Name: Clostridium isatidis Wv6
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 2812

Type strain:

Species: Clostridium isatidis

Strain Designation: Wv6, Vv6

Culture col. no.: DSM 15098, NCFB 3071, NCIMB 703071, CIP 107118

Strain history: CIP <- 2001, NCIMB <- V. Dillon, Reading University, UK: strain Vv6

NCBI tax ID(s): 182773 (species)

SI-ID 62136

NCIMB 703071, CIP 107118, NCFB3071, DSM 15098

Other strains from Clostridium isatidis

C. isatidis STH00048(ZIMET), GT19951221, MCRL0129, ...

Section

Clostridium isatidis Wv6 is an anaerobe, spore-forming, mesophilic bacterium that was isolated from fermenting woad vat.

Gram-positive
spore-forming
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 isatidis**
	Full Scientific Name (LPSN)	Clostridium isatidis Padden et al. 1999

Information on morphological and physiological properties Morphology

[Ref.: #120283]	Gram stain	positive
[Ref.: #69480]	Gram stain	positive Confidence in %100

[Ref.: #120283]	Cell shape	rod-shaped

[Ref.: #120283]	Motility	yes

Information on culture and growth conditions Culture and growth conditions

[Ref.: #5710]

Culture medium

CHOPPED MEAT MEDIUM WITH CARBOHYDRATES (DSMZ Medium 110)

[Ref.: #5710]

Culture medium growth

[Ref.: #5710]

Culture medium link

Medium recipe at MediaDive

[Ref.: #5710]

Culture medium composition

expand / minimize

[Ref.: #33606]

Culture medium

MEDIUM 417 - for Clostridium isotidis

[Ref.: #33606]

Culture medium growth

[Ref.: #33606]

Culture medium composition

expand / minimize

[Ref.: #120283]

Culture medium

CIP Medium 417

[Ref.: #120283]

Culture medium growth

[Ref.: #120283]

Culture medium link

Medium recipe provided by DSMZ

		Temperature
[Ref.: #5710]	growth	37 °C
[Ref.: #33606]	growth	37 °C
[Ref.: #120283]	growth	37 °C

[Ref.: #5710]	Temperature range	mesophilic
[Ref.: #33606]	Temperature range	mesophilic
[Ref.: #120283]	Temperature range	mesophilic

Information on physiology and metabolism Physiology and metabolism

[Ref.: #5710]	Oxygen tolerance	anaerobe
[Ref.: #69480]	Oxygen tolerance	anaerobe Confidence in %98.648

[Ref.: #69481]	Ability of spore formation	yes Confidence in %100
[Ref.: #69480]	Ability of spore formation	yes Confidence in %96.328

