Clostridium gasigenes (DSM 12272, DB1A)

Name: Clostridium gasigenes (DSM 12272, DB1A)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 2793

Type strain

Strain Designation DB1A

Culture col. no. DSM 12272 DB1A

NCBI tax ID(s) 1121314 94869

Special Collections DSMZ

History <- D. M. Broda, University of Waikato, Hamilton, New Zealand; DB1A <- D. M. Broda {1993}

Links

Clostridium gasigenes DB1A is an anaerobe, psychrophilic prokaryote that was isolated from vakuum-packed chilled lamb.

anaerobe psychrophilic genome sequence 16S sequence

Name and taxonomic classification

SI-ID 49264

DSM 12272,ATCC BAA-158,CIP 106517

@ref 20215

Last LPSN update 2025-12-16 09:47:23

Domain Bacillati

Phylum Bacillota

Class Clostridia

Order Eubacteriales

Family Clostridiaceae

Genus Clostridium

Species Clostridium gasigenes

Full scientific name Clostridium gasigenes Broda et al. 2000

Morphology

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
4666	PY + X MEDIUM (DSMZ Medium 104b)		Medium recipe at MediaDive	Name: PY + X MEDIUM (DSMZ Medium 104b) Composition: Yeast extract 10.0 g/l D-Glucose 5.0 g/l Trypticase peptone 5.0 g/l Meat peptone 5.0 g/l L-Cysteine HCl x H2O 0.5 g/l NaHCO3 0.4 g/l NaCl 0.08 g/l KH2PO4 0.04 g/l K2HPO4 0.04 g/l MgSO4 x 7 H2O 0.02 g/l CaCl2 x 2 H2O 0.01 g/l Sodium resazurin 0.0005 g/l Distilled water
4666	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
4666	positive	growth	20	psychrophilic

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
4666	anaerobe
125439	anaerobe	99.4

Pathway annotation

Computationally determined by

@ref	pathway	enzyme coverage	annotated reactions
66794	anapleurotic synthesis of oxalacetate	100	1 of 1
66794	adipate degradation	100	2 of 2
66794	L-lactaldehyde degradation	100	3 of 3
66794	starch degradation	100	10 of 10
66794	cis-vaccenate biosynthesis	100	2 of 2
66794	methylglyoxal degradation	100	5 of 5
66794	ppGpp biosynthesis	100	4 of 4
66794	palmitate biosynthesis	100	22 of 22
66794	CMP-KDO biosynthesis	100	4 of 4
66794	coenzyme A metabolism	100	4 of 4
66794	CDP-diacylglycerol biosynthesis	100	2 of 2
66794	UDP-GlcNAc biosynthesis	100	3 of 3
66794	suberin monomers biosynthesis	100	2 of 2
66794	C4 and CAM-carbon fixation	100	8 of 8
66794	cellulose degradation	100	5 of 5
66794	folate polyglutamylation	100	1 of 1
66794	pyrimidine metabolism	93.33	42 of 45
66794	d-mannose degradation	88.89	8 of 9
66794	chorismate metabolism	88.89	8 of 9
66794	gluconeogenesis	87.5	7 of 8
66794	flavin biosynthesis	86.67	13 of 15
66794	alanine metabolism	86.21	25 of 29
66794	photosynthesis	85.71	12 of 14
66794	tetrahydrofolate metabolism	85.71	12 of 14
66794	purine metabolism	85.11	80 of 94
66794	vitamin B1 metabolism	84.62	11 of 13
66794	NAD metabolism	83.33	15 of 18
66794	vitamin B12 metabolism	82.35	28 of 34
66794	threonine metabolism	80	8 of 10
66794	hydrogen production	80	4 of 5
66794	peptidoglycan biosynthesis	80	12 of 15
66794	metabolism of amino sugars and derivatives	80	4 of 5
66794	glycogen metabolism	80	4 of 5
66794	heme metabolism	78.57	11 of 14
66794	glutamate and glutamine metabolism	78.57	22 of 28
66794	valine metabolism	77.78	7 of 9
66794	serine metabolism	77.78	7 of 9
66794	aspartate and asparagine metabolism	77.78	7 of 9
66794	glycolysis	76.47	13 of 17
66794	biotin biosynthesis	75	3 of 4
66794	glycogen biosynthesis	75	3 of 4
66794	acetate fermentation	75	3 of 4
66794	butanoate fermentation	75	3 of 4
66794	propanol degradation	71.43	5 of 7
66794	cardiolipin biosynthesis	71.43	5 of 7
66794	ubiquinone biosynthesis	71.43	5 of 7
66794	reductive acetyl coenzyme A pathway	71.43	5 of 7
66794	phenylalanine metabolism	69.23	9 of 13
66794	urea cycle	69.23	9 of 13
66794	molybdenum cofactor biosynthesis	66.67	6 of 9
66794	acetoin degradation	66.67	2 of 3
66794	CO2 fixation in Crenarchaeota	66.67	6 of 9
66794	enterobactin biosynthesis	66.67	2 of 3
66794	cyanate degradation	66.67	2 of 3
66794	octane oxidation	66.67	2 of 3
66794	formaldehyde oxidation	66.67	2 of 3
66794	histidine metabolism	65.52	19 of 29
66794	citric acid cycle	64.29	9 of 14
66794	non-pathway related	63.16	24 of 38
66794	isoleucine metabolism	62.5	5 of 8
66794	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	62.5	5 of 8
66794	degradation of sugar alcohols	62.5	10 of 16
66794	oxidative phosphorylation	60.44	55 of 91
66794	4-hydroxyphenylacetate degradation	60	6 of 10
66794	Entner Doudoroff pathway	60	6 of 10
66794	degradation of aromatic, nitrogen containing compounds	58.33	7 of 12
66794	lipid metabolism	58.06	18 of 31
66794	isoprenoid biosynthesis	57.69	15 of 26
66794	glutathione metabolism	57.14	8 of 14
66794	cysteine metabolism	55.56	10 of 18
66794	proline metabolism	54.55	6 of 11
66794	d-xylose degradation	54.55	6 of 11
66794	arginine metabolism	54.17	13 of 24
66794	methionine metabolism	53.85	14 of 26
66794	sulfate reduction	53.85	7 of 13
66794	leucine metabolism	53.85	7 of 13
66794	sulfopterin metabolism	50	2 of 4
66794	phenylmercury acetate degradation	50	1 of 2
66794	selenocysteine biosynthesis	50	3 of 6
66794	pantothenate biosynthesis	50	3 of 6
66794	propionate fermentation	50	5 of 10
66794	glycolate and glyoxylate degradation	50	3 of 6
66794	aminopropanol phosphate biosynthesis	50	1 of 2
66794	toluene degradation	50	2 of 4
66794	dTDPLrhamnose biosynthesis	50	4 of 8
66794	tryptophan metabolism	50	19 of 38
66794	ethanol fermentation	50	1 of 2
66794	ketogluconate metabolism	50	4 of 8
66794	vitamin E metabolism	50	2 of 4
66794	lysine metabolism	47.62	20 of 42
66794	degradation of pentoses	46.43	13 of 28
66794	pentose phosphate pathway	45.45	5 of 11
66794	metabolism of disaccharids	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	glycine metabolism	40	4 of 10
66794	arachidonate biosynthesis	40	2 of 5
66794	phosphatidylethanolamine bioynthesis	38.46	5 of 13
66794	vitamin B6 metabolism	36.36	4 of 11
66794	phenol degradation	35	7 of 20
66794	polyamine pathway	34.78	8 of 23
66794	IAA biosynthesis	33.33	1 of 3
66794	arachidonic acid metabolism	33.33	6 of 18
66794	allantoin degradation	33.33	3 of 9
66794	degradation of hexoses	33.33	6 of 18
66794	phenylpropanoid biosynthesis	30.77	4 of 13
66794	myo-inositol biosynthesis	30	3 of 10
66794	benzoyl-CoA degradation	28.57	2 of 7
66794	ascorbate metabolism	27.27	6 of 22
66794	3-phenylpropionate degradation	26.67	4 of 15
66794	lactate fermentation	25	1 of 4
66794	methanogenesis from CO2	25	3 of 12
66794	cyclohexanol degradation	25	1 of 4
66794	4-hydroxymandelate degradation	22.22	2 of 9

