Propionibacterium acidifaciens (DSM 21887, CCUG 57100, CIP 110570)

Name: Propionibacterium acidifaciens (DSM 21887, CCUG 57100, CIP 110570)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 12659

Type strain

Strain Designation C3M-31, C3M_31

Culture col. no. DSM 21887 CCUG 57100 CIP 110570 C3M-31 C3M_31 1 more

NCBI tax ID(s) 1122994 556499

Special Collections DSMZ CCUG JCM CIP Literature strains

History <- J. Downes <- W. Wade, King's College London, United Kingdom; C3M-31 CCUG 57100 <-- J. Downes <-- W. Wade C3M_31. CIP <- 2013, DSMZ <- J. Downes <- W. Wade, King's College London, UK: strain C3M-31

Links

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

Gram-positive anaerobe mesophilic genome sequence 16S sequence

Name and taxonomic classification

SI-ID 403725

LMG 31299,NCTC 13654,JCM 16571,DSM 21887,CCUG 57100,CIP 110570

@ref 20215

Last LPSN update 2026-02-09 11:20:54

Domain Bacteria

Phylum Actinomycetota

Class Actinomycetes

Order Propionibacteriales

Family Propionibacteriaceae

Genus Propionibacterium

Species Propionibacterium acidifaciens

Full scientific name Propionibacterium acidifaciens Downes and Wade 2009

Morphology

Cell morphology

@ref	Gram stain	Cell length	Cell width	Cell shape	Confidence
29297	positive	2.6 µm	0.75 µm
115997	positive			rod-shaped
125438					97.5
125439	positive				94

Colony morphology

61190

Incubation period2 days

Pigmentation

29297

Productionyes

Culture and growth conditions

Culture medium

@ref	Name	Medium link	Composition
16021	SCHAEDLER BROTH (ROTH; 5772) (DSMZ Medium 1669)	Medium recipe at MediaDive	Name: SCHAEDLER BROTH (Roth; 5772) (DSMZ Medium 1669) Composition: Glucose 5.83 g/l Casein peptone 5.66 g/l Yeast extract 5.0 g/l Peptone mixture 5.0 g/l Tris 3.0 g/l NaCl 1.66 g/l Soy peptone 1.0 g/l K2HPO4 0.83 g/l L-Cysteine HCl x H2O 0.4 g/l Hemin 0.01 g/l Resazurin 0.001 g/l Distilled water
16021	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
16021	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
115997	CIP Medium 20	Medium recipe at CIP

Culture temp

@ref	Growth	Type	Temperature (°C)	Range
16021	positive	growth	35	mesophilic
61190	positive	growth	37	mesophilic
67770	positive	growth	37	mesophilic

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance
29297	anaerobe
61190	anaerobe

Spore formation

@ref	Spore formation	Confidence
29297
125439		92.2

Observation

29297

Observationaggregates in chains

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
29297	30089 ChEBI	acetate	+	carbon source
29297	22599 ChEBI	arabinose	+	carbon source
68380	29016 ChEBI	arginine	-	hydrolysis	from API rID32A
29297	17057 ChEBI	cellobiose	+	carbon source
68380	16024 ChEBI	D-mannose	+	fermentation	from API rID32A
29297	28757 ChEBI	fructose	+	carbon source
29297	17234 ChEBI	glucose	+	carbon source
68380	29985 ChEBI	L-glutamate	-	degradation	from API rID32A
29297	17716 ChEBI	lactose	+	carbon source
29297	17306 ChEBI	maltose	+	carbon source
29297	29864 ChEBI	mannitol	+	carbon source
29297	37684 ChEBI	mannose	+	carbon source
29297	28053 ChEBI	melibiose	+	carbon source
68380	17632 ChEBI	nitrate	-	reduction	from API rID32A
29297	17272 ChEBI	propionate	+	carbon source
29297	16634 ChEBI	raffinose	+	carbon source
68380	16634 ChEBI	raffinose	+	fermentation	from API rID32A
29297	26546 ChEBI	rhamnose	+	carbon source
29297	33942 ChEBI	ribose	+	carbon source
29297	17814 ChEBI	salicin	+	carbon source
29297	30031 ChEBI	succinate	+	carbon source
29297	17992 ChEBI	sucrose	+	carbon source
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-arabinosidase	-	3.2.1.55	from API rID32A
68380	alpha-fucosidase	-	3.2.1.51	from API rID32A
29297	alpha-galactosidase	+	3.2.1.22
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	beta-glucuronidase	-	3.2.1.31	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	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
16021	-	-	+	+	-	+	-	-	-	-	+	+	-	-	-	-	-	+	+	-	+	-	-	+	-	-	-	-	-
16021	-	-	+	+	-	+	-	-	-	-	+	+	-	-	-	-	-	+	+	-	+	+	-	+	-	-	-	-	-

