Clostridioides difficile (CIP 107932, CD196)

Name: Clostridioides difficile (CIP 107932, CD196)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 134676

Type strain

Strain Designation CD196

Culture col. no. CIP 107932 CD196

NCBI tax ID(s) 499176 1496

Special Collections CIP

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

Links

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

spore-forming Gram-positive rod-shaped anaerobe genome sequence Bacteria

Name and taxonomic classification

SI-ID 361807

CIP 107932

@ref 20215

Last LPSN update 2026-05-29 08:38:23

Domain Bacteria

Phylum Bacillota

Class Clostridia

Order Peptostreptococcales

Family Peptostreptococcaceae

Genus Clostridioides

Species Clostridioides difficile

Full scientific name Clostridioides difficile (Hall and O'Toole 1935) Lawson et al. 2016

Synonyms (3)

"Peptoclostridium difficile"
"Bacillus difficilis"
Clostridium difficile

BacDive ID	Other strains from **Clostridioides difficile** (81)	Type strain
2582	C. difficile 1780, McClung 1780, 90556-M6S, 10008, DSM ... (type strain)
2583	C. difficile AA1, DSM 12056
2584	C. difficile A90, DSM 12057
22963	C. difficile R20291, DSM 27147, NCTC 13366
23853	C. difficile 630, DSM 27543, ATCC BAA-1382, NCTC 13307
23854	C. difficile 1470, DSM 27544, ATCC 43598, NCTC 13569, ...
23855	C. difficile 630 Delta erm, DSM 28645
134703	C. difficile CIP 109239
135237	C. difficile W 1194, CIP 104903, ATCC 43594, CCUG 37779
135760	C. difficile CIP 110322
137137	C. difficile CIP 109238
137139	C. difficile CIP 109240, ATCC 43255, CCUG 19126, VPI 10463
138126	C. difficile 2149, CIP 104905, ATCC 43600, CCUG 37784
138128	C. difficile 545, CIP 104904, ATCC 43596, CCUG 37766
141963	C. difficile CCUG 8884
141965	C. difficile CCUG 9004
141966	C. difficile CCUG 9018
143578	C. difficile CCUG 20309
143948	C. difficile CCUG 22019
143949	C. difficile CCUG 22020
143950	C. difficile CCUG 22023
145666	C. difficile CCUG 29183
148544	C. difficile CCUG 35620
149446	C. difficile CCUG 37767
149447	C. difficile CCUG 37768
149448	C. difficile CCUG 37769
149449	C. difficile CCUG 37770
149450	C. difficile CCUG 37771
149451	C. difficile CCUG 37772
149452	C. difficile CCUG 37773
149453	C. difficile CCUG 37774
149454	C. difficile CCUG 37775
149455	C. difficile CCUG 37776
149456	C. difficile CCUG 37777
149457	C. difficile CCUG 37778
149458	C. difficile CCUG 37780, ATCC 43593
149459	C. difficile CCUG 37781, ATCC 43597
149460	C. difficile CCUG 37783, ATCC 43599
149461	C. difficile CCUG 37785, ATCC 43601
149462	C. difficile CCUG 37787, ATCC 43603
149536	C. difficile CCUG 37922
151958	C. difficile CCUG 45344
151959	C. difficile CCUG 45345
152338	C. difficile CCUG 46468
152339	C. difficile CCUG 46469
152340	C. difficile CCUG 46470
154467	C. difficile CCUG 53741
154468	C. difficile CCUG 53742
154474	C. difficile CCUG 53749
154520	C. difficile CCUG 54206
156075	C. difficile CCUG 60275, LBM 08.01.040
156076	C. difficile CCUG 60276, LBM 08.01.058
156768	C. difficile CCUG 64977
156771	C. difficile CCUG 65028
157662	C. difficile 4167/2013 1, DSM 27638
157663	C. difficile 4167/2013 2, DSM 27639
157664	C. difficile 4167/2013 3, DSM 27640
157665	C. difficile SC037-01-01, 6551/2013, DSM 28196
157666	C. difficile SC052-01-01, DSM 29688
157667	C. difficile SC009-01-01, DSM 29745
157668	C. difficile SC052-02-01, DSM 29747
157669	C. difficile CD-16-113, D/6474/2015, DSM 102978
157670	C. difficile 3525/15, Goe-91, DSM 105001
158911	C. difficile 3022, CD3022, DSM 101085
165126	C. difficile JCM 5243
165127	C. difficile JCM 5244
165128	C. difficile JCM 5245
165129	C. difficile JCM 5246
165130	C. difficile JCM 5247
165131	C. difficile JCM 5248
165132	C. difficile JCM 5249
165133	C. difficile JCM 5250
165134	C. difficile JCM 5251
165135	C. difficile JCM 5252
165136	C. difficile JCM 5253
165137	C. difficile JCM 5254
165138	C. difficile JCM 5256
165139	C. difficile JCM 5257
165140	C. difficile JCM 5258
176413	C. difficile RT 023, DSM 102859
176414	C. difficile RT 127, DSM 102860

