Name: Clostridioides difficile CD196
Creator: BacDive
License: https://creativecommons.org/licenses/by/4.0/

Strain identifier

BacDive ID: 134676

Type strain:

Species: Clostridioides difficile

Strain Designation: CD196

Culture col. no.: CIP 107932

Strain history: CIP <- 2003, J.P. Carlier, Inst. Pasteur, Paris, France: strain AIP 196-84, Clostridium difficile

NCBI tax ID(s): 499176 (strain), 1496 (species)

SI-ID 361807

CIP 107932

Special Collections

Other strains from Clostridioides difficile

Section

Clostridioides difficile CD196 is an anaerobe, spore-forming, mesophilic bacterium of the family Peptostreptococcaceae.

Gram-positive
rod-shaped
spore-forming
anaerobe
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.: #33182]	Gram stain	positive

[Ref.: #33182]	Cell shape	rod-shaped

[Ref.: #33182]	Motility	no

Information on culture and growth conditions Culture and growth conditions

[Ref.: #33182]

Culture medium

MEDIUM 20 - for Anaerobic bacteria

[Ref.: #33182]

Culture medium growth

[Ref.: #33182]

Culture medium composition

expand / minimize

[Ref.: #33182]

Culture medium

CIP Medium 20

[Ref.: #33182]

Culture medium growth

[Ref.: #33182]

Culture medium link

Medium recipe provided by DSMZ

	Temperatures	Kind of temperature		Temperature
[Ref.: #33182]			growth	37 °C

Information on physiology and metabolism Physiology and metabolism

[Ref.: #33182]	Oxygen tolerance	anaerobe
[Ref.: #69480]	Oxygen tolerance	anaerobe Confidence in %90.809

[Ref.: #33182]	Ability of spore formation	yes
[Ref.: #69481]	Ability of spore formation	yes Confidence in %98

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #33182]	cellobiose ChEBI	-	degradation
[Ref.: #33182]	D-arabinose ChEBI	-	degradation
[Ref.: #33182]	D-fructose ChEBI	+	degradation
[Ref.: #33182]	D-glucose ChEBI	+	degradation
[Ref.: #33182]	D-xylose ChEBI	-	degradation
[Ref.: #33182]	esculin ChEBI	+	hydrolysis
[Ref.: #33182]	lactose ChEBI	-	degradation
[Ref.: #33182]	maltose ChEBI	-	degradation
[Ref.: #33182]	nitrate ChEBI	-	reduction
[Ref.: #33182]	nitrate ChEBI	+	respiration
[Ref.: #33182]	nitrite ChEBI	-	reduction
[Ref.: #33182]	salicin ChEBI	-	degradation
[Ref.: #33182]	sucrose ChEBI	-	degradation
	Only first 10 entries are displayed. Click here to see all.

	Metabolite production	Metabolite	Production
[Ref.: #33182]		indole ChEBI	no

	Enzyme	Enzyme activity	EC number
[Ref.: #68382]	acid phosphatase	-	3.1.3.2	* from API zym
[Ref.: #68382]	alkaline phosphatase	-	3.1.3.1	* from API zym
[Ref.: #68382]	alpha-chymotrypsin	-	3.4.21.1	* from API zym
[Ref.: #68382]	alpha-fucosidase	-	3.2.1.51	* from API zym
[Ref.: #68382]	alpha-galactosidase	-	3.2.1.22	* from API zym
[Ref.: #68382]	alpha-glucosidase	-	3.2.1.20	* from API zym
[Ref.: #68382]	alpha-mannosidase	-	3.2.1.24	* from API zym
[Ref.: #33182]	amylase	-
[Ref.: #33182]	beta-galactosidase	+	3.2.1.23
[Ref.: #68382]	beta-galactosidase	-	3.2.1.23	* from API zym
[Ref.: #68382]	beta-glucosidase	-	3.2.1.21	* from API zym
[Ref.: #68382]	beta-glucuronidase	-	3.2.1.31	* from API zym
[Ref.: #33182]	caseinase	-	3.4.21.50
[Ref.: #33182]	catalase	-	1.11.1.6
[Ref.: #68382]	cystine arylamidase	-	3.4.11.3	* from API zym
[Ref.: #33182]	DNase	-
[Ref.: #68382]	esterase (C 4)	-		* from API zym
[Ref.: #68382]	esterase lipase (C 8)	-		* from API zym
[Ref.: #33182]	gelatinase	-
[Ref.: #33182]	lecithinase	-
[Ref.: #68382]	leucine arylamidase	-	3.4.11.1	* from API zym
[Ref.: #33182]	lipase	-
[Ref.: #68382]	lipase (C 14)	-		* from API zym
[Ref.: #68382]	N-acetyl-beta-glucosaminidase	-	3.2.1.52	* from API zym
[Ref.: #68382]	naphthol-AS-BI-phosphohydrolase	-		* from API zym
[Ref.: #33182]	oxidase	-
[Ref.: #33182]	protease	-
[Ref.: #68382]	trypsin	-	3.4.21.4	* from API zym
[Ref.: #33182]	tween esterase	-
[Ref.: #33182]	urease	-	3.5.1.5
[Ref.: #68382]	valine arylamidase	-		* from API zym
	Only first 10 entries are displayed. Click here to see all.