	Pathway	Enzyme coverage	Annotated reactions
	Pathway annotation	Computationally determined by
[Ref.: #66794]	C4 and CAM-carbon fixation	100	8 of 8
[Ref.: #66794]	L-lactaldehyde degradation	100	3 of 3
[Ref.: #66794]	starch degradation	100	10 of 10
[Ref.: #66794]	methylglyoxal degradation	100	5 of 5
[Ref.: #66794]	cis-vaccenate biosynthesis	100	2 of 2
[Ref.: #66794]	palmitate biosynthesis	100	22 of 22
[Ref.: #66794]	gluconeogenesis	100	8 of 8
[Ref.: #66794]	reductive acetyl coenzyme A pathway	100	7 of 7
[Ref.: #66794]	ribulose monophosphate pathway	100	2 of 2
[Ref.: #66794]	formaldehyde oxidation	100	3 of 3
[Ref.: #66794]	suberin monomers biosynthesis	100	2 of 2
[Ref.: #66794]	folate polyglutamylation	100	1 of 1
[Ref.: #66794]	anapleurotic synthesis of oxalacetate	100	1 of 1
[Ref.: #66794]	CDP-diacylglycerol biosynthesis	100	2 of 2
[Ref.: #66794]	teichoic acid biosynthesis	100	1 of 1
[Ref.: #66794]	coenzyme A metabolism	100	4 of 4
[Ref.: #66794]	UDP-GlcNAc biosynthesis	100	3 of 3
[Ref.: #66794]	threonine metabolism	90	9 of 10
[Ref.: #66794]	chorismate metabolism	88.89	8 of 9
[Ref.: #66794]	ubiquinone biosynthesis	85.71	6 of 7
[Ref.: #66794]	photosynthesis	85.71	12 of 14
[Ref.: #66794]	vitamin B1 metabolism	84.62	11 of 13
[Ref.: #66794]	glycine betaine biosynthesis	80	4 of 5
[Ref.: #66794]	Entner Doudoroff pathway	80	8 of 10
[Ref.: #66794]	hydrogen production	80	4 of 5
[Ref.: #66794]	peptidoglycan biosynthesis	80	12 of 15
[Ref.: #66794]	glycogen metabolism	80	4 of 5
[Ref.: #66794]	valine metabolism	77.78	7 of 9
[Ref.: #66794]	aspartate and asparagine metabolism	77.78	7 of 9
[Ref.: #66794]	pyrimidine metabolism	77.78	35 of 45
[Ref.: #66794]	glycolysis	76.47	13 of 17
[Ref.: #66794]	sulfopterin metabolism	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]	ppGpp biosynthesis	75	3 of 4
[Ref.: #66794]	cardiolipin biosynthesis	71.43	5 of 7
[Ref.: #66794]	phenylalanine metabolism	69.23	9 of 13
[Ref.: #66794]	degradation of sugar alcohols	68.75	11 of 16
[Ref.: #66794]	purine metabolism	68.09	64 of 94
[Ref.: #66794]	d-mannose degradation	66.67	6 of 9
[Ref.: #66794]	octane oxidation	66.67	2 of 3
[Ref.: #66794]	acetoin degradation	66.67	2 of 3
[Ref.: #66794]	NAD metabolism	66.67	12 of 18
[Ref.: #66794]	molybdenum cofactor biosynthesis	66.67	6 of 9
[Ref.: #66794]	serine metabolism	66.67	6 of 9
[Ref.: #66794]	cyanate degradation	66.67	2 of 3
[Ref.: #66794]	non-pathway related	65.79	25 of 38
[Ref.: #66794]	oxidative phosphorylation	63.74	58 of 91
[Ref.: #66794]	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	62.5	5 of 8
[Ref.: #66794]	dTDPLrhamnose biosynthesis	62.5	5 of 8
[Ref.: #66794]	isoprenoid biosynthesis	61.54	16 of 26
[Ref.: #66794]	myo-inositol biosynthesis	60	6 of 10
[Ref.: #66794]	metabolism of amino sugars and derivatives	60	3 of 5
[Ref.: #66794]	histidine metabolism	58.62	17 of 29
[Ref.: #66794]	propanol degradation	57.14	4 of 7
[Ref.: #66794]	tryptophan metabolism	55.26	21 of 38
[Ref.: #66794]	alanine metabolism	55.17	16 of 29
[Ref.: #66794]	d-xylose degradation	54.55	6 of 11
[Ref.: #66794]	pentose phosphate pathway	54.55	6 of 11
[Ref.: #66794]	methionine metabolism	53.85	14 of 26
[Ref.: #66794]	urea cycle	53.85	7 of 13
[Ref.: #66794]	flavin biosynthesis	53.33	8 of 15
[Ref.: #66794]	toluene degradation	50	2 of 4
[Ref.: #66794]	ethanol fermentation	50	1 of 2
[Ref.: #66794]	glutamate and glutamine metabolism	50	14 of 28
[Ref.: #66794]	tetrahydrofolate metabolism	50	7 of 14
[Ref.: #66794]	dolichol and dolichyl phosphate biosynthesis	50	1 of 2
[Ref.: #66794]	glycolate and glyoxylate degradation	50	3 of 6
[Ref.: #66794]	vitamin E metabolism	50	2 of 4
[Ref.: #66794]	CMP-KDO biosynthesis	50	2 of 4
[Ref.: #66794]	phenylmercury acetate degradation	50	1 of 2
[Ref.: #66794]	ketogluconate metabolism	50	4 of 8
[Ref.: #66794]	butanoate fermentation	50	2 of 4
[Ref.: #66794]	glutathione metabolism	50	7 of 14
[Ref.: #66794]	adipate degradation	50	1 of 2
[Ref.: #66794]	arginine metabolism	50	12 of 24
[Ref.: #66794]	cysteine metabolism	50	9 of 18
[Ref.: #66794]	leucine metabolism	46.15	6 of 13
[Ref.: #66794]	proline metabolism	45.45	5 of 11
[Ref.: #66794]	metabolism of disaccharids	45.45	5 of 11
[Ref.: #66794]	lysine metabolism	45.24	19 of 42
[Ref.: #66794]	lipid metabolism	45.16	14 of 31
[Ref.: #66794]	CO2 fixation in Crenarchaeota	44.44	4 of 9
[Ref.: #66794]	citric acid cycle	42.86	6 of 14
[Ref.: #66794]	propionate fermentation	40	4 of 10
[Ref.: #66794]	arachidonate biosynthesis	40	2 of 5
[Ref.: #66794]	cellulose degradation	40	2 of 5
[Ref.: #66794]	bacilysin biosynthesis	40	2 of 5
[Ref.: #66794]	glycine metabolism	40	4 of 10
[Ref.: #66794]	arachidonic acid metabolism	38.89	7 of 18
[Ref.: #66794]	phosphatidylethanolamine bioynthesis	38.46	5 of 13
[Ref.: #66794]	tyrosine metabolism	35.71	5 of 14
[Ref.: #66794]	polyamine pathway	34.78	8 of 23
[Ref.: #66794]	sphingosine metabolism	33.33	2 of 6
[Ref.: #66794]	lipid A biosynthesis	33.33	3 of 9
[Ref.: #66794]	methane metabolism	33.33	1 of 3
[Ref.: #66794]	degradation of hexoses	33.33	6 of 18
[Ref.: #66794]	degradation of aromatic, nitrogen containing compounds	33.33	4 of 12
[Ref.: #66794]	nitrate assimilation	33.33	3 of 9
[Ref.: #66794]	IAA biosynthesis	33.33	1 of 3
[Ref.: #66794]	selenocysteine biosynthesis	33.33	2 of 6
[Ref.: #66794]	degradation of pentoses	32.14	9 of 28
[Ref.: #66794]	phenylpropanoid biosynthesis	30.77	4 of 13
[Ref.: #66794]	coenzyme M biosynthesis	30	3 of 10
[Ref.: #66794]	4-hydroxyphenylacetate degradation	30	3 of 10
[Ref.: #66794]	vitamin B6 metabolism	27.27	3 of 11
[Ref.: #66794]	ascorbate metabolism	27.27	6 of 22
[Ref.: #66794]	carnitine metabolism	25	2 of 8
[Ref.: #66794]	cyclohexanol degradation	25	1 of 4
[Ref.: #66794]	lactate fermentation	25	1 of 4
[Ref.: #66794]	biotin biosynthesis	25	1 of 4
[Ref.: #66794]	degradation of sugar acids	24	6 of 25
[Ref.: #66794]	sulfate reduction	23.08	3 of 13
		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.: #5710]	Sample type/isolated from	fermenting woad vat
[Ref.: #5710]	Geographic location (country and/or sea, region)	Reading
[Ref.: #5710]	Country	United Kingdom
[Ref.: #5710]	Country ISO 3 Code	GBR
[Ref.: #5710]	Continent	Europe

