMB 10671

[Ref.: #72155]

SI-ID 265463

Literature:

Topic	Title	Authors	Journal	DOI	Year
Metabolism	Completion of the gut microbial epi-bile acid pathway.	Doden HL, Wolf PG, Gaskins HR, Anantharaman K, Alves JMP, Ridlon JM	Gut Microbes	10.1080/19490976.2021.1907271	2021	*
Pathogenicity	Growth-Inhibiting and morphostructural effects of constituents identified in Asarum heterotropoides root on human intestinal bacteria.	Perumalsamy H, Jung MY, Hong SM, Ahn YJ	BMC Complement Altern Med	10.1186/1472-6882-13-245	2013	*

References

#1176

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 2630

#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 )

#51161 Culture Collection University of Gothenburg (CCUG) ; Curators of the CCUG; CCUG 32755

#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;

#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) .

#72155

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-ID265463.1 )

* 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 paraputrificum in external resources:
SILVA
BRENDA
PANGAEA
StrainInfo
GBIF

Clostridium paraputrificum strain NCTC11833

Change proposal

Change proposal