API® zym:

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

	API ID	Control	2-naphthyl phosphateAlkaline phosphatase	2-naphthyl butyrateEsterase (C 4)	2-naphtyl caprylateEsterase Lipase (C 8)	2-naphthyl myristateLipase (C 14)	L-leucyl-2-naphthylamideLeucine arylamidase	L-valyl-2-naphthylamideValine arylamidase	L-cystyl-2-naphthylamideCystine arylamidase	N-benzoyl-DL-arginine-2-naphthylamideTrypsin	N-glutaryl-phenylalanine-2-naphthylamidealpha- Chymotrypsin	2-naphthyl phosphateAcid phosphatase	Naphthol-AS-BI-phosphateNaphthol-AS-BI-phosphohydrolase	6-Br-2-naphthyl-alphaD-galactpyranosidealpha- Galactosidase	2-naphthyl-betaD-galactpyranosidebeta- Galactosidase	Naphthol-AS-BI-betaD-glucuronidebeta- Glucuronidase	2-naphthyl-alphaD-glucopyranosidealpha- Glucosidase	6-Br-2-naphthyl-betaD-glucopyranosidebeta- Glucosidase	1-naphthyl-N-acetyl-betaD-glucosaminideN-acetyl-beta- glucosaminidase	6-Br-2-naphthyl-alphaD-mannopyranosidealpha- Mannosidase	2-naphthyl-alphaL-fucopyranosidealpha- Fucosidase
[Ref.: #33182]	10756	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-

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

[Ref.: #33182]	Sample type/isolated from	Human, Feces
[Ref.: #33182]	Geographic location (country and/or sea, region)	Reims
[Ref.: #33182]	Country	France
[Ref.: #33182]	Country ISO 3 Code	FRA
[Ref.: #33182]	Continent	Europe
[Ref.: #33182]	Isolation date	1984

[Ref.: #33182]	Geographic location (country and/or sea, region)	Reims
[Ref.: #33182]	Country	France
[Ref.: #33182]	Country ISO 3 Code	FRA
[Ref.: #33182]	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.: #33182]

Biosafety level

Risk group (French classification)

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 CD196	GCA_021378415	complete	GenBank ENA	645462 tax ID	*
[Ref.: #66792]	Clostridioides difficile CIP 107932	GCA_000155045	chromosome	GenBank ENA	499176 tax ID	*
[Ref.: #66792]	Clostridioides difficile CD196	GCA_000449605	contig	GenBank ENA	645462 tax ID	*
[Ref.: #66792]	Clostridium difficile CIP 107932	499176.4	wgs	PATRIC	499176 tax ID	*
[Ref.: #66792]	Clostridioides difficile CIP 107932	642791606	draft	JGI IMG/M	499176 tax ID	*
[Ref.: #66792]	Clostridioides difficile CD196	2541047488	draft	JGI IMG/M	645462 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: Clostridioides difficile CIP 107932 CIP 107932 NCBI: GCA_000155045.1
[Ref.: #69481]	spore-forming	spore-formingⓘ	yes	98	no

