Pedococcus ginsenosidimutans (DSM 21006, KCTC 19419, LMG 24462)

Name: Pedococcus ginsenosidimutans (DSM 21006, KCTC 19419, LMG 24462)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 6304

Type strain

Strain Designation BXN5-13

Culture col. no. DSM 21006 KCTC 19419 LMG 24462 BXN5-13 JCM 18961

NCBI tax ID(s) 490570

Special Collections DSMZ JCM KCTC Wink compendium Literature strains

Links

Pedococcus ginsenosidimutans BXN5-13 is an aerobe, mesophilic, Gram-positive prokaryote that was isolated from soil of a ginseng field.

Gram-positive coccus-shaped aerobe mesophilic genome sequence 16S sequence

Name and taxonomic classification

SI-ID 323917

LMG 24462,DSM 21006,KCTC 19419,JCM 18961

@ref 20215

Last LPSN update 2025-12-16 09:48:17

Domain Bacillati

Phylum Actinomycetota

Class Actinomycetes

Order Micrococcales

Family Intrasporangiaceae

Genus Pedococcus

Species Pedococcus ginsenosidimutans

Full scientific name Pedococcus ginsenosidimutans (Wang et al. 2011) Nouioui et al. 2018

Synonyms (1)

Phycicoccus ginsenosidimutans

Morphology

Cell morphology

@ref	Gram stain	Cell width	Cell shape	Motility
29835	positive	0.5 µm	coccus-shaped
67771	positive

Colony morphology

@ref	Colony color	Incubation period	Medium used
21352	Brown beige (1011)	10-14 days	ISP 2
21352	Maize yellow (1006)	10-14 days	ISP 3
21352		10-14 days	ISP 4
21352		10-14 days	ISP 5
21352		10-14 days	ISP 7
21352		10-14 days	suter with tyrosine
21352		10-14 days	suter without tyrosine

Multicellular morphology

@ref	Forms multicellular complex	Medium name
21352		ISP 2
21352		ISP 3
21352		ISP 4
21352		ISP 5
21352		ISP 7
21352		Suter with tyrosine
21352		Suter without tyrosine

