Clostridium innocuum (DSM 29132, A-C3-1)

Name: Clostridium innocuum (DSM 29132, A-C3-1)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 130921

Type strain

Strain Designation A-C3-1

Culture col. no. DSM 29132 A-C3-1

NCBI tax ID(s) 1522

Special Collections DSMZ Mouse DZIF

History <- T. Clavel, TU Munich, Freising-Weihenstephan, Germany; A-C3-1

Links

Clostridium innocuum A-C3-1 is an anaerobe bacterium that was isolated from caecal content; wildtype C57BL/6 mouse.

anaerobe genome sequence 16S sequence Bacteria

Name and taxonomic classification

SI-ID 407410

DSM 29132

@ref 20215

Last LPSN update 2026-02-09 11:31:20

Domain Bacteria

Phylum Bacillota

Class Clostridia

Order Eubacteriales

Family Clostridiaceae

Genus Clostridium

Species Clostridium innocuum

Full scientific name Clostridium innocuum Smith and King 1962 (Approved Lists 1980)

BacDive ID	Other strains from **Clostridium innocuum** (10)	Type strain
2603	C. innocuum B-3, DSM 1286, ATCC 14501, NCIB 10674, JCM ... (type strain)
130922	C. innocuum I46, DSM 26113
2604	C. innocuum SB23, DSM 22910
149069	C. innocuum CCUG 36812
151996	C. innocuum CCUG 45485
152489	C. innocuum CCUG 46922
155352	C. innocuum CCUG 57429
158912	C. innocuum BSM-380-WT-2D, DSM 100998
158913	C. innocuum H4_16, DSM 108163
160008	C. innocuum Cla-CZ-133, DSM 107457

Morphology

Cell morphology

@ref	Motility	Confidence
125439		91.2

Colony morphology

22213

Incubation period2-3 days

Culture and growth conditions

Culture medium

@ref	Name	Medium link	Composition
22213	FASTIDIOUS ANAEROBE AGAR (DSMZ Medium 1203)	Medium recipe at MediaDive	Name: FASTIDIOUS ANAEROBE AGAR (DSMZ Medium 1203) Composition: Horse blood 100.0 g/l Fastidious Anaerobe Agar 45.7 g/l Distilled water
22213	CHOPPED MEAT MEDIUM (DSMZ Medium 78)	Medium recipe at MediaDive	Name: CHOPPED MEAT MEDIUM (DSMZ Medium 78) Composition: Ground beef 500.0 g/l Casitone 30.0 g/l Agar 15.0 g/l Ethanol 9.5 g/l (optional) K2HPO4 5.0 g/l Yeast extract 5.0 g/l L-Cysteine HCl 0.5 g/l Haemin 0.005 g/l (optional) Resazurin 0.001 g/l Vitamin K3 0.0005 g/l (optional) Vitamin K1 (optional) NaOH (optional) Distilled water
22213	WILKINS-CHALGREN ANAEROBE BROTH (DSMZ Medium 339)	Medium recipe at MediaDive	Name: WILKINS-CHALGREN ANAEROBE BROTH (DSMZ Medium 339) Composition: dehydrated Wilkins-Chalgren medium 33.0 g/l L-Cysteine HCl 0.3 g/l Sodium resazurin 0.0005 g/l Distilled water

Culture temp

@ref	Growth	Type	Temperature (°C)
22213	positive	growth	37

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
22213	anaerobe
125439	obligate aerobe	94.9