	Trait	Model	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Clostridioides difficile CIP 107932 CIP 107932 NCBI: GCA_000155045.1
[Ref.: #69480]	gram-positive	gram-positiveⓘ	yes	56.83	no
[Ref.: #69480]	anaerobic	anaerobicⓘ	yes	90.809	no
[Ref.: #69480]	aerobic	aerobicⓘ	no	97.236	no
[Ref.: #69480]	spore-forming	spore-formingⓘ	yes	65.356	no
[Ref.: #69480]	thermophilic	thermophileⓘ	no	91.739	yes
[Ref.: #69480]	flagellated	motile2+ⓘ	yes	75.714	no

Availability in culture collections External links

[Ref.: #33182]

Culture collection no.

CIP 107932

[Ref.: #92157]

SI-ID 361807

Literature:

Only first 10 entries are displayed. Click here to see all.

Topic	Title	Authors	Journal	DOI	Year
Pathogenicity	Clostridioides difficile strain-dependent and strain-independent adaptations to a microaerobic environment.	Weiss A, Lopez CA, Beavers WN, Rodriguez J, Skaar EP	Microb Genom	10.1099/mgen.0.000738	2021	*
Metabolism	Analysis of metabolic evolution in bacteria using whole-genome metabolic models.	Bryant WA, Faruqi AA, Pinney JW	J Comput Biol	10.1089/cmb.2013.0079	2013	*
Pathogenicity	Fidaxomicin inhibits toxin production in Clostridium difficile.	Babakhani F, Bouillaut L, Sears P, Sims C, Gomez A, Sonenshein AL	J Antimicrob Chemother	10.1093/jac/dks450	2012	*
Metabolism	Secretome analysis of Clostridium difficile strains.	Boetzkes A, Felkel KW, Zeiser J, Jochim N, Just I, Pich A	Arch Microbiol	10.1007/s00203-012-0802-5	2012	*
Pathogenicity	Assessing the role of p-cresol tolerance in Clostridium difficile.	Dawson LF, Stabler RA, Wren BW	J Med Microbiol	10.1099/jmm.0.47744-0	2008	*
Genetics	ADP-ribosylating binary toxin genes of Clostridium difficile strain CCUG 20309.	Chang SY, Song KP	DNA Seq	10.3109/10425170109047564	2001	*
Enzymology	Production of a complete binary toxin (actin-specific ADP-ribosyltransferase) by Clostridium difficile CD196.	Perelle S, Gibert M, Bourlioux P, Corthier G, Popoff MR	Infect Immun	10.1128/iai.65.4.1402-1407.1997	1997	*
Pathogenicity	Actin-specific ADP-ribosyltransferase produced by a Clostridium difficile strain.	Popoff MR, Rubin EJ, Gill DM, Boquet P	Infect Immun	10.1128/iai.56.9.2299-2306.1988	1988	*
Pathogenicity	Inhibition of spore germination, growth, and toxin activity of clinically relevant C. difficile strains by gut microbiota derived secondary bile acids.	Thanissery R, Winston JA, Theriot CM	Anaerobe	10.1016/j.anaerobe.2017.03.004	2017	*
Pathogenicity	Clostridium-DT(DB): a comprehensive database for potential drug targets of Clostridium difficile.	Jadhav A, Ezhilarasan V, Prakash Sharma O, Pan A	Comput Biol Med	10.1016/j.compbiomed.2013.01.009	2013	*
	A Small Molecule-Screening Pipeline to Evaluate the Therapeutic Potential of 2-Aminoimidazole Molecules Against Clostridium difficile.	Thanissery R, Zeng D, Doyle RG, Theriot CM	Front Microbiol	10.3389/fmicb.2018.01206	2018	*
	Comparative genomic analysis of Clostridium difficile ribotype 027 strains including the newly sequenced strain NCKUH-21 isolated from a patient in Taiwan.	Suzuki H, Tomita M, Tsai PJ, Ko WC, Hung YP, Huang IH, Chen JW	Gut Pathog	10.1186/s13099-017-0219-4	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 )

#33182 Collection of Institut Pasteur ; Curators of the CIP; CIP 107932

#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) .

#68382

Automatically annotated from API zym .

#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 )

#92157

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-ID361807.1 )

* These data were automatically processed and therefore are not curated

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