Clostridium puniceum (DSM 2619, ATCC 43978, NCIMB 11596)

Name: Clostridium puniceum (DSM 2619, ATCC 43978, NCIMB 11596)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 2649

Type strain

Strain Designation BL 70/20

Culture col. no. DSM 2619 ATCC 43978 NCIMB 11596 BL 70/20

NCBI tax ID(s) 29367

Special Collections DSMZ

History <- NCIMB <- B.M. Lund, BL 70/20

Links

Clostridium puniceum BL 70/20 is an anaerobe, mesophilic prokaryote that was isolated from rotting potatoes.

anaerobe mesophilic genome sequence 16S sequence

Name and taxonomic classification

SI-ID 46857

ATCC 43978,NCIMB 11596,DSM 2619,NCIB 11596,BCRC 14491,CCRC 14491,ICMP 12529,VTT E-032439

@ref 20215

Last LPSN update 2025-12-16 09:47:21

Domain Bacillati

Phylum Bacillota

Class Clostridia

Order Eubacteriales

Family Clostridiaceae

Genus Clostridium

Species Clostridium puniceum

Full scientific name Clostridium puniceum Lund et al. 1981

Morphology

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
1169	CHOPPED MEAT MEDIUM WITH CARBOHYDRATES (DSMZ Medium 110)		Medium recipe at MediaDive	Name: CHOPPED MEAT MEDIUM WITH CARBOHYDRATES (DSMZ Medium 110) Composition: Ground beef 500.0 g/l Casitone 30.0 g/l Agar 15.0 g/l K2HPO4 5.0 g/l Yeast extract 5.0 g/l D-Glucose 4.0 g/l Starch 1.0 g/l Maltose 1.0 g/l Cellobiose 1.0 g/l L-Cysteine HCl 0.5 g/l Ethanol 0.19 g/l Vitamin K3 0.05 g/l Hemin 0.005 g/l Sodium resazurin 0.0005 g/l Vitamin K1 NaOH Distilled water

Culture temp

@ref	Growth	Type	Temperature (°C)	Range
1169	positive	growth	30	mesophilic

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
1169	anaerobe
125439	facultative anaerobe	97.1