Spore formation

@ref	Spore formation	Confidence
125439		96.3

Pathway annotation

Computationally determined by

@ref	pathway	enzyme coverage	annotated reactions
66794	cellulose degradation	100	5 of 5
66794	cardiolipin biosynthesis	100	7 of 7
66794	pentose phosphate pathway	100	11 of 11
66794	adipate degradation	100	2 of 2
66794	ribulose monophosphate pathway	100	2 of 2
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	L-lactaldehyde degradation	100	3 of 3
66794	teichoic acid biosynthesis	100	1 of 1
66794	suberin monomers biosynthesis	100	2 of 2
66794	anapleurotic synthesis of oxalacetate	100	1 of 1
66794	folate polyglutamylation	100	1 of 1
66794	degradation of sugar alcohols	93.75	15 of 16
66794	peptidoglycan biosynthesis	93.33	14 of 15
66794	vitamin B1 metabolism	92.31	12 of 13
66794	threonine metabolism	90	9 of 10
66794	aspartate and asparagine metabolism	88.89	8 of 9
66794	chorismate metabolism	88.89	8 of 9
66794	valine metabolism	88.89	8 of 9
66794	flavin biosynthesis	86.67	13 of 15
66794	palmitate biosynthesis	86.36	19 of 22
66794	reductive acetyl coenzyme A pathway	85.71	6 of 7
66794	Entner Doudoroff pathway	80	8 of 10
66794	starch degradation	80	8 of 10
66794	glycogen metabolism	80	4 of 5
66794	photosynthesis	78.57	11 of 14
66794	heme metabolism	78.57	11 of 14
66794	d-mannose degradation	77.78	7 of 9
66794	NAD metabolism	77.78	14 of 18
66794	serine metabolism	77.78	7 of 9
66794	purine metabolism	77.66	73 of 94
66794	pyrimidine metabolism	75.56	34 of 45
66794	lactate fermentation	75	3 of 4
66794	glycogen biosynthesis	75	3 of 4
66794	isoleucine metabolism	75	6 of 8
66794	acetate fermentation	75	3 of 4
66794	C4 and CAM-carbon fixation	75	6 of 8
66794	butanoate fermentation	75	3 of 4
66794	glutamate and glutamine metabolism	75	21 of 28
66794	ppGpp biosynthesis	75	3 of 4
66794	alanine metabolism	72.41	21 of 29
66794	propanol degradation	71.43	5 of 7
66794	glycolysis	70.59	12 of 17
66794	phenylalanine metabolism	69.23	9 of 13
66794	methane metabolism	66.67	2 of 3
66794	glycolate and glyoxylate degradation	66.67	4 of 6
66794	octane oxidation	66.67	2 of 3
66794	cyanate degradation	66.67	2 of 3
66794	formaldehyde oxidation	66.67	2 of 3
66794	acetoin degradation	66.67	2 of 3
66794	CO2 fixation in Crenarchaeota	66.67	6 of 9
66794	d-xylose degradation	63.64	7 of 11
66794	dTDPLrhamnose biosynthesis	62.5	5 of 8
66794	gluconeogenesis	62.5	5 of 8
66794	ketogluconate metabolism	62.5	5 of 8
66794	histidine metabolism	62.07	18 of 29
66794	oxidative phosphorylation	61.54	56 of 91
66794	methionine metabolism	61.54	16 of 26
66794	non-pathway related	60.53	23 of 38
66794	phenylacetate degradation (aerobic)	60	3 of 5
66794	glycine betaine biosynthesis	60	3 of 5
66794	hydrogen production	60	3 of 5
66794	factor 420 biosynthesis	60	3 of 5
66794	methylglyoxal degradation	60	3 of 5
66794	metabolism of amino sugars and derivatives	60	3 of 5
66794	citric acid cycle	57.14	8 of 14
66794	tetrahydrofolate metabolism	57.14	8 of 14
66794	tryptophan metabolism	55.26	21 of 38
66794	metabolism of disaccharids	54.55	6 of 11
66794	proline metabolism	54.55	6 of 11
66794	leucine metabolism	53.85	7 of 13
66794	sphingosine metabolism	50	3 of 6
66794	ethanol fermentation	50	1 of 2
66794	CMP-KDO biosynthesis	50	2 of 4
66794	myo-inositol biosynthesis	50	5 of 10
66794	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	50	4 of 8
66794	isoprenoid biosynthesis	50	13 of 26
66794	degradation of pentoses	50	14 of 28
66794	sulfopterin metabolism	50	2 of 4
66794	toluene degradation	50	2 of 4
66794	glycine metabolism	50	5 of 10
66794	cis-vaccenate biosynthesis	50	1 of 2
66794	selenocysteine biosynthesis	50	3 of 6
66794	phenylmercury acetate degradation	50	1 of 2
66794	cysteine metabolism	50	9 of 18
66794	urea cycle	46.15	6 of 13
66794	sulfate reduction	46.15	6 of 13
66794	arginine metabolism	45.83	11 of 24
66794	molybdenum cofactor biosynthesis	44.44	4 of 9
66794	nitrate assimilation	44.44	4 of 9
66794	degradation of hexoses	44.44	8 of 18
66794	tyrosine metabolism	42.86	6 of 14
66794	ubiquinone biosynthesis	42.86	3 of 7
66794	lipid metabolism	41.94	13 of 31
66794	degradation of aromatic, nitrogen containing compounds	41.67	5 of 12
66794	lysine metabolism	40.48	17 of 42
66794	gallate degradation	40	2 of 5
66794	4-hydroxyphenylacetate degradation	40	4 of 10
66794	phenylpropanoid biosynthesis	38.46	5 of 13
66794	phosphatidylethanolamine bioynthesis	38.46	5 of 13
66794	ascorbate metabolism	36.36	8 of 22
66794	degradation of sugar acids	36	9 of 25
66794	glutathione metabolism	35.71	5 of 14
66794	IAA biosynthesis	33.33	1 of 3
66794	acetyl CoA biosynthesis	33.33	1 of 3
66794	enterobactin biosynthesis	33.33	1 of 3
66794	lipid A biosynthesis	33.33	3 of 9
66794	coenzyme M biosynthesis	30	3 of 10
66794	phenol degradation	30	6 of 20
66794	propionate fermentation	30	3 of 10
66794	benzoyl-CoA degradation	28.57	2 of 7
66794	vitamin B6 metabolism	27.27	3 of 11
66794	3-phenylpropionate degradation	26.67	4 of 15
66794	biotin biosynthesis	25	1 of 4
66794	cyclohexanol degradation	25	1 of 4
66794	carnitine metabolism	25	2 of 8
66794	vitamin B12 metabolism	23.53	8 of 34
66794	allantoin degradation	22.22	2 of 9
66794	4-hydroxymandelate degradation	22.22	2 of 9