Morphology

Cell morphology

@ref	Gram stain	Cell shape	Motility
33182	positive	rod-shaped

Colony morphology

33182

Hemolysis ability0

Culture and growth conditions

Culture medium

@ref	Name	Growth	Composition	Medium link
33182	MEDIUM 20 - for Anaerobic bacteria		Agar (15.000 g);Glucose (5.000 g);Yeast extract (20.000 g);Tryptone (30.000 g);Cysteine hydrochloride (0.500 g);distilled water (1000.000 ml);Hemin solution -M00149 (25.000 ml)
33182	CIP Medium 20			Medium recipe at CIP

Culture temp

@ref	Growth	Type	Temperature (°C)
33182	positive	growth	37

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
33182	anaerobe
125438	anaerobe	90.809
125439	facultative anaerobe	98.325

Spore formation

33182

Spore formationyes

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
33182	17057 ChEBI	cellobiose	-	degradation
33182	17108 ChEBI	D-arabinose	-	degradation
33182	15824 ChEBI	D-fructose	+	degradation
33182	17634 ChEBI	D-glucose	+	degradation
33182	65327 ChEBI	D-xylose	-	degradation
33182	4853 ChEBI	esculin	+	hydrolysis
33182	17716 ChEBI	lactose	-	degradation
33182	17306 ChEBI	maltose	-	degradation
33182	17632 ChEBI	nitrate	-	reduction
33182	17632 ChEBI	nitrate	+	respiration
33182	16301 ChEBI	nitrite	-	reduction
33182	17814 ChEBI	salicin	-	degradation
33182	17992 ChEBI	sucrose	-	degradation

Metabolite production

@ref	Chebi-ID	Metabolite	Production
33182	35581 ChEBI	indole

Enzymes

@ref	Value	Activity	Ec
68382	acid phosphatase	-	3.1.3.2	from API zym
68382	alkaline phosphatase	-	3.1.3.1	from API zym
68382	alpha-chymotrypsin	-	3.4.21.1	from API zym
68382	alpha-fucosidase	-	3.2.1.51	from API zym
68382	alpha-galactosidase	-	3.2.1.22	from API zym
68382	alpha-glucosidase	-	3.2.1.20	from API zym
68382	alpha-mannosidase	-	3.2.1.24	from API zym
33182	amylase	-
68382	beta-galactosidase	-	3.2.1.23	from API zym
33182	beta-galactosidase	+	3.2.1.23
68382	beta-glucosidase	-	3.2.1.21	from API zym
68382	beta-glucuronidase	-	3.2.1.31	from API zym
33182	caseinase	-	3.4.21.50
33182	catalase	-	1.11.1.6
68382	cystine arylamidase	-	3.4.11.3	from API zym
33182	DNase	-
68382	esterase (C 4)	-		from API zym
68382	esterase lipase (C 8)	-		from API zym
33182	gelatinase	-
33182	lecithinase	-
68382	leucine arylamidase	-	3.4.11.1	from API zym
33182	lipase	-
68382	lipase (C 14)	-		from API zym
68382	N-acetyl-beta-glucosaminidase	-	3.2.1.52	from API zym
68382	naphthol-AS-BI-phosphohydrolase	-		from API zym
33182	oxidase	-
33182	protease	-
68382	trypsin	-	3.4.21.4	from API zym
33182	tween esterase	-
33182	urease	-	3.5.1.5
68382	valine arylamidase	-		from API zym

API zym

@ref	Control	Alkaline phosphatase	Esterase (C 4)	2-naphtyl caprylateEsterase Lipase (C 8)	Lipase (C 14)	L-leucyl-2-naphthylamideLeucine arylamidase	L-valyl-2-naphthylamideValine arylamidase	L-cystyl-2-naphthylamideCystine arylamidase	Trypsin	alpha- Chymotrypsin	Acid phosphatase	Naphthol-AS-BI-phosphateNaphthol-AS-BI-phosphohydrolase	alpha- Galactosidase	beta- Galactosidase	beta- Glucuronidase	alpha- Glucosidase	beta- Glucosidase	N-acetyl-beta- glucosaminidase	alpha- Mannosidase	alpha- Fucosidase
33182	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-

Isolation, sampling and environmental information

Isolation

@ref	Sample type	Host species	Geographic location	Country	Country ISO 3 Code	Continent	Isolation date
33182			Reims	France	FRA	Europe
33182	Human, Feces	Homo sapiens	Reims	France	FRA	Europe	1984

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
33182	2	Risk group (French classification)

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
66792	ASM8522v1 assembly for Clostridioides difficile CD196	complete	GCA_000085225	645462.3	646311914	645462	99.02
66792	ASM2137841v1 assembly for Clostridioides difficile CD196	complete	GCA_021378415	645462.89	8005870720	645462	98.97
66792	cdeaa assembly for Clostridioides difficile CIP 107932	chromosome	GCA_000155045	499176.4	642791606	499176	76.2
66792	ASM44960v2 assembly for Clostridioides difficile CD196	contig	GCA_000449605	645462.16	2541047488	645462	0

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: ASM8522v1 assembly for Clostridioides difficile CD196
NCBI: GCA_000085225

