Name: Clostridioides difficile 630
Creator: BacDive
License: https://creativecommons.org/licenses/by/4.0/

Strain identifier

BacDive ID: 23853

Type strain:

Species: Clostridioides difficile

Strain Designation: 630

Culture col. no.: DSM 27543, ATCC BAA-1382, NCTC 13307

Strain history: <- P. Bracegirdle, NCTC <- P. Mullany <- H. Hächler <- J. Wüst; 630

NCBI tax ID(s): 1496 (species)

Special Collections

DSMZ
DZIF

Other strains from Clostridioides difficile

Section

Clostridioides difficile 630 is an anaerobe, spore-forming, mesophilic human pathogen that was isolated from clinical isolate.

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	09-12-2024 (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	"Peptoclostridium* difficile"*
	Synonym	"Bacillus* difficilis"*
	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.: #20942]	Type of hemolysis	gamma
[Ref.: #20942]	Incubation period	1-2 days

Information on culture and growth conditions Culture and growth conditions

[Ref.: #20942]

Culture medium

CHOPPED MEAT MEDIUM (DSMZ Medium 78)

[Ref.: #20942]

Culture medium growth

[Ref.: #20942]

Culture medium link

Medium recipe at MediaDive

[Ref.: #20942]

Culture medium composition

expand / minimize

[Ref.: #20942]

Culture medium

FASTIDIOUS ANAEROBE AGAR (DSMZ Medium 1203)

[Ref.: #20942]

Culture medium growth

[Ref.: #20942]

Culture medium link

Medium recipe at MediaDive

[Ref.: #20942]

Culture medium composition

expand / minimize

	Temperatures	Kind of temperature		Temperature
[Ref.: #20942]			growth	37 °C

Information on physiology and metabolism Physiology and metabolism

[Ref.: #20942]	Oxygen tolerance	anaerobe
[Ref.: #69480]	Oxygen tolerance	anaerobe Confidence in %92.319

[Ref.: #68367]	Ability of spore formation	yes * from API 20A
[Ref.: #69481]	Ability of spore formation	yes Confidence in %100

	Metabolite	Utilization activity	Kind of utilization tested
[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.: #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]	sucrose ChEBI	-	builds acid from	* from API 20A
[Ref.: #68380]	tryptophan ChEBI	-	energy source	* from API rID32A, API 20A
[Ref.: #68380]	urea ChEBI	-	hydrolysis	* from API rID32A, API 20A
	Only first 10 entries are displayed. Click here to see all.

	Metabolite production	Metabolite	Production
[Ref.: #68380]		indole ChEBI	no	* from API rID32A, API 20A

	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]	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-glucuronidase	-	3.2.1.31	* from API rID32A
[Ref.: #20942]	catalase	+	1.11.1.6
[Ref.: #68367]	catalase	+	1.11.1.6	* from API 20A
[Ref.: #20942]	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]	leucyl glycin arylamidase	-	3.4.11.1	* 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.: #20942]	2446	-	-	+	+	-	-	-	+	+	-	+	+	-	+	+	+	-	+/-	-	+	not determinedn.d.	not determinedn.d.	not determinedn.d.	not determinedn.d.
[Ref.: #20942]	2442	-	-	+	+	-	-	-	+	+	-	+	+	-	-	+	+	-	+/-	-	+/-	not determinedn.d.	not determinedn.d.	not determinedn.d.	not determinedn.d.
[Ref.: #20942]	2412	-	-	+	+	-	-	-	+	+	-	+	+	-	+/-	+	+	-	+/-	-	-	not determinedn.d.	not determinedn.d.	not determinedn.d.	not determinedn.d.
[Ref.: #20942]	2411	-	-	+	+	-	-	-	+/-	+/-	-	+	+	-	-	+	+	-	-	-	-	not determinedn.d.	not determinedn.d.	not determinedn.d.	not determinedn.d.
[Ref.: #20942]	2355	-	-	+	+	-	-	-	+	+	-	+	+	-	+/-	+	+	-	+/-	-	+	+	+	+	-
[Ref.: #20942]	2354	-	-	+	+	-	-	-	+	+	-	+	+	-	+	+	+	-	+	-	+/-	not determinedn.d.	not determinedn.d.	not determinedn.d.	not determinedn.d.

