Clostridioides difficile (DSM 28645, 630 Delta erm)

Name: Clostridioides difficile (DSM 28645, 630 Delta erm)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 23855

Type strain

Strain Designation 630 Delta erm

Culture col. no. DSM 28645 630 Delta erm

NCBI tax ID(s) 1496

Special Collections DSMZ DZIF

History DSMZ <- R. Gerhard <- N. P. Minton <- H. A. Hussain; 630 Delta erm

Links

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

spore-forming rod-shaped anaerobe human pathogen genome sequence Bacteria

Name and taxonomic classification

SI-ID 397186

DSM 28645

@ref 20215

Last LPSN update 2026-05-29 08:30:30

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, ...
134676	C. difficile CD196, CIP 107932
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	Cell shape	Gram stain
68367	rod-shaped		from API 20A
68367		positive	from API 20A

Colony morphology

@ref	Type of hemolysis	Hemolysis ability	Incubation period
20944	gamma	0	1-2 days

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
20944	FASTIDIOUS ANAEROBE AGAR (DSMZ Medium 1203)		Medium recipe at MediaDive	Name: FASTIDIOUS ANAEROBE AGAR (DSMZ Medium 1203) Composition: Horse blood 100.0 g/l Fastidious Anaerobe Agar 45.7 g/l Distilled water
20944	CHOPPED MEAT MEDIUM (DSMZ Medium 78)		Medium recipe at MediaDive	Name: CHOPPED MEAT MEDIUM (DSMZ Medium 78) Composition: Ground beef 500.0 g/l Casitone 30.0 g/l Agar 15.0 g/l Ethanol 9.5 g/l (optional) K2HPO4 5.0 g/l Yeast extract 5.0 g/l L-Cysteine HCl 0.5 g/l Haemin 0.005 g/l (optional) Resazurin 0.001 g/l Vitamin K3 0.0005 g/l (optional) Vitamin K1 (optional) NaOH (optional) Distilled water

Culture temp

@ref	Growth	Type	Temperature (°C)
20944	positive	growth	37

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
20944	anaerobe
125438	anaerobe	92.319
125439	facultative anaerobe	99.769

Spore formation

@ref	Spore formation	Confidence
68367			from API 20A
125439		98.87

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
68380	29016 ChEBI	arginine	-	hydrolysis	from API rID32A
68367	17634 ChEBI	D-glucose	+	builds acid from	from API 20A
68367	16899 ChEBI	D-mannitol	+	builds acid from	from API 20A
68380	16024 ChEBI	D-mannose	+	fermentation	from API rID32A
68367	16024 ChEBI	D-mannose	+	builds acid from	from API 20A
68367	65327 ChEBI	D-xylose	+	builds acid from	from API 20A
68367	4853 ChEBI	esculin	+	hydrolysis	from API 20A
68367	5291 ChEBI	gelatin	+	hydrolysis	from API 20A
68367	17754 ChEBI	glycerol	-	builds acid from	from API 20A
68367	30849 ChEBI	L-arabinose	-	builds acid from	from API 20A
68380	29985 ChEBI	L-glutamate	-	degradation	from API rID32A
68367	62345 ChEBI	L-rhamnose	-	builds acid from	from API 20A
68367	17716 ChEBI	lactose	-	builds acid from	from API 20A
68367	17306 ChEBI	maltose	-	builds acid from	from API 20A
68367	6731 ChEBI	melezitose	+	builds acid from	from API 20A
68380	17632 ChEBI	nitrate	-	reduction	from API rID32A
68380	16634 ChEBI	raffinose	-	fermentation	from API rID32A
68367	16634 ChEBI	raffinose	-	builds acid from	from API 20A
68367	17814 ChEBI	salicin	+	builds acid from	from API 20A
68367	17992 ChEBI	sucrose	-	builds acid from	from API 20A
68367	27082 ChEBI	trehalose	+	builds acid from	from API 20A
68380	27897 ChEBI	tryptophan	-	energy source	from API rID32A
68367	27897 ChEBI	tryptophan	-	energy source	from API 20A
68380	16199 ChEBI	urea	-	hydrolysis	from API rID32A
68367	16199 ChEBI	urea	-	hydrolysis	from API 20A

Metabolite production

@ref	Chebi-ID	Metabolite	Production
68380	35581 ChEBI	indole		from API rID32A
68367	35581 ChEBI	indole		from API 20A

Metabolite tests

@ref	Chebi-ID	Metabolite	Indole test
68380	35581 ChEBI	indole	-	from API rID32A
68367	35581 ChEBI	indole	-	from API 20A

