Name: Clostridioides difficile 630 Delta erm
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 23855

Type strain:

Species: Clostridioides difficile

Strain Designation: 630 Delta erm

Culture col. no.: DSM 28645

Strain history: <- R. Gerhard <- N. P. Minton <- H. A. Hussain; 630 Delta erm

NCBI tax ID(s): 1496 (species)

SI-ID 397186

DSM 28645

Other strains from Clostridioides difficile

Section

Clostridioides difficile 630 Delta erm is an anaerobe, spore-forming, mesophilic human pathogen of the family Peptostreptococcaceae.

rod-shaped
spore-forming
anaerobe
human pathogen
mesophilic
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	*Peptostreptococcaceae*
	Genus	*Clostridioides*
	Species	**Clostridioides difficile**
	Full Scientific Name (LPSN)	Clostridioides difficile (Hall and O'Toole 1935) Lawson et al. 2016

	Synonym	"Bacillus* difficilis"*
	Synonym	"Peptoclostridium* difficile"*
	Synonym	Clostridium difficile

Information on morphological and physiological properties Morphology

[Ref.: #68367]	Gram stain	positive * from API 20A

[Ref.: #68367]	Cell shape	rod-shaped * from API 20A

[Ref.: #20944]	Type of hemolysis	gamma
[Ref.: #20944]	Incubation period	1-2 days

Information on culture and growth conditions Culture and growth conditions

[Ref.: #20944]

Culture medium

FASTIDIOUS ANAEROBE AGAR (DSMZ Medium 1203)

[Ref.: #20944]

Culture medium growth

[Ref.: #20944]

Culture medium link

Medium recipe at MediaDive

[Ref.: #20944]

Culture medium composition

expand / minimize

[Ref.: #20944]

Culture medium

CHOPPED MEAT MEDIUM (DSMZ Medium 78)

[Ref.: #20944]

Culture medium growth

[Ref.: #20944]

Culture medium link

Medium recipe at MediaDive

[Ref.: #20944]

Culture medium composition

expand / minimize

	Temperatures	Kind of temperature		Temperature
[Ref.: #20944]			growth	37 °C

[Ref.: #20944]

Temperature range

mesophilic

Information on physiology and metabolism Physiology and metabolism

[Ref.: #20944]

Oxygen tolerance

anaerobe

[Ref.: #68367]

Ability of spore formation

yes * from API 20A

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #68380]	arginine ChEBI	-	hydrolysis	* from API rID32A
[Ref.: #68367]	D-glucose ChEBI	+	builds acid from	* from API 20A
[Ref.: #68367]	D-mannitol ChEBI	+	builds acid from	* from API 20A
[Ref.: #68367]	D-mannose ChEBI	+	builds acid from	* from API 20A
[Ref.: #68380]	D-mannose ChEBI	+	fermentation	* from API rID32A
[Ref.: #68367]	D-xylose ChEBI	+	builds acid from	* from API 20A
[Ref.: #68367]	esculin ChEBI	+	hydrolysis	* from API 20A
[Ref.: #68367]	gelatin ChEBI	+	hydrolysis	* from API 20A
[Ref.: #68367]	glycerol ChEBI	-	builds acid from	* from API 20A
[Ref.: #68367]	L-arabinose ChEBI	-	builds acid from	* from API 20A
[Ref.: #68380]	L-glutamate ChEBI	-	degradation	* from API rID32A
[Ref.: #68367]	L-rhamnose ChEBI	-	builds acid from	* from API 20A
[Ref.: #68367]	lactose ChEBI	-	builds acid from	* from API 20A
[Ref.: #68367]	maltose ChEBI	-	builds acid from	* from API 20A
[Ref.: #68367]	melezitose ChEBI	+	builds acid from	* from API 20A
[Ref.: #68380]	nitrate ChEBI	-	reduction	* from API rID32A
[Ref.: #68367]	raffinose ChEBI	-	builds acid from	* from API 20A
[Ref.: #68380]	raffinose ChEBI	-	fermentation	* from API rID32A
[Ref.: #68367]	salicin ChEBI	+	builds acid from	* from API 20A
[Ref.: #68367]	sucrose ChEBI	-	builds acid from	* from API 20A
[Ref.: #68367]	trehalose ChEBI	+	builds acid from	* from API 20A
[Ref.: #68367]	tryptophan ChEBI	-	energy source	* from API 20A, API rID32A
[Ref.: #68367]	urea ChEBI	-	hydrolysis	* from API 20A, API rID32A
	Only first 10 entries are displayed. Click here to see all.

