Name: Propionibacterium acidifaciens C3M-31
Creator: BacDive
License: https://creativecommons.org/licenses/by/4.0/

Strain identifier

BacDive ID: 12659

Type strain:

Species: Propionibacterium acidifaciens

Strain Designation: C3M-31, C3M_31

Culture col. no.: DSM 21887, CCUG 57100, CIP 110570, JCM 16571

Strain history: CIP <- 2013, DSMZ <- J. Downes <- W. Wade, King's College London, UK: strain C3M-31

NCBI tax ID(s): 1122994 (strain), 556499 (species)

SI-ID 403725

DSM 21887, CCUG 57100, CIP 110570

Special Collections

Section

Propionibacterium acidifaciens C3M-31 is an anaerobe, Gram-positive human pathogen that was isolated from human oral cavity from middle depth of carious lesion.

Gram-positive
anaerobe
human pathogen
16S sequence
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	*Actinomycetota*
	Class	*Actinomycetes*
	Order	*Propionibacteriales*
	Family	*Propionibacteriaceae*
	Genus	*Propionibacterium*
	Species	**Propionibacterium acidifaciens**
	Full Scientific Name (LPSN)	Propionibacterium acidifaciens Downes and Wade 2009

Information on morphological and physiological properties Morphology

[Ref.: #29297]	Gram stain	positive
[Ref.: #115997]	Gram stain	positive

[Ref.: #29297]	Cell length	2.6 µm

[Ref.: #29297]	Cell width	0.75 µm

[Ref.: #29297]	Motility	no
[Ref.: #115997]	Motility	no
[Ref.: #69480]	Motility	no Confidence in %97.5

[Ref.: #115997]	Cell shape	rod-shaped

[Ref.: #61190]

Incubation period

2 days

[Ref.: #29297]

Pigment production

yes

Information on culture and growth conditions Culture and growth conditions

[Ref.: #16021]

Culture medium

SCHAEDLER BROTH (ROTH; 5772) (DSMZ Medium 1669)

[Ref.: #16021]

Culture medium growth

[Ref.: #16021]

Culture medium link

Medium recipe at MediaDive

[Ref.: #16021]

Culture medium composition

expand / minimize

[Ref.: #16021]

Culture medium

COLUMBIA BLOOD MEDIUM (DSMZ Medium 693)

[Ref.: #16021]

Culture medium growth

[Ref.: #16021]

Culture medium link

Medium recipe at MediaDive

[Ref.: #16021]

Culture medium composition

expand / minimize

[Ref.: #16021]

Culture medium

PYG MEDIUM (MODIFIED) (DSMZ Medium 104)

[Ref.: #16021]

Culture medium growth

[Ref.: #16021]

Culture medium link

Medium recipe at MediaDive

[Ref.: #16021]

Culture medium composition

expand / minimize

[Ref.: #115997]

Culture medium

CIP Medium 20

[Ref.: #115997]

Culture medium growth

[Ref.: #115997]

Culture medium link

Medium recipe provided by DSMZ

		Temperature
[Ref.: #16021]	growth	35 °C
[Ref.: #61190]	growth	37 °C
[Ref.: #67770]	growth	37 °C

Information on physiology and metabolism Physiology and metabolism

[Ref.: #29297]	Oxygen tolerance	anaerobe
[Ref.: #61190]	Oxygen tolerance	anaerobe

[Ref.: #29297]

Ability of spore formation

[Ref.: #29297]