Enzymes

@ref	Value	Activity	Ec
68380	alanine arylamidase	-	3.4.11.2	from API rID32A
68380	alkaline phosphatase	-	3.1.3.1	from API rID32A
68380	alpha-arabinosidase	-	3.2.1.55	from API rID32A
68380	alpha-fucosidase	-	3.2.1.51	from API rID32A
68380	alpha-galactosidase	-	3.2.1.22	from API rID32A
68380	alpha-glucosidase	-	3.2.1.20	from API rID32A
68380	arginine dihydrolase	-	3.5.3.6	from API rID32A
68380	beta-galactosidase	-	3.2.1.23	from API rID32A
68380	beta-Galactosidase 6-phosphate	-		from API rID32A
68380	beta-glucosidase	-	3.2.1.21	from API rID32A
68367	beta-glucosidase	+	3.2.1.21	from API 20A
68380	beta-glucuronidase	-	3.2.1.31	from API rID32A
20944	cytochrome-c oxidase	-	1.9.3.1
68367	gelatinase	+		from API 20A
68380	glutamate decarboxylase	-	4.1.1.15	from API rID32A
68380	glutamyl-glutamate arylamidase	-		from API rID32A
68380	glycin arylamidase	-		from API rID32A
68380	histidine arylamidase	-		from API rID32A
68380	L-arginine arylamidase	-		from API rID32A
68380	N-acetyl-beta-glucosaminidase	-	3.2.1.52	from API rID32A
68380	phenylalanine arylamidase	-		from API rID32A
68380	proline-arylamidase	+	3.4.11.5	from API rID32A
68380	pyrrolidonyl arylamidase	-	3.4.19.3	from API rID32A
68380	serine arylamidase	-		from API rID32A
68380	tryptophan deaminase	-	4.1.99.1	from API rID32A
68380	tyrosine arylamidase	-		from API rID32A
68380	urease	-	3.5.1.5	from API rID32A
68367	urease	-	3.5.1.5	from API 20A

API 20A

@ref	IND	URE	GLU	MAN	LAC	SAC	MAL	SAL	XYL	ARA	GEL	ESC	GLY	CEL	MNE	MLZ	RAF	SOR	RHA	TRE	CAT	Spores presentSPOR	GramGRAM	Morphology coccus="+" rod="-"COCC
20944	-	-	+	+	-	-	-	+	+	-	+	+	-	+/-	+	+	-	-	-	+	+	+	+	-
20944	-	-	+	+	-	-	-	+	+	-	+	+	-	+	+	+	-	+/-	-	+	+/-	+	+	-

API rID32A

@ref	URE	ADH (Arg)	alpha GAL	beta GAL	beta-Galactosidase 6-phosphatebeta GP	alpha GLU	beta GLU	alpha ARA	beta GUR	beta-N-Acetyl-beta-glucosaminidasebeta NAG	MNE	RAF	GDC	alpha FUC	Reduction of nitrateNIT	IND	PAL	L-arginine arylamidaseArgA	ProA	LGA	Phenylalanine arylamidasePheA	Leucine arylamidaseLeuA	PyrA	Tyrosine arylamidaseTyrA	Alanine arylamidaseAlaA	Glycin arylamidaseGlyA	Histidine arylamidaseHisA	Glutamyl-glutamate arylamidaseGGA	Serine arylamidaseSerA
20944	-	-	-	-	-	-	-	-	-	-	+	-	-	-	-	-	-	-	+	-	-	-	-	-	-	-	-	-	-
20944	-	-	-	-	-	-	-	-	-	-	+	-	-	-	-	-	-	-	+	+/-	-	+/-	-	-	-	-	-	-	-

Isolation, sampling and environmental information

Isolation

@ref	Country	Country ISO 3 Code	Continent
20944	United Kingdom	GBR	Europe

Interaction and safety

Risk assessment

@ref	Pathogenicity human	Pathogenicity animal	Biosafety level	Biosafety level comment
20944			2	Risk group (German classification)

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
124043	ASM208006v1 assembly for Clostridioides difficile 630 delta erm	complete	GCA_002080065	1496.2021	2871977330	1496	98.75

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: ASM208006v1 assembly for Clostridioides difficile 630 delta erm
NCBI: GCA_002080065

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	gram_stain	BacteriaNetⓘ	positive	51.81	no
125439	oxygen_tolerance	BacteriaNetⓘ	facultative anaerobe	99.77	no
125439	motility	BacteriaNetⓘ	yes	87.73	no
125439	spore_formation	BacteriaNetⓘ	yes	98.87	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Clostridioides difficile strain 630 delta erm
PATRIC: 1496.2021