	Metabolite production	Metabolite	Production
[Ref.: #68367]		indole ChEBI	no	* from API 20A, API rID32A

	Physiological tests	Metabolite	Indole test
[Ref.: #68380]		indole ChEBI	-	* from API rID32A, API 20A

	Enzyme	Enzyme activity	EC number
[Ref.: #68380]	alanine arylamidase	-	3.4.11.2	* from API rID32A
[Ref.: #68380]	alkaline phosphatase	-	3.1.3.1	* from API rID32A
[Ref.: #68380]	alpha-arabinosidase	-	3.2.1.55	* from API rID32A
[Ref.: #68380]	alpha-fucosidase	-	3.2.1.51	* from API rID32A
[Ref.: #68380]	alpha-galactosidase	-	3.2.1.22	* from API rID32A
[Ref.: #68380]	alpha-glucosidase	-	3.2.1.20	* from API rID32A
[Ref.: #68380]	arginine dihydrolase	-	3.5.3.6	* from API rID32A
[Ref.: #68380]	beta-galactosidase	-	3.2.1.23	* from API rID32A
[Ref.: #68380]	beta-Galactosidase 6-phosphate	-		* from API rID32A
[Ref.: #68367]	beta-glucosidase	+	3.2.1.21	* from API 20A
[Ref.: #68380]	beta-glucosidase	-	3.2.1.21	* from API rID32A
[Ref.: #68380]	beta-glucuronidase	-	3.2.1.31	* from API rID32A
[Ref.: #20944]	cytochrome-c oxidase	-	1.9.3.1
[Ref.: #68367]	gelatinase	+		* from API 20A
[Ref.: #68380]	glutamate decarboxylase	-	4.1.1.15	* from API rID32A
[Ref.: #68380]	glutamyl-glutamate arylamidase	-		* from API rID32A
[Ref.: #68380]	glycin arylamidase	-		* from API rID32A
[Ref.: #68380]	histidine arylamidase	-		* from API rID32A
[Ref.: #68380]	L-arginine arylamidase	-		* from API rID32A
[Ref.: #68380]	N-acetyl-beta-glucosaminidase	-	3.2.1.52	* from API rID32A
[Ref.: #68380]	phenylalanine arylamidase	-		* from API rID32A
[Ref.: #68380]	proline-arylamidase	+	3.4.11.5	* from API rID32A
[Ref.: #68380]	pyrrolidonyl arylamidase	-	3.4.19.3	* from API rID32A
[Ref.: #68380]	serine arylamidase	-		* from API rID32A
[Ref.: #68380]	tryptophan deaminase	-	4.1.99.1	* from API rID32A
[Ref.: #68380]	tyrosine arylamidase	-		* from API rID32A
[Ref.: #68380]	urease	-	3.5.1.5	* from API rID32A, API 20A
	Only first 10 entries are displayed. Click here to see all.

API® 20A:

Note that the displayed test results represent raw data and therefore may deviate!

	API ID	Indole productionIND	Urease/urea hydrolysisURE	Acid from D-glucoseGLU	Acid from D-mannitolMAN	Acid from lactoseLAC	Acid from sucroseSAC	Acid from maltoseMAL	Acid from salicinSAL	Acid from D-xyloseXYL	Acid from L-arabinoseARA	Gelatinase/gelatin hydrolysisGEL	Esculin hydrolysis/beta-glucosidaseESC	Acid from glycerolGLY	Acid from cellobioseCEL	Acid from D-mannoseMNE	Acid from melezitoseMLZ	Acid from raffinoseRAF	Acid from sorbitolSOR	Acid from L-rhamnoseRHA	Acid from trehaloseTRE	CatalaseCAT	Spores presentSPOR	GramGRAM	Morphology coccus="+" rod="-"COCC
[Ref.: #20944]	2109	-	-	+	+	-	-	-	+	+	-	+	+	-	+/-	+	+	-	-	-	+	+	+	+	-
[Ref.: #20944]	2108	-	-	+	+	-	-	-	+	+	-	+	+	-	+	+	+	-	+/-	-	+	+/-	+	+	-

API® rID32A:

Note that the displayed test results represent raw data and therefore may deviate!

