Name: Clostridium innocuum B-3
Creator: BacDive
License: https://creativecommons.org/licenses/by/4.0/

Strain identifier

BacDive ID: 2603

Type strain:

Species: Clostridium innocuum

Strain Designation: B-3

Culture col. no.: DSM 1286, ATCC 14501, NCIB 10674, JCM 1292, BCRC 14517, CCUG 24036, CCUG 35868, CCUG 36763, KCTC 5183, NCIMB 10674

Strain history: ATCC 14501 <-- L. DS. Smith B-3 <-- CDC (E. King) <-- Murfreesboro Med. Clinic, TN, USA.

NCBI tax ID(s): 1522 (species)

SI-ID 92603

ATCC 14501, CCUG 24036, DSM 1286, NCIB 10674, CCUG 35868, CCUG 36763, NCIMB 10674, JCM 1292, CCRC 14517, BCRC 14517, KCTC 5183, LMG 28905

Special Collections

Other strains from Clostridium innocuum

Section

Clostridium innocuum B-3 is an anaerobe, spore-forming, mesophilic bacterium that was isolated from appendiceal abscess.

spore-forming
anaerobe
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 innocuum**
	Full Scientific Name (LPSN)	Clostridium innocuum Smith and King 1962 (Approved Lists 1980)

Information on culture and growth conditions Culture and growth conditions

[Ref.: #606]

Culture medium

CHOPPED MEAT MEDIUM (DSMZ Medium 78)

[Ref.: #606]

Culture medium growth

[Ref.: #606]

Culture medium link

Medium recipe at MediaDive

[Ref.: #606]

Culture medium composition

expand / minimize

	Temperatures	Kind of temperature		Temperature
[Ref.: #606]			growth	37 °C
[Ref.: #67770]			growth	37 °C

Information on physiology and metabolism Physiology and metabolism

[Ref.: #606]

Oxygen tolerance

anaerobe

[Ref.: #69481]

Ability of spore formation

yes Confidence in %95

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

[Ref.: #67770]	Sample type/isolated from	Appendiceal abscess
* marker position based on {}

Isolation sources categories

#Host Body-Site	#Gastrointestinal tract	#Large intestine
#Host Body-Site	#Other	#Abscess

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence AB971793 (>99% sequence identity) for [Clostridium] innocuum subclade from Microbeatlas

Aquatic Samples	1
Soil Samples	1
Animal Samples	1573
Plant Samples
Total Samples	1575

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

[Ref.: #606]

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.: #67770]	[Clostridium] innocuum gene for 16S ribosomal RNA, partial sequence, strain: JCM 1292	AB971793	1501	GenBank ENA	1522 tax ID
[Ref.: #606]	[Clostridium] innocuum strain B-3 16S ribosomal RNA gene, partial sequence	M23732	1543	GenBank ENA	1522 tax ID
[Ref.: #20218]	Clostridium innocuum strain DSM 1286 16S ribosomal RNA gene, partial sequence	HM245947	832	GenBank ENA	1522 tax ID	*

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	[Clostridium] innocuum ATCC 14501	GCA_012317185	complete	GenBank ENA	1522 tax ID	*
[Ref.: #66792]	[Clostridium] innocuum ATCC 14501	GCA_018458805	scaffold	GenBank ENA	1522 tax ID	*
[Ref.: #66792]	[Clostridium] innocuum strain ATCC 14501	1522.132	complete	PATRIC	1522 tax ID	*
[Ref.: #66792]	[Clostridium] innocuum strain ATCC 14501	1522.172	wgs	PATRIC	1522 tax ID	*

[Ref.: #606]	GC-content	44.0 mol%
[Ref.: #67770]	GC-content	44 mol%	thermal denaturation, midpoint method (Tm)
[Ref.: #67770]	GC-content	44.5 mol%	genome sequence analysis

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

	Trait	Model	Prediction	Confidence in %	In training data
	Predictions from GenomeNet Sporulation v. 1 based on: [Clostridium] innocuum ATCC 14501 NCBI: GCA_012317185.1
[Ref.: #69481]	spore-forming	spore-formingⓘ	yes	95	no

	Trait	Model	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: [Clostridium] innocuum ATCC 14501 NCBI: GCA_012317185.1
[Ref.: #69480]	gram-positive	gram-positiveⓘ	yes	77.482	no
[Ref.: #69480]	anaerobic	anaerobicⓘ	yes	83.449	yes
[Ref.: #69480]	aerobic	aerobicⓘ	no	96.798	yes
[Ref.: #69480]	spore-forming	spore-formingⓘ	no	52.977	no
[Ref.: #69480]	thermophilic	thermophileⓘ	no	92.29	yes
[Ref.: #69480]	flagellated	motile2+ⓘ	no	78.009	no

Availability in culture collections External links

[Ref.: #606]

Culture collection no.

DSM 1286, ATCC 14501, NCIB 10674, JCM 1292, BCRC 14517, CCUG 24036, CCUG 35868, CCUG 36763, KCTC 5183, NCIMB 10674

[Ref.: #72134]

SI-ID 92603

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Description of a new member of the family Erysipelotrichaceae: Dakotella fusiforme gen. nov., sp. nov., isolated from healthy human feces.	Ghimire S, Wongkuna S, Scaria J	PeerJ	10.7717/peerj.10071	2020	*
Genetics	Complete Genome Sequence of Clostridium innocuum Strain ATCC 14501.	Cherny KE, Ozer EA, Kochan TJ, Kociolek LK	Microbiol Resour Announc	10.1128/MRA.00452-20	2020	*
Phylogeny	Description of Absiella argi gen. nov., sp. nov., and transfer of Eubacterium dolichum and Eubacterium tortuosum to the genus Absiella as Absiella dolichum comb. nov. and Absiella tortuosum comb. nov.	Paek J, Shin Y, Kim JS, Kim H, Kook JK, Paek WK, Chang YH	Anaerobe	10.1016/j.anaerobe.2017.07.006	2017	*
Genetics	Mechanism of intrinsic resistance to vancomycin in Clostridium innocuum NCIB 10674.	David V, Bozdogan B, Mainardi JL, Legrand R, Gutmann L, Leclercq R	J Bacteriol	10.1128/JB.186.11.3415-3422.2004	2004	*
Pathogenicity	Low-level vancomycin resistance in Clostridium innocuum.	Mory F, Lozniewski A, David V, Carlier JP, Dubreuil L, Leclercq R	J Clin Microbiol	10.1128/JCM.36.6.1767-1768.1998	1998	*

References

#606	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 1286

#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 )

#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) .

#69481

Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch: Predictions based on the model GenomeNet Sporulation v. 1 . ( DOI 10.21203/rs.3.rs-2527258/v1 )

#72134

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-ID92603.1 )

* These data were automatically processed and therefore are not curated

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[Clostridium] innocuum ATCC 14501

[Clostridium] innocuum ATCC 14501

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