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Host	#Human	-
#Host Body-Site	#Oral cavity and airways	-
#Host Body-Site	#Other	#Wound

Isolation

@ref	Sample type	Sampling date	Geographic location	Country	Country ISO 3 Code	Continent
16021	human oral cavity from middle depth of carious lesion		London	United Kingdom	GBR	Europe
61190	Human oral cavity,carious lesion	2001-11-01	London	United Kingdom	GBR	Europe
67770	Human mouth
115997	Human, Oral cavity from middle depth of carious lesion		London	United Kingdom	GBR	Europe

Taxonmaps

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

Interaction and safety

Risk assessment

@ref	Pathogenicity human	Biosafety level	Biosafety level comment
16021	yes, in single cases	1	Risk group (German classification) According to TRBA 466
115997		1	Risk group (French classification) According to TRBA 466

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
67770	ASM42660v1 assembly for Propionibacterium acidifaciens DSM 21887	scaffold	GCA_000426605	1122994.3	2524614803	1122994	59.57

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
16021	Propionibacterium acidifaciens strain C3M_31 16S ribosomal RNA gene, partial sequence	EU979537	1442		556499
67770	Propionibacterium acidifaciens gene for 16S ribosomal RNA, partial sequence	AB565481	1481		556499

GC content

@ref	GC-content (mol%)	Method
16021	70	high performance liquid chromatography (HPLC)
29297	70

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Propionibacterium acidifaciens DSM 21887
NCBI: GCA_000426605

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	no	92.20	no
125439	motility	BacteriaNetⓘ	no	52.80	no
125439	gram_stain	BacteriaNetⓘ	positive	94.00	no
125439	oxygen_tolerance	BacteriaNetⓘ	anaerobe	85.30	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Propionibacterium acidifaciens DSM 21887
PATRIC: 1122994.3

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	yes	88.15	yes
125438	anaerobic	anaerobicⓘ	no	68.17	no
125438	spore-forming	spore-formingⓘ	no	79.31	no
125438	aerobic	aerobicⓘ	no	64.78	no
125438	thermophilic	thermophileⓘ	no	89.71	yes
125438	flagellated	motile2+ⓘ	no	97.50	yes