Pathway annotation

Computationally determined by

@ref	pathway	enzyme coverage	annotated reactions
66794	cellulose degradation	100	5 of 5
66794	CMP-KDO biosynthesis	100	4 of 4
66794	adipate degradation	100	2 of 2
66794	gluconeogenesis	100	8 of 8
66794	C4 and CAM-carbon fixation	100	8 of 8
66794	threonine metabolism	100	10 of 10
66794	palmitate biosynthesis	100	22 of 22
66794	ppGpp biosynthesis	100	4 of 4
66794	methylglyoxal degradation	100	5 of 5
66794	L-lactaldehyde degradation	100	3 of 3
66794	cis-vaccenate biosynthesis	100	2 of 2
66794	folate polyglutamylation	100	1 of 1
66794	anapleurotic synthesis of oxalacetate	100	1 of 1
66794	formaldehyde oxidation	100	3 of 3
66794	coenzyme A metabolism	100	4 of 4
66794	CDP-diacylglycerol biosynthesis	100	2 of 2
66794	suberin monomers biosynthesis	100	2 of 2
66794	UDP-GlcNAc biosynthesis	100	3 of 3
66794	vitamin B1 metabolism	92.31	12 of 13
66794	chorismate metabolism	88.89	8 of 9
66794	d-mannose degradation	88.89	8 of 9
66794	pyrimidine metabolism	88.89	40 of 45
66794	aspartate and asparagine metabolism	88.89	8 of 9
66794	alanine metabolism	86.21	25 of 29
66794	tetrahydrofolate metabolism	85.71	12 of 14
66794	reductive acetyl coenzyme A pathway	85.71	6 of 7
66794	photosynthesis	85.71	12 of 14
66794	phenylalanine metabolism	84.62	11 of 13
66794	selenocysteine biosynthesis	83.33	5 of 6
66794	glycolysis	82.35	14 of 17
66794	flavin biosynthesis	80	12 of 15
66794	metabolism of amino sugars and derivatives	80	4 of 5
66794	Entner Doudoroff pathway	80	8 of 10
66794	glycogen metabolism	80	4 of 5
66794	hydrogen production	80	4 of 5
66794	peptidoglycan biosynthesis	80	12 of 15
66794	starch degradation	80	8 of 10
66794	serine metabolism	77.78	7 of 9
66794	CO2 fixation in Crenarchaeota	77.78	7 of 9
66794	purine metabolism	76.6	72 of 94
66794	butanoate fermentation	75	3 of 4
66794	isoleucine metabolism	75	6 of 8
66794	sulfopterin metabolism	75	3 of 4
66794	glutamate and glutamine metabolism	75	21 of 28
66794	glycogen biosynthesis	75	3 of 4
66794	acetate fermentation	75	3 of 4
66794	vitamin B12 metabolism	73.53	25 of 34
66794	NAD metabolism	72.22	13 of 18
66794	cardiolipin biosynthesis	71.43	5 of 7
66794	propanol degradation	71.43	5 of 7
66794	heme metabolism	71.43	10 of 14
66794	myo-inositol biosynthesis	70	7 of 10
66794	phosphatidylethanolamine bioynthesis	69.23	9 of 13
66794	degradation of sugar alcohols	68.75	11 of 16
66794	enterobactin biosynthesis	66.67	2 of 3
66794	octane oxidation	66.67	2 of 3
66794	degradation of hexoses	66.67	12 of 18
66794	valine metabolism	66.67	6 of 9
66794	cyanate degradation	66.67	2 of 3
66794	acetoin degradation	66.67	2 of 3
66794	methane metabolism	66.67	2 of 3
66794	molybdenum cofactor biosynthesis	66.67	6 of 9
66794	non-pathway related	65.79	25 of 38
66794	histidine metabolism	65.52	19 of 29
66794	methionine metabolism	65.38	17 of 26
66794	oxidative phosphorylation	64.84	59 of 91
66794	d-xylose degradation	63.64	7 of 11
66794	metabolism of disaccharids	63.64	7 of 11
66794	proline metabolism	63.64	7 of 11
66794	pentose phosphate pathway	63.64	7 of 11
66794	ketogluconate metabolism	62.5	5 of 8
66794	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	62.5	5 of 8
66794	dTDPLrhamnose biosynthesis	62.5	5 of 8
66794	lipid metabolism	61.29	19 of 31
66794	factor 420 biosynthesis	60	3 of 5
66794	lysine metabolism	59.52	25 of 42
66794	arginine metabolism	58.33	14 of 24
66794	tryptophan metabolism	57.89	22 of 38
66794	ubiquinone biosynthesis	57.14	4 of 7
66794	degradation of pentoses	57.14	16 of 28
66794	polyamine pathway	56.52	13 of 23
66794	leucine metabolism	53.85	7 of 13
66794	sulfate reduction	53.85	7 of 13
66794	urea cycle	53.85	7 of 13
66794	lactate fermentation	50	2 of 4
66794	mannosylglycerate biosynthesis	50	1 of 2
66794	kanosamine biosynthesis II	50	1 of 2
66794	pantothenate biosynthesis	50	3 of 6
66794	aminopropanol phosphate biosynthesis	50	1 of 2
66794	glycolate and glyoxylate degradation	50	3 of 6
66794	propionate fermentation	50	5 of 10
66794	glycine metabolism	50	5 of 10
66794	ethanol fermentation	50	1 of 2
66794	phenylmercury acetate degradation	50	1 of 2
66794	ribulose monophosphate pathway	50	1 of 2
66794	degradation of aromatic, nitrogen containing compounds	50	6 of 12
66794	cysteine metabolism	50	9 of 18
66794	quinate degradation	50	1 of 2
66794	glutathione metabolism	50	7 of 14
66794	degradation of sugar acids	48	12 of 25
66794	isoprenoid biosynthesis	46.15	12 of 26
66794	vitamin B6 metabolism	45.45	5 of 11
66794	nitrate assimilation	44.44	4 of 9
66794	lipid A biosynthesis	44.44	4 of 9
66794	tyrosine metabolism	42.86	6 of 14
66794	citric acid cycle	42.86	6 of 14
66794	aclacinomycin biosynthesis	42.86	3 of 7
66794	arachidonate biosynthesis	40	2 of 5
66794	coenzyme M biosynthesis	40	4 of 10
66794	lipoate biosynthesis	40	2 of 5
66794	phenylpropanoid biosynthesis	38.46	5 of 13
66794	ascorbate metabolism	36.36	8 of 22
66794	IAA biosynthesis	33.33	1 of 3
66794	4-hydroxymandelate degradation	33.33	3 of 9
66794	1,4-dihydroxy-6-naphthoate biosynthesis	33.33	2 of 6
66794	arachidonic acid metabolism	33.33	6 of 18
66794	acetyl CoA biosynthesis	33.33	1 of 3
66794	allantoin degradation	33.33	3 of 9
66794	4-hydroxyphenylacetate degradation	30	3 of 10
66794	benzoyl-CoA degradation	28.57	2 of 7
66794	dolichyl-diphosphooligosaccharide biosynthesis	27.27	3 of 11
66794	toluene degradation	25	1 of 4
66794	carnitine metabolism	25	2 of 8
66794	cyclohexanol degradation	25	1 of 4
66794	biotin biosynthesis	25	1 of 4
66794	methanogenesis from CO2	25	3 of 12
66794	carotenoid biosynthesis	22.73	5 of 22