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Engineered	#Food production	#Bottled, canned, packed food
#Engineered	#Food production	#Meat

Isolation

@ref	Sample type	Country	Country ISO 3 Code	Continent
4666	vakuum-packed chilled lamb	New Zealand	NZL	Australia and Oceania

Taxonmaps

69479

Global distribution of 16S sequence AF092548 (>99% sequence identity) for Clostridium gasigenes subclade from Microbeatlas

Aquatic Samples	865
Soil Samples	729
Animal Samples	975
Plant Samples	92
Total Samples	2661

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
4666	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	IMG-taxon 2634166322 annotated assembly for Clostridium gasigenes DSM 12272	scaffold	GCA_900104115	94869.18	2634166322	94869	66.87

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
4666	Clostridium gasigenes 16S ribosomal RNA gene, partial sequence	AF092548	1483		94869

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Clostridium gasigenes DSM 12272
NCBI: GCA_900104115

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	yes	82.80	no
125439	motility	BacteriaNetⓘ	yes	78.50	no
125439	gram_stain	BacteriaNetⓘ	positive	77.00	no
125439	oxygen_tolerance	BacteriaNetⓘ	anaerobe	99.40	no

Literature

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Comparative Genome Analysis and Phenotypic Characterization of Clostridium gasigenes CGAS001 Isolated From Chilled Vacuum-Packed Lamb Meat.	Wambui J, Cernela N, Corti S, Stephan R	Front Microbiol	10.3389/fmicb.2020.02048	2020
Phylogeny	Clostridium gasigenes sp. nov., a psychrophile causing spoilage of vacuum-packed meat.	Broda DM, Saul DJ, Lawson PA, Bell RG, Musgrave DR	Int J Syst Evol Microbiol	10.1099/00207713-50-1-107	2000

References

#4666	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 12272
#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 .
#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 gasigenes (DSM 12272, DB1A)

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

Taxonmaps

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_900104115

16S sequences

Genome-based predictions

Predictions

Literature

Literature

References

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