Observation

aggregates in chains

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #29297]	acetate ChEBI	+	carbon source
[Ref.: #29297]	arabinose ChEBI	+	carbon source
[Ref.: #68380]	arginine ChEBI	-	hydrolysis	* from API rID32A
[Ref.: #29297]	cellobiose ChEBI	+	carbon source
[Ref.: #68380]	D-mannose ChEBI	+	fermentation	* from API rID32A
[Ref.: #29297]	fructose ChEBI	+	carbon source
[Ref.: #29297]	glucose ChEBI	+	carbon source
[Ref.: #68380]	L-glutamate ChEBI	-	degradation	* from API rID32A
[Ref.: #29297]	lactose ChEBI	+	carbon source
[Ref.: #29297]	maltose ChEBI	+	carbon source
[Ref.: #29297]	mannitol ChEBI	+	carbon source
[Ref.: #29297]	mannose ChEBI	+	carbon source
[Ref.: #29297]	melibiose ChEBI	+	carbon source
[Ref.: #68380]	nitrate ChEBI	-	reduction	* from API rID32A
[Ref.: #29297]	propionate ChEBI	+	carbon source
[Ref.: #29297]	raffinose ChEBI	+	carbon source
[Ref.: #68380]	raffinose ChEBI	+	fermentation	* from API rID32A
[Ref.: #29297]	rhamnose ChEBI	+	carbon source
[Ref.: #29297]	ribose ChEBI	+	carbon source
[Ref.: #29297]	salicin ChEBI	+	carbon source
[Ref.: #29297]	succinate ChEBI	+	carbon source
[Ref.: #29297]	sucrose ChEBI	+	carbon source
[Ref.: #68380]	tryptophan ChEBI	-	energy source	* from API rID32A
[Ref.: #68380]	urea ChEBI	-	hydrolysis	* from API rID32A
	Only first 10 entries are displayed. Click here to see all.

	Metabolite production	Metabolite	Production
[Ref.: #68380]		indole ChEBI	no	* from API rID32A

	Physiological tests	Metabolite	Indole test
[Ref.: #68380]		indole ChEBI	-	* from API rID32A

	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.: #29297]	alpha-galactosidase	+	3.2.1.22
[Ref.: #68380]	alpha-galactosidase	+	3.2.1.22	* from API rID32A
[Ref.: #68380]	alpha-glucosidase	+	3.2.1.20	* from API rID32A
[Ref.: #68380]	arginine dihydrolase	-	3.5.3.6	* from API rID32A
[Ref.: #68380]	beta-galactosidase	+	3.2.1.23	* from API rID32A
[Ref.: #68380]	beta-Galactosidase 6-phosphate	-		* from API rID32A
[Ref.: #68380]	beta-glucosidase	-	3.2.1.21	* from API rID32A
[Ref.: #68380]	beta-glucuronidase	-	3.2.1.31	* from API rID32A
[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
	Only first 10 entries are displayed. Click here to see all.

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.: #16021]	12753	-	-	+	+	-	+	-	-	-	-	+	+	-	-	-	-	-	+	+	-	+	-	-	+	-	-	-	-	-
[Ref.: #16021]	12752	-	-	+	+	-	+	-	-	-	-	+	+	-	-	-	-	-	+	+	-	+	+	-	+	-	-	-	-	-

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

[Ref.: #16021]	Sample type/isolated from	human oral cavity from middle depth of carious lesion
[Ref.: #16021]	Geographic location (country and/or sea, region)	London
[Ref.: #16021]	Country	United Kingdom
[Ref.: #16021]	Country ISO 3 Code	GBR
[Ref.: #16021]	Continent	Europe

[Ref.: #61190]	Sample type/isolated from	Human oral cavity,carious lesion
[Ref.: #61190]	Sampling date	2001-11-01
[Ref.: #61190]	Geographic location (country and/or sea, region)	London
[Ref.: #61190]	Country	United Kingdom
[Ref.: #61190]	Country ISO 3 Code	GBR
[Ref.: #61190]	Continent	Europe

[Ref.: #67770]	Sample type/isolated from	Human mouth

[Ref.: #115997]	Sample type/isolated from	Human, Oral cavity from middle depth of carious lesion
[Ref.: #115997]	Geographic location (country and/or sea, region)	London
[Ref.: #115997]	Country	United Kingdom
[Ref.: #115997]	Country ISO 3 Code	GBR
[Ref.: #115997]	Continent	Europe
* marker position based on {}

Isolation sources categories

#Host	#Human	-
#Host Body-Site	#Oral cavity and airways	-
#Host Body-Site	#Other	#Wound

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence EU979537 (>99% sequence identity) for Propionibacterium acidifaciens subclade from Microbeatlas