	API ID	Urease/urea hydrolysisURE	Arginine dihydrolaseADH (Arg)	alpha-Galactosidasealpha GAL	beta-Galactosidasebeta GAL	beta-Galactosidase 6-phosphatebeta GP	alpha-Glucosidasealpha GLU	beta-Glucosidasebeta GLU	alpha-Arabinosidasealpha ARA	beta-Glucuronidasebeta GUR	beta-N-Acetyl-beta-glucosaminidasebeta NAG	Fermentation of D-mannoseMNE	Fermentation of raffinoseRAF	Glutamate decarboxylaseGDC	alpha-Fucosidasealpha FUC	Reduction of nitrateNIT	Indole productionIND	Alkaline phosphatasePAL	L-arginine arylamidaseArgA	Proline arylamidaseProA	Leucyl glycin arylamidaseLGA	Phenylalanine arylamidasePheA	Leucine arylamidaseLeuA	Pyrrolidonyl arylamidasePyrA	Tyrosine arylamidaseTyrA	Alanine arylamidaseAlaA	Glycin arylamidaseGlyA	Histidine arylamidaseHisA	Glutamyl-glutamate arylamidaseGGA	Serine arylamidaseSerA
[Ref.: #20944]	13280	-	-	-	-	-	-	-	-	-	-	+	-	-	-	-	-	-	-	+	-	-	-	-	-	-	-	-	-	-
[Ref.: #20944]	12469	-	-	-	-	-	-	-	-	-	-	+	-	-	-	-	-	-	-	+	+/-	-	+/-	-	-	-	-	-	-	-

Information on isolation source, the sampling and environmental conditions Isolation, sampling and environmental information

[Ref.: #20944]	Country	United Kingdom
[Ref.: #20944]	Country ISO 3 Code	GBR
[Ref.: #20944]	Continent	Europe
* marker position based on {}

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

[Ref.: #20944]	Pathogenicity (human)	yes
[Ref.: #20944]	Pathogenicity (animal)	yes
[Ref.: #20944]	Biosafety level	2	Risk group (German classification) According to TRBA 466

Information on genomic background e.g. entries in nucleic sequence databass Sequence information

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Clostridioides difficile strain 630 delta erm	1496.2352	plasmid	PATRIC	1496 tax ID	*
[Ref.: #66792]	Clostridioides difficile strain 630 delta erm	1496.2021	complete	PATRIC	1496 tax ID	*

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

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Clostridioides difficile strain 630 delta erm PATRIC: 1496.2021
[Ref.: #69480]	motile	yes	75.324	no
[Ref.: #69480]	gram-positive	yes	92.023	yes
[Ref.: #69480]	anaerobic	yes	98.664	no
[Ref.: #69480]	aerobic	no	97.893	no
[Ref.: #69480]	halophile	no	92.504	no
[Ref.: #69480]	spore-forming	yes	94.993	yes
[Ref.: #69480]	glucose-util	yes	87.275	no
[Ref.: #69480]	flagellated	no	69.697	no
[Ref.: #69480]	thermophile	no	93.381	yes
[Ref.: #69480]	glucose-ferment	yes	56.74	no

Availability in culture collections External links

[Ref.: #20944]

Culture collection no.

DSM 28645

[Ref.: #87870]

SI-ID 397186

Literature:

Topic	Title	Authors	Journal	DOI	Year
Metabolism	Characterization of Clostridioides difficile DSM 101085 with A-B-CDT+ Phenotype from a Late Recurrent Colonization.	Riedel T, Neumann-Schaal M, Wittmann J, Schober I, Hofmann JD, Lu CW, Dannheim A, Zimmermann O, Lochner M, Gross U, Overmann J	Genome Biol Evol	10.1093/gbe/evaa072	2020	*
Genetics	Manual curation and reannotation of the genomes of Clostridium difficile 630Deltaerm and C. difficile 630.	Dannheim H, Riedel T, Neumann-Schaal M, Bunk B, Schober I, Sproer C, Chibani CM, Gronow S, Liesegang H, Overmann J, Schomburg D	J Med Microbiol	10.1099/jmm.0.000427	2017	*

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 )

#20944

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 28645

#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) .

#68367

Automatically annotated from API 20A .

#68380

Automatically annotated from API rID32A .

#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) .

#87870

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-ID397186.1 )

* These data were automatically processed and therefore are not curated

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Clostridioides difficile strain 630 delta erm

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