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Host	#Mammals	#Muridae (Mouse/Rat)
#Host Body-Site	#Gastrointestinal tract	#Large intestine
#Host Body Product	#Gastrointestinal tract	#Caecal content

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent
22213	caecal content; wildtype C57BL/6 mouse	Freising	Germany	DEU	Europe

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
22213	2	Risk group (German classification)

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID
66792	ASM2462296v1 assembly for [Clostridium] innocuum DSM 29132	contig	GCA_024622965	1522.289	8067332837	1522

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
22213	[Clostridium] innocuum strain A-C3-1 16S ribosomal RNA gene, partial sequence	GQ456207	1440		1522

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: [Clostridium] innocuum DSM 29132
NCBI: GCA_024622965

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	yes	96.30	no
125439	motility	BacteriaNetⓘ	yes	91.20	no
125439	gram_stain	BacteriaNetⓘ	variable	89.70	no
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	94.90	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: [Clostridium] innocuum DSM 29132
NCBI: GCA_024622965.1

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	yes	76.01	no
125438	anaerobic	anaerobicⓘ	yes	85.95	yes
125438	aerobic	aerobicⓘ	no	96.78	no
125438	spore-forming	spore-formingⓘ	no	56.05	no
125438	thermophilic	thermophileⓘ	no	90.82	no
125438	flagellated	motile2+ⓘ	no	80.94	no

Literature

References

#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 )
#22213	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 29132
#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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