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

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

[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

[Ref.: #20942]

Temperature range

mesophilic

Information on physiology and metabolism Physiology and metabolism

[Ref.: #20942]	Oxygen tolerance	anaerobe
[Ref.: #69480]	Oxygen tolerance	anaerobe Confidence in %99.628

[Ref.: #68367]	Ability of spore formation	yes * from API 20A
[Ref.: #69481]	Ability of spore formation	yes Confidence in %100
[Ref.: #69480]	Ability of spore formation	yes Confidence in %99.728

	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.: #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]	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]	2195	-	-	+	+	-	-	-	+	+	-	+	+	-	+	+	+	-	+/-	-	+	not determinedn.d.	not determinedn.d.	not determinedn.d.	not determinedn.d.
[Ref.: #20942]	2191	-	-	+	+	-	-	-	+	+	-	+	+	-	-	+	+	-	+/-	-	+/-	not determinedn.d.	not determinedn.d.	not determinedn.d.	not determinedn.d.
[Ref.: #20942]	2161	-	-	+	+	-	-	-	+	+	-	+	+	-	+/-	+	+	-	+/-	-	-	not determinedn.d.	not determinedn.d.	not determinedn.d.	not determinedn.d.
[Ref.: #20942]	2160	-	-	+	+	-	-	-	+/-	+/-	-	+	+	-	-	+	+	-	-	-	-	not determinedn.d.	not determinedn.d.	not determinedn.d.	not determinedn.d.
[Ref.: #20942]	2104	-	-	+	+	-	-	-	+	+	-	+	+	-	+/-	+	+	-	+/-	-	+	+	+	+	-
[Ref.: #20942]	2103	-	-	+	+	-	-	-	+	+	-	+	+	-	+	+	+	-	+	-	+/-	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]	13126	-	+	-	-	-	-	+/-	-	-	-	+	-	-	-	-	-	-	-	+	-	-	-	-	-	-	-	-	-	-
[Ref.: #20942]	13115	-	+/-	-	-	-	-	+/-	-	-	-	+	-	-	-	-	-	-	-	+	-	-	-	-	-	-	-	-	-	-
[Ref.: #20942]	12995	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	+	-	-	-	-	-	-	-	-	-	-
[Ref.: #20942]	12466	-	-	-	-	-	-	+/-	-	-	-	-	-	-	-	-	-	-	-	+	-	-	+	-	-	-	-	-	-	-

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	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	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	yes	100	no

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Clostridioides difficile 630 630 NCBI: GCA_000009205.1
[Ref.: #69480]	motile	yes	75.324	no
[Ref.: #69480]	flagellated	no	69.697	no
[Ref.: #69480]	gram-positive	yes	92.023	yes
[Ref.: #69480]	anaerobic	yes	98.664	yes
[Ref.: #69480]	halophile	no	92.504	no
[Ref.: #69480]	spore-forming	yes	94.993	yes
[Ref.: #69480]	thermophile	no	93.381	no
[Ref.: #69480]	glucose-util	yes	87.275	no
[Ref.: #69480]	aerobic	no	97.893	no
[Ref.: #69480]	glucose-ferment	yes	56.74	no
[Ref.: #69480]	motile	yes	75.324	no
[Ref.: #69480]	flagellated	no	69.697	no
[Ref.: #69480]	gram-positive	yes	92.023	yes
[Ref.: #69480]	anaerobic	yes	98.664	yes
[Ref.: #69480]	halophile	no	92.504	no
[Ref.: #69480]	spore-forming	yes	94.993	yes
[Ref.: #69480]	thermophile	no	93.381	no
[Ref.: #69480]	glucose-util	yes	87.275	no
[Ref.: #69480]	aerobic	no	97.893	no
[Ref.: #69480]	glucose-ferment	yes	56.74	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

Change proposal

You found an error in BacDive? Please tell us about it!

Note that changes will be reviewed and judged. If your changes are legitimate, changes will occur within the next BacDive update. Only proposed changes supported by the according reference will be reviewed. The BacDive team reserves the right to reject proposed changes.

Search for species Clostridioides difficile in external resources:
SILVA
BRENDA
PANGAEA
StrainInfo
GBIF

Peptoclostridium difficile strain NCTC13307

Clostridioides difficile 630 630

Change proposal

Change proposal