[Ref.: #120283]	Sample type/isolated from	Woad vat
[Ref.: #120283]	Country	United Kingdom
[Ref.: #120283]	Country ISO 3 Code	GBR
[Ref.: #120283]	Continent	Europe
* marker position based on {}

Isolation sources categories

#Engineered

#Industrial

#Engineered product

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence X98395 (>99% sequence identity) for Clostridium from Microbeatlas

Aquatic Samples	34
Soil Samples	58
Animal Samples	300
Plant Samples	23
Total Samples	415

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

[Ref.: #5710]	Biosafety level	1	Risk group (German classification) According to TRBA 466
[Ref.: #120283]	Biosafety level	2	Risk group (French classification)

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.: #5710]	Clostridium sp. 16S rRNA gene	X98395	1332	ENA	1506 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Clostridium isatidis DSM 15098	GCA_002285495	complete	GenBank	182773 tax ID	*
[Ref.: #66792]	Clostridium isatidis strain DSM 15098	182773.3	complete	PATRIC	182773 tax ID	*
[Ref.: #66792]	Clostridium isatidis DSM 15098	2877451605	complete	JGI IMG/M	182773 tax ID	*

[Ref.: #5710]

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 GenomeNet Sporulation v. 1 based on: Clostridium isatidis DSM 15098 NCBI: GCA_002285495.1
[Ref.: #69481]	spore-forming	yes	100	no

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Clostridium isatidis DSM 15098 NCBI: GCA_002285495.1
[Ref.: #69480]	flagellated	no	50.809	no
[Ref.: #69480]	gram-positive	yes	82.711	no
[Ref.: #69480]	anaerobic	yes	98.152	yes
[Ref.: #69480]	aerobic	no	99.463	yes
[Ref.: #69480]	halophile	no	85.812	no
[Ref.: #69480]	spore-forming	yes	93.776	no
[Ref.: #69480]	glucose-util	yes	85.844	no
[Ref.: #69480]	thermophile	no	91.489	yes
[Ref.: #69480]	motile	yes	79.801	no
[Ref.: #69480]	glucose-ferment	yes	72.092	no

Availability in culture collections External links

[Ref.: #5710]

Culture collection no.

DSM 15098, NCFB 3071, NCIMB 703071, CIP 107118

[Ref.: #72338]

SI-ID 62136

Literature:

Topic	Title	Authors	Journal	DOI	Year
Metabolism	Implementation of a biotechnological process for vat dyeing with woad.	Osimani A, Aquilanti L, Baldini G, Silvestri G, Butta A, Clementi F	J Ind Microbiol Biotechnol	10.1007/s10295-012-1139-4	2012	*
Phylogeny	An indigo-reducing moderate thermophile from a woad vat, Clostridium isatidis sp. nov.	Padden AN, Dillon VM, Edmonds J, Collins MD, Alvarez N, John P	Int J Syst Bacteriol	10.1099/00207713-49-3-1025	1999	*

References

#5710

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 15098

#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 )

#33606 ; Curators of the CIP;

#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 .

#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 )

#72338

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-ID62136.1 )

#120283 Collection of Institut Pasteur ; Curators of the CIP; CIP 107118
* These data were automatically processed and therefore are not curated

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Clostridium isatidis DSM 15098

Clostridium isatidis DSM 15098

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