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	yes	59.33	yes
125438	anaerobic	anaerobicⓘ	yes	92.32	no
125438	spore-forming	spore-formingⓘ	yes	61.68	no
125438	aerobic	aerobicⓘ	no	97.85	yes
125438	thermophilic	thermophileⓘ	no	91.23	yes
125438	flagellated	motile2+ⓘ	yes	75.65	no

Literature

Topic	Title	Authors	Journal	DOI	Year
	Rifaximin resistance in Clostridioides difficile is associated with specific rpoB alleles and multilocus sequence typing (MLST) clades.	Schwanbeck J, Laukien F, Riedel T, Bunk B, Halama P, Sproer C, Overmann J, Cooper P, Kusumawati RL, Gross U, Bohne W, Zautner AE.	BMC Microbiol	10.1186/s12866-025-04164-4	2025
	Genomic analysis of a novel ST11(PR34365) Clostridioides difficile strain isolated from the human fecal of a CDI patient in Guizhou, China.	Yang Y, Shu L, Ling P, Yang J, Shao R, Cheng Y, Luo S, Wei X, Guan Z, Chen Z, Liao J, Qi X, Cui G, Hong W.	Open Life Sci	10.1515/biol-2025-1067	2025
Metabolism	Formation of the pyruvoyl-dependent proline reductase Prd from Clostridioides difficile requires the maturation enzyme PrdH.	Behlendorf C, Diwo M, Neumann-Schaal M, Fuchs M, Korner D, Jansch L, Faber F, Blankenfeldt W.	PNAS Nexus	10.1093/pnasnexus/pgae249	2024
	Clostridioides difficile minimal nutrient requirements for flagellar motility.	Schwanbeck J, Oehmig I, Gross U, Bohne W.	Front Microbiol	10.3389/fmicb.2023.1172707	2023
Metabolism	Thiol Metabolism and Volatile Metabolome of Clostridioides difficile.	Biwer P, Neumann-Schaal M, Henke P, Jahn D, Schulz S.	Front Microbiol	10.3389/fmicb.2022.864587	2022
	Clostridioides difficile Single Cell Swimming Strategy: A Novel Motility Pattern Regulated by Viscoelastic Properties of the Environment.	Schwanbeck J, Oehmig I, Gross U, Zautner AE, Bohne W.	Front Microbiol	10.3389/fmicb.2021.715220	2021
	Clostridioides difficile Activates Human Mucosal-Associated Invariant T Cells.	Bernal I, Hofmann JD, Bulitta B, Klawonn F, Michel AM, Jahn D, Neumann-Schaal M, Bruder D, Jansch L.	Front Microbiol	10.3389/fmicb.2018.02532	2018
	PrsA2 (CD630_35000) of Clostridioides difficile Is an Active Parvulin-Type PPIase and a Virulence Modulator.	Unal CM, Berges M, Smit N, Schiene-Fischer C, Priebe C, Strowig T, Jahn D, Steinert M.	Front Microbiol	10.3389/fmicb.2018.02913	2018
	Pleiotropic Clostridioides difficile Cyclophilin PpiB Controls Cysteine-Tolerance, Toxin Production, the Central Metabolism and Multiple Stress Responses.	Unal CM, Karagoz MS, Berges M, Priebe C, Borrero de Acuna JM, Wissing J, Jansch L, Jahn D, Steinert M.	Front Pharmacol	10.3389/fphar.2019.00340	2019
Pathogenicity	Transcriptional licensing is required for Pyrin inflammasome activation in human macrophages and bypassed by mutations causing familial Mediterranean fever.	Mangan MSJ, Mangan MSJ, Gorki F, Krause K, Heinz A, Pankow A, Ebert T, Jahn D, Hiller K, Hornung V, Maurer M, Schmidt FI, Gerhard R, Latz E.	PLoS Biol	10.1371/journal.pbio.3001351	2022
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
#68367	Automatically annotated from API 20A .
#68380	Automatically annotated from API rID32A .
#124043	Isabel Schober, Julia Koblitz: Data extracted from sequence databases, automatically matched based on designation and taxonomy .
#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 (DSM 28645, 630 Delta erm)

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

Metabolite tests

Enzymes

API 20A

API rID32A

Isolation, sampling and environmental information

Isolation

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_002080065

Genome-based predictions

Predictions

Literature

Literature

References

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