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Host	#Plants	#Decomposing plant
#Host	#Plants	#Herbaceous plants (Grass,Crops)
#Host Body-Site	#Plant	#Root (Rhizome)

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent
1169	rotting potatoes	Norwich	United Kingdom	GBR	Europe

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
1169	1	Risk group (German classification) According to TRBA 466

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
66792	ASM200634v1 assembly for Clostridium puniceum DSM 2619	contig	GCA_002006345	29367.3	8111044261	29367	29.29

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
20218	Clostridium puniceum 16S rRNA gene, strain DSM 2619	X73444	1449		29367
1169	C.puniceum gene for 16S ribosomal RNA	X71857	1491		29367

GC content

1169

GC-content (mol%)28.0-29.0

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Clostridium puniceum DSM 2619
NCBI: GCA_002006345

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	yes	79.80	no
125439	motility	BacteriaNetⓘ	yes	81.10	no
125439	gram_stain	BacteriaNetⓘ	positive	81.90	no
125439	oxygen_tolerance	BacteriaNetⓘ	facultative anaerobe	97.10	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Clostridium puniceum strain DSM 2619
PATRIC: 29367.3

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	yes	59.45	no
125438	anaerobic	anaerobicⓘ	yes	89.66	no
125438	spore-forming	spore-formingⓘ	yes	72.88	no
125438	thermophilic	thermophileⓘ	no	96.20	yes
125438	aerobic	aerobicⓘ	no	93.76	yes
125438	flagellated	motile2+ⓘ	yes	77.75	no

Literature

Topic	Title	Authors	Journal	DOI	Year
	Clostridium btbubcensis BJN0001, a potentially new species isolated from the cellar mud of Chinese strong-flavor baijiu, produces ethanol, acetic acid and butyric acid from glucose.	Xu Y, Wu M, Niu J, Huang H, Nie Z, Fu Z, Zhang C, Zhao Z, Lu H, Li X, Sun B.	3 Biotech	10.1007/s13205-022-03271-7	2022
	Draft Genome Sequences of Two Clostridium Isolates from the Poultry Gastrointestinal Tract.	Keshri J, Ramirez R, Chalghoumi R, Garrish JK, Seal BS, Oakley BB.	Microbiol Resour Announc	10.1128/mra.00137-20	2020
Phylogeny	Bacterial-biota dynamics of eight bryophyte species from different ecosystems.	Koua FH, Kimbara K, Tani A.	Saudi J Biol Sci	10.1016/j.sjbs.2014.07.009	2015
Phylogeny	Microbial solvent formation revisited by comparative genome analysis.	Poehlein A, Solano JDM, Flitsch SK, Krabben P, Winzer K, Reid SJ, Jones DT, Green E, Minton NP, Daniel R, Durre P.	Biotechnol Biofuels	10.1186/s13068-017-0742-z	2017
Enzymology	Degradation of cyanophycin by Sedimentibacter hongkongensis strain KI and Citrobacter amalonaticus strain G Isolated from an anaerobic bacterial consortium.	Obst M, Krug A, Luftmann H, Steinbuchel A.	Appl Environ Microbiol	10.1128/aem.71.7.3642-3652.2005	2005

References

#1169	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 2619
#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 )
#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 )
#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 .
#126262	A. Lissin, I. Schober, J. F. Witte, H. Lüken, A. Podstawka, J. Koblitz, B. Bunk, P. Dawyndt, P. Vandamme, P. de Vos, J. Overmann, L. C. Reimer: StrainInfo—the central database for linked microbial strain identifiers. ( DOI 10.1093/database/baaf059 )

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Clostridium puniceum (DSM 2619, ATCC 43978, NCIMB 11596)

Name and taxonomic classification

Morphology

Culture and growth conditions

Culture medium

Culture temp

Physiology and metabolism

Oxygen tolerance

Pathway annotation

Isolation, sampling and environmental information

Isolation source categories

Isolation

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_002006345

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

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