Cutibacterium porci (DSM 101006, WCA-380-WT-3A, JCM 34386)

Name: Cutibacterium porci (DSM 101006, WCA-380-WT-3A, JCM 34386)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 159049

Type strain

Strain Designation WCA-380-WT-3A

Culture col. no. DSM 101006 WCA-380-WT-3A JCM 34386

NCBI tax ID(s) 2605781

Special Collections DSMZ JCM Pig DZIF

History <- T. Clavel , TU Munich, Freising-Weihenstephan, Germany; WCA-380-WT-3A B. Abt; DSMZ, Germany; DSM 101006 (=WCA-380-WT-3A) <-- T. Clavel; RWTH Aachen, Germany.

Links

Cutibacterium porci WCA-380-WT-3A is a bacterium that was isolated from feces; pig, 8 weeks old, wild type.

genome sequence 16S sequence Bacteria

Name and taxonomic classification

SI-ID 398607

JCM 34386,DSM 101006

@ref 20215

Last LPSN update 2026-02-09 11:38:30

Domain Bacteria

Phylum Actinomycetota

Class Actinomycetes

Order Propionibacteriales

Family Propionibacteriaceae

Genus Cutibacterium

Species Cutibacterium porci

Full scientific name Cutibacterium porci Wylensek et al. 2021

Morphology

Cell morphology

@ref	Motility	Confidence	Gram stain
125438		94
125438		91.941	positive

Culture and growth conditions

Culture medium

@ref	Name	Medium link	Composition
65872	WILKINS-CHALGREN ANAEROBE BROTH (DSMZ Medium 339)	Medium recipe at MediaDive	Name: WILKINS-CHALGREN ANAEROBE BROTH (DSMZ Medium 339) Composition: dehydrated Wilkins-Chalgren medium 33.0 g/l L-Cysteine HCl 0.3 g/l Sodium resazurin 0.0005 g/l Distilled water
65872	PYG MEDIUM (MODIFIED) (DSMZ Medium 104)	Medium recipe at MediaDive	Name: PYG MEDIUM (modified) (DSMZ Medium 104) Composition: Yeast extract 10.0 g/l Peptone 5.0 g/l Trypticase peptone 5.0 g/l Beef extract 5.0 g/l Glucose 5.0 g/l L-Cysteine HCl x H2O 0.5 g/l NaHCO3 0.4 g/l NaCl 0.08 g/l K2HPO4 0.04 g/l KH2PO4 0.04 g/l MgSO4 x 7 H2O 0.02 g/l CaCl2 x 2 H2O 0.01 g/l Hemin 0.005 g/l Ethanol 0.0038 g/l Resazurin 0.001 g/l Tween 80 Vitamin K1 NaOH Distilled water
65872	COLUMBIA BLOOD MEDIUM (DSMZ Medium 693)	Medium recipe at MediaDive	Name: COLUMBIA BLOOD MEDIUM (DSMZ Medium 693) Composition: Defibrinated sheep blood 50.0 g/l Columbia agar base

Culture temp

@ref	Growth	Type	Temperature (°C)
65872	positive	growth	37
67770	positive	growth	37

Physiology and metabolism

Spore formation

@ref	Spore formation	Confidence
125439		95.3

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
68380	29016 ChEBI	arginine	+	hydrolysis	from API rID32A
68380	16024 ChEBI	D-mannose	+	fermentation	from API rID32A
68380	29985 ChEBI	L-glutamate	-	degradation	from API rID32A
68380	17632 ChEBI	nitrate	-	reduction	from API rID32A
68380	16634 ChEBI	raffinose	-	fermentation	from API rID32A
68380	27897 ChEBI	tryptophan	-	energy source	from API rID32A
68380	16199 ChEBI	urea	-	hydrolysis	from API rID32A

Metabolite production

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

Metabolite tests

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

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-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
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	leucine arylamidase	-	3.4.11.1	from API rID32A
68380	leucyl glycin arylamidase	+	3.4.11.1	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

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
65872	-	+	-	+	-	+	-	+/-	+/-	-	+	-	-	-	-	-	-	+	+	+	-	-	-	-	+	+	-	-	+

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Host Body Product	#Gastrointestinal tract	#Feces (Stool)
#Host	#Mammals	#Suidae (Pig,Swine)

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent	Latitude	Longitude
65872	feces; pig, 8 weeks old, wild type	Kranzberg (Bavaria)	Germany	DEU	Europe	48	11 48/11
67770	Feces of a German Landrace pig	Freising	Germany	DEU	Europe

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
65872	2	Risk group (German classification)

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
66792	ASM969631v1 assembly for Cutibacterium porci WCA-380-WT-3A	contig	GCA_009696315	2605781.3	2902680501	2605781	73.4

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
65872	Cutibacterium porci strain WCA-380-WT-3A 16S ribosomal RNA gene, partial sequence	MN537454	1457		2652271

GC content

@ref	GC-content (mol%)	Method
67770	58.8	genome sequence analysis

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Cutibacterium porci WCA-380-WT-3A
NCBI: GCA_009696315

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	no	95.30	no
125439	motility	BacteriaNetⓘ	no	66.10	no
125439	gram_stain	BacteriaNetⓘ	positive	68.80	no
125439	oxygen_tolerance	BacteriaNetⓘ	anaerobe	77.80	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Cutibacterium sp. WCA-380-WT-3A
PATRIC: 2605781.3

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	yes	91.94	no
125438	anaerobic	anaerobicⓘ	no	74.01	no
125438	spore-forming	spore-formingⓘ	no	80.53	no
125438	aerobic	aerobicⓘ	no	65.83	no
125438	thermophilic	thermophileⓘ	no	93.59	yes
125438	flagellated	motile2+ⓘ	no	94.00	no

Literature

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 )
#65872	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 101006
#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) .
#67770	Japan Collection of Microorganism (JCM) ; Curators of the JCM;
#68380	Automatically annotated from API rID32A .
#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 )

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