Literature

Topic	Title	Authors	Journal	DOI	Year
	Metatranscriptomic analysis shows functional alterations in subgingival biofilm in young smokers with periodontitis: a pilot study.	Casarin RCV, Silva RVCD, Paz HES, Stolf CS, Carvalho LM, Noronha MF, Sallum AW, Monteiro MF.	J Appl Oral Sci	10.1590/1678-7757-2024-0031	2024
Metabolism	Comparative Genomics of Sigma Factors in Acidithiobacillia Sheds Light into the Transcriptional Regulatory Networks Involved in Biogeochemical Dynamics in Extreme Acidic Environments.	Sepulveda-Rebolledo P, Gonzalez-Rosales C, Dopson M, Perez-Rueda E, Holmes DS, Valdes JH.	Microorganisms	10.3390/microorganisms13061199	2025
	Draft Genome Sequences of Sphingomonas mucosissima DSM 17494 and Sphingomonas dokdonensis DSM 21029.	Poehlein A, Wubbeler JH, Daniel R, Steinbuchel A.	Genome Announc	10.1128/genomea.00889-17	2017
Genetics	Beyond the ABCs-Discovery of Three New Plasmid Types in Rhodobacterales (RepQ, RepY, RepW).	Freese HM, Ringel V, Overmann J, Petersen J.	Microorganisms	10.3390/microorganisms10040738	2022
Enzymology	Two Cases of Urinary Tract Infection Caused by Propionimicrobium lymphophilum.	Williams GD.	J Clin Microbiol	10.1128/jcm.00438-15	2015
Pathogenicity	Procyanidin-Cell Wall Interactions within Apple Matrices Decrease the Metabolization of Procyanidins by the Human Gut Microbiota and the Anti-Inflammatory Effect of the Resulting Microbial Metabolome In Vitro.	Le Bourvellec C, Bagano Vilas Boas P, Lepercq P, Comtet-Marre S, Auffret P, Ruiz P, Bott R, Renard CMGC, Dufour C, Chatel JM, Mosoni P.	Nutrients	10.3390/nu11030664	2019
Genetics	Integrated Multi-omics Investigations Reveal the Key Role of Synergistic Microbial Networks in Removing Plasticizer Di-(2-Ethylhexyl) Phthalate from Estuarine Sediments.	Wei ST, Chen YL, Wu YW, Wu TY, Lai YL, Wang PH, Ismail W, Lee TH, Chiang YR.	mSystems	10.1128/msystems.00358-21	2021
Phylogeny	Helcococcus ovis, an emerging pathogen in bovine valvular endocarditis.	Kutzer P, Schulze C, Engelhardt A, Wieler LH, Nordhoff M.	J Clin Microbiol	10.1128/jcm.00867-08	2008
Phylogeny	Analysis of early bacterial communities on volcanic deposits on the island of Miyake (Miyake-jima), Japan: a 6-year study at a fixed site.	Fujimura R, Sato Y, Nishizawa T, Nanba K, Oshima K, Hattori M, Kamijo T, Ohta H.	Microbes Environ	10.1264/jsme2.me11207	2012
	Clostridium butyricum-altered lung microbiome is associated with enhanced anti-influenza effects via G-protein-coupled receptor120.	Hagihara M, Yamashita M, Ariyoshi T, Minemura A, Yoshida C, Higashi S, Oka K, Takahashi M, Ota A, Maenaka A, Iwasaki K, Hirai J, Shibata Y, Umemura T, Mori T, Kato H, Asai N, Mikamo H.	iScience	10.1016/j.isci.2025.113502	2025
Phylogeny	Sphingomonas panaciterrae sp. nov., a plant growth-promoting bacterium isolated from soil of a ginseng field.	Sukweenadhi J, Kim YJ, Kang CH, Farh Mel-A, Nguyen NL, Hoang VA, Choi ES, Yang DC.	Arch Microbiol	10.1007/s00203-015-1134-z	2015
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 )
#25713	IJSEM 2778 2009 ( DOI 10.1099/ijs.0.010470-0 , PubMed 19625418 )
#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
#61190	Culture Collection University of Gothenburg (CCUG) ; Curators of the CCUG; CCUG 57100
#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 .
#115997	Collection of Institut Pasteur ; Curators of the CIP; CIP 110570
#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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Propionibacterium acidifaciens (DSM 21887, CCUG 57100, CIP 110570)

Name and taxonomic classification

Morphology

Cell morphology

Colony morphology

Pigmentation

Culture and growth conditions

Culture medium

Culture temp

Physiology and metabolism

Oxygen tolerance

Spore formation

Observation

Metabolite utilization

Metabolite production

Metabolite tests

Enzymes

API rID32A

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_000426605

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

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