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.: #20942]	14476	-	+	-	-	-	-	+/-	-	-	-	+	-	-	-	-	-	-	-	+	-	-	-	-	-	-	-	-	-	-
[Ref.: #20942]	14465	-	+/-	-	-	-	-	+/-	-	-	-	+	-	-	-	-	-	-	-	+	-	-	-	-	-	-	-	-	-	-
[Ref.: #20942]	14345	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	+	-	-	-	-	-	-	-	-	-	-
[Ref.: #20942]	13814	-	-	-	-	-	-	+/-	-	-	-	-	-	-	-	-	-	-	-	+	-	-	+	-	-	-	-	-	-	-

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

[Ref.: #20942]	Sample type/isolated from	clinical isolate
[Ref.: #20942]	Country	Switzerland
[Ref.: #20942]	Country ISO 3 Code	CHE
[Ref.: #20942]	Continent	Europe
* marker position based on {}

Isolation sources categories

#Infection	#Medical environment	#Clinic
#Infection	#Patient	-
#Infection	#Patient	#Specimen

What are isolation sources categories?

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

[Ref.: #20942]	Pathogenicity (human)	yes
[Ref.: #20942]	Pathogenicity (animal)	yes
[Ref.: #20942]	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:

Only first 5 entries are displayed. Click here to see all.

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Clostridioides difficile 630	2588253713	draft	JGI IMG/M	272563 tax ID	*
[Ref.: #66792]	Clostridioides difficile 630	GCA_000932055	complete	GenBank ENA	272563 tax ID	*
[Ref.: #66792]	Clostridioides difficile 630	272563.206	plasmid	PATRIC	272563 tax ID	*
[Ref.: #66792]	Peptoclostridium difficile 630	272563.120	complete	PATRIC	272563 tax ID	*
[Ref.: #66792]	Peptoclostridium difficile strain NCTC13307	1496.877	complete	PATRIC	1496 tax ID	*
[Ref.: #66792]	Clostridioides difficile NCTC13307	2663762959	complete	JGI IMG/M	1496 tax ID	*

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: Peptoclostridium difficile strain NCTC13307 PATRIC: 1496.877
[Ref.: #69481]	spore-forming	spore-formingⓘ	yes	100	no

	Trait	Model	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Clostridioides difficile 630 630 NCBI: GCA_000009205.2
[Ref.: #69480]	gram-positive	gram-positiveⓘ	yes	59.331	yes
[Ref.: #69480]	anaerobic	anaerobicⓘ	yes	92.319	yes
[Ref.: #69480]	aerobic	aerobicⓘ	no	97.852	yes
[Ref.: #69480]	spore-forming	spore-formingⓘ	yes	61.68	yes
[Ref.: #69480]	thermophilic	thermophileⓘ	no	91.233	yes
[Ref.: #69480]	flagellated	motile2+ⓘ	yes	75.646	no

Availability in culture collections External links

[Ref.: #20942]

Culture collection no.

DSM 27543, ATCC BAA-1382, NCTC 13307

Literature:

Topic	Title	Authors	Journal	DOI	Year
Cultivation	Generation of a fully erythromycin-sensitive strain of Clostridioides difficile using a novel CRISPR-Cas9 genome editing system.	Ingle P, Groothuis D, Rowe P, Huang H, Cockayne A, Kuehne SA, Jiang W, Gu Y, Humphreys CM, Minton NP	Sci Rep	10.1038/s41598-019-44458-y	2019	*
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	*
	In vitro Study of Lactobacillus paracasei CNCM I-1518 in Healthy and Clostridioides difficile Colonized Elderly Gut Microbiota.	Fehlbaum S, Chassard C, Schwab C, Voolaid M, Fourmestraux C, Derrien M, Lacroix C	Front Nutr	10.3389/fnut.2019.00184	2019	*

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 )

#20942

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 27543

#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) .

#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 )

* These data were automatically processed and therefore are not curated

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Peptoclostridium difficile strain NCTC13307

Clostridioides difficile 630 630

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