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	oxygen_tolerance	BacteriaNetⓘ	facultative anaerobe	98.33	no
125439	gram_stain	BacteriaNetⓘ	positive	70.64	no
125439	spore_formation	BacteriaNetⓘ	yes	82.44	no
125439	motility	BacteriaNetⓘ	yes	78.82	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Clostridioides difficile CIP 107932 CIP 107932
NCBI: GCA_000155045.1

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	yes	56.83	no
125438	anaerobic	anaerobicⓘ	yes	90.81	no
125438	aerobic	aerobicⓘ	no	97.24	no
125438	spore-forming	spore-formingⓘ	yes	65.36	no
125438	thermophilic	thermophileⓘ	no	91.74	yes
125438	flagellated	motile2+ⓘ	yes	75.71	no

Literature

Topic	Title	Authors	Journal	DOI	Year
	Recognition of extracellular DNA by type IV pili promotes biofilm formation by Clostridioides difficile.	Ronish LA, Sidner B, Yu Y, Piepenbrink KH.	J Biol Chem	10.1016/j.jbc.2022.102449	2022
Pathogenicity	Cwl0971, a novel peptidoglycan hydrolase, plays pleiotropic roles in Clostridioides difficile R20291.	Zhu D, Patabendige HMLW, Tomlinson BR, Wang S, Hussain S, Flores D, He Y, Shaw LN, Sun X.	Environ Microbiol	10.1111/1462-2920.15529	2021
Metabolism	Cwp22, a novel peptidoglycan cross-linking enzyme, plays pleiotropic roles in Clostridioides difficile.	Zhu D, Zhu D, Bullock J, He Y, Sun X.	Environ Microbiol	10.1111/1462-2920.14706	2019
Metabolism	Motility and flagellar glycosylation in Clostridium difficile.	Twine SM, Reid CW, Aubry A, McMullin DR, Fulton KM, Austin J, Logan SM.	J Bacteriol	10.1128/jb.00861-09	2009
	The First Two Clostridium difficile Ribotype 027/ST1 Isolates Identified in Beijing, China-an Emerging Problem or a Neglected Threat?	Cheng JW, Xiao M, Kudinha T, Xu ZP, Hou X, Sun LY, Zhang L, Fan X, Kong F, Xu YC.	Sci Rep	10.1038/srep18834	2016
Genetics	Analysis of ultra low genome conservation in Clostridium difficile.	Scaria J, Ponnala L, Janvilisri T, Yan W, Mueller LA, Chang YF.	PLoS One	10.1371/journal.pone.0015147	2010
Proteome	Structure of Clostridium difficile PilJ exhibits unprecedented divergence from known type IV pilins.	Piepenbrink KH, Maldarelli GA, de la Pena CF, Mulvey GL, Snyder GA, De Masi L, von Rosenvinge EC, Gunther S, Armstrong GD, Donnenberg MS, Sundberg EJ.	J Biol Chem	10.1074/jbc.m113.534404	2014
Metabolism	Clostridium difficile is an autotrophic bacterial pathogen.	Kopke M, Straub M, Durre P.	PLoS One	10.1371/journal.pone.0062157	2013
Phylogeny	Fourteen-genome comparison identifies DNA markers for severe-disease-associated strains of Clostridium difficile.	Forgetta V, Oughton MT, Marquis P, Brukner I, Blanchette R, Haub K, Magrini V, Mardis ER, Gerding DN, Loo VG, Miller MA, Mulvey MR, Rupnik M, Dascal A, Dewar K.	J Clin Microbiol	10.1128/jcm.00391-11	2011
	Sequence similarity of Clostridium difficile strains by analysis of conserved genes and genome content is reflected by their ribotype affiliation.	Kurka H, Ehrenreich A, Ludwig W, Monot M, Rupnik M, Barbut F, Indra A, Dupuy B, Liebl W.	PLoS One	10.1371/journal.pone.0086535	2014
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
	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
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

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 .
#125438	Julia Koblitz, Lorenz Christian Reimer, Rüdiger Pukall, Jörg Overmann: Predicting bacterial phenotypic traits through improved machine learning using high-quality, curated datasets. 2024 ( DOI 10.1101/2024.08.12.607695 )
#125439	Philipp Münch, René Mreches, Martin Binder, Hüseyin Anil Gündüz, Xiao-Yin To, Alice McHardy: deepG: Deep Learning for Genome Sequence Data. R package version 0.3.1 .
#126262	A. Lissin, I. Schober, J. F. Witte, H. Lüken, A. Podstawka, J. Koblitz, B. Bunk, P. Dawyndt, P. Vandamme, P. de Vos, J. Overmann, L. C. Reimer: StrainInfo—the central database for linked microbial strain identifiers. ( DOI 10.1093/database/baaf059 )

Content

About us

Clostridioides difficile (CIP 107932, CD196)

Name and taxonomic classification

Morphology

Cell morphology

Colony morphology

Culture and growth conditions

Culture medium

Culture temp

Physiology and metabolism

Oxygen tolerance

Spore formation

Metabolite utilization

Metabolite production

Enzymes

API zym

Isolation, sampling and environmental information

Isolation

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_000085225

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

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