Aquatic Samples	605
Soil Samples	272
Animal Samples	17851
Plant Samples	116
Total Samples	18844

Information on possible application of the strain and its possible interaction with e.g. potential hosts Safety information

[Ref.: #16021]	Pathogenicity (human)	yes, in single cases
[Ref.: #16021]	Biosafety level	1	Risk group (German classification) According to TRBA 466
[Ref.: #115997]	Biosafety level	1	Risk group (French classification)

Information on genomic background e.g. entries in nucleic sequence databass Sequence information

16S Sequence information:

	Sequence accession description	Seq. accession number	Sequence length (bp)	Sequence database	Associated NCBI tax ID
[Ref.: #16021]	Propionibacterium acidifaciens strain C3M_31 16S ribosomal RNA gene, partial sequence	EU979537	1442	GenBank ENA	556499 tax ID
[Ref.: #67770]	Propionibacterium acidifaciens gene for 16S ribosomal RNA, partial sequence	AB565481	1481	GenBank ENA	556499 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #67770]	Propionibacterium acidifaciens DSM 21887	GCA_000426605	scaffold	GenBank ENA	1122994 tax ID
[Ref.: #66792]	Propionibacterium acidifaciens DSM 21887	1122994.3	wgs	PATRIC	1122994 tax ID	*
[Ref.: #66792]	Propionibacterium acidifaciens DSM 21887	2524614803	draft	JGI IMG/M	1122994 tax ID	*

[Ref.: #16021]	GC-content	70 mol%	high performance liquid chromatography (HPLC)
[Ref.: #29297]	GC-content	70 mol%

Data predicted using genome information as a basis Genome-based predictions

	Trait	Model	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Propionibacterium acidifaciens DSM 21887 PATRIC: 1122994.3
[Ref.: #69480]	gram-positive	gram-positiveⓘ	yes	88.148	yes
[Ref.: #69480]	anaerobic	anaerobicⓘ	no	68.167	no
[Ref.: #69480]	spore-forming	spore-formingⓘ	no	79.311	no
[Ref.: #69480]	aerobic	aerobicⓘ	no	64.776	no
[Ref.: #69480]	thermophilic	thermophileⓘ	no	89.712	yes
[Ref.: #69480]	flagellated	motile2+ⓘ	no	97.5	yes

Availability in culture collections External links

[Ref.: #16021]

Culture collection no.

DSM 21887, CCUG 57100, CIP 110570, JCM 16571

[Ref.: #81871]

SI-ID 403725

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Propionibacterium ruminifibrarum sp. nov., isolated from cow rumen fibrous content.	Vaidya JD, Hornung BVH, Smidt H, Edwards JE, Plugge CM	Int J Syst Evol Microbiol	10.1099/ijsem.0.003544	2019	*
Phylogeny	Propionibacterium acidifaciens sp. nov., isolated from the human mouth.	Downes J, Wade WG	Int J Syst Evol Microbiol	10.1099/ijs.0.010470-0	2009	*

References

#16021

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 21887

#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 )

#29297

Barberan A, Caceres Velazquez H, Jones S, Fierer N.: Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information. mSphere 2: 2017 ( DOI 10.1128/mSphere.00237-17 , PubMed 28776041 ) - originally annotated from #25713 (see below)

#61190 Culture Collection University of Gothenburg (CCUG) ; Curators of the CCUG; CCUG 57100

#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 .

#69479

João F Matias Rodrigues, Janko Tackmann,Gregor Rot, Thomas SB Schmidt, Lukas Malfertheiner, Mihai Danaila,Marija Dmitrijeva, Daniela Gaio, Nicolas Näpflin and Christian von Mering. University of Zurich.: MicrobeAtlas 1.0 beta .

#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) .

#81871

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-ID403725.1 )

#115997 Collection of Institut Pasteur ; Curators of the CIP; CIP 110570

#25713

IJSEM 2778 2009 ( DOI 10.1099/ijs.0.010470-0 , PubMed 19625418 )

* These data were automatically processed and therefore are not curated

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Propionibacterium acidifaciens DSM 21887

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