Pigmentation

29835

Productionyes

Culture and growth conditions

Culture medium

@ref	Name	Medium link	Composition
9079	R2A MEDIUM (DSMZ Medium 830)	Medium recipe at MediaDive	Name: R2A MEDIUM (DSMZ Medium 830) Composition: Agar 15.0 g/l Casamino acids 0.5 g/l Starch 0.5 g/l Glucose 0.5 g/l Proteose peptone 0.5 g/l Yeast extract 0.5 g/l K2HPO4 0.3 g/l Na-pyruvate 0.3 g/l MgSO4 x 7 H2O 0.05 g/l Distilled water
21352	ISP 2		Name: ISP 2 / Yeast Malt Agar (5265); 5265 Composition Malt extract 10.0 g/l Yeast extract 4.0 g/l Glucose 4.0 g/l Agar 15.0 g/l Preparation: Sterilisation: 20 minutes at 121°C pH before sterilisation: 7.0 Usage: Maintenance and Taxonomy Organisms: All Actinomycetes
21352	ISP 3		Name: ISP 3; 5315 Composition Dog oat flakes 20.0 g/l Trace element solution (5314) 2.5 ml/l Agar 18.0 g/l Preparation: Oat flakes are cooked for 20 minutes, trace element solution and agar are added (in the case of non rolled oat flakes the suspension has to bee filtrated). Sterilisation: 20 minutes at 121°C pH before sterilisation: 7.8 Usage: Maintenance and taxonomy (e.g. SEM As liquid medium for metabolite production) Organisms: All Actinomycetes Trace element solution 5314 Name: Trace element solution 5314; 5314 Composition CaCl2 x H2O 3.0 g/l Fe-III-citrate 1.0 g/l MnSO4 0.2 g/l ZnCl2 0.1 g/l CuSO4 x 5 H2O 0.025 g/l Sodium tetra borate 0.2 g/l CoCl2 x 6 H2O 0.004 g/l Sodium molybdate 0.01 g/l Preparation: Use double destillated water. Sterilisation: 20 minutes at 121°C pH before sterilisation: Usage: Trace element solution for different media Organisms:
21352	ISP 4		Name: ISP 4; DSM 547 Solution I: Difco soluble starch, 10.0 g. Make a paste of the starch with a small amount of cold distilled water and bring to a volume of 500 ml. Solution II: CaCO3 2.0 g K2HPO4 (anhydrous) 1.0 g MgSO4 x 7 H2O 1.0 g NaCl 1.0 g (NH4)2SO4 2.0 g Distilled water 500.0 ml Trace salt solution (see below) 1.0 ml The pH should be between 7.0 and 7.4. Do not adjust if it is within this range. Mix solutions I and II together. Add 20.0 g agar. Liquify agar by steaming at 100°C for 10 to 20 min. Trace element solution: FeSO4 x 7 H2O 0.1 g MnCl2 x 4 H2O 0.1 g ZnSO4 x 7 H2O 0.1 g Distilled water 100.0 ml
21352	ISP 5		Name: ISP 5 (5323) Composition L-Asparagine 1.0 g/l Glycerol 10.0 g/l K2HPO4 1.0 g/l Salt solution (see preparation) 1.0 ml/l Agar 20.0 g/l Preparation: Salt solution 1.0 g FeSO4 x 7 H2O 1.0 g MnCl2 x 4 H2O 1.0 g ZNSO4 x 7 H2O in 100 ml water Sterilisation: 20 minutes at 121°C pH before sterilisation: 7.2 Usage: Maintenance and taxonomy Organisms: All Actinomycetes
21352	ISP 7		Name: ISP 7 (5322) Composition Glycerol 15.0 g/l L-Tyrosine 0.5 g/l L-Asparagine 1.0 g/l K2HPO4 0.5 g/l NaCl 0.5 g/l FeSO4 x 7 H2O 0.01 g/l Trace element solution 5343 1.0 ml/l Agar 20.0 Sterilisation: 20 minutes at 121°C pH before sterilisation: 7.3 Usage: Production of melanoid pigments Organisms: All Actinomycetes
21352	suter with tyrosine		Name: Synthetically suter medium (5337) with and without tyrosine - see Kutzner,H.J., R. M. Kroppensted and F. Korn-Wendisch. (1986) Composition: Glycerol 15.0 g/l Tyrosine 1.0 (optional, see preparation comment) L-arginine 5.0 g/l L-glutamic acid 5.0 g/l L-methionine 0.3 g/l L-isoleucine 0.3 g/l K2HPO4 0.5 g/l MgSO4 x 7 H2O 0.2 g/l Agar 20.0 g/l Trace element solution (5341) 1.0 ml Composition of Trace element solution (5341): CuSO4 x 5 H2O 10.0 g/l CaCl2 x 2 H2O 10.0 g/l FeSO4 x 7 H2O 10.0 g/l ZnSO4 x 7 H2O 10.0 g/l MnSO4 x 7 H2O 40.0 g/l Preparation: Control medium is prepared without tyrosine Sterilisation: 20 minutes at 121°C pH before sterilisation: Usage: Production of melanoid pigment Organisms: All Actinomycetes
21352	suter without tyrosine		Name: Synthetically suter medium (5337) with and without tyrosine - see Kutzner,H.J., R. M. Kroppensted and F. Korn-Wendisch. (1986) Composition: Glycerol 15.0 g/l Tyrosine 1.0 (optional, see preparation comment) L-arginine 5.0 g/l L-glutamic acid 5.0 g/l L-methionine 0.3 g/l L-isoleucine 0.3 g/l K2HPO4 0.5 g/l MgSO4 x 7 H2O 0.2 g/l Agar 20.0 g/l Trace element solution (5341) 1.0 ml Composition of Trace element solution (5341): CuSO4 x 5 H2O 10.0 g/l CaCl2 x 2 H2O 10.0 g/l FeSO4 x 7 H2O 10.0 g/l ZnSO4 x 7 H2O 10.0 g/l MnSO4 x 7 H2O 40.0 g/l Preparation: Control medium is prepared without tyrosine Sterilisation: 20 minutes at 121°C pH before sterilisation: Usage: Production of melanoid pigment Organisms: All Actinomycetes

Culture temp

@ref	Growth	Type	Temperature (°C)	Range
9079	positive	growth	28	mesophilic
29835	positive	growth	10-37
29835	positive	optimum	30	mesophilic
67770	positive	growth	28	mesophilic
67771	positive	growth	30	mesophilic

Culture pH

@ref	Ability	Type	PH	PH range
29835	positive	optimum	7
29835	positive	growth	05-10	alkaliphile

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance
29835	aerobe
67771	aerobe

Spore formation

29835

Spore formationno

Halophily

@ref	Salt	Growth	Tested relation	Concentration
21352	NaCl	positive	growth	0 %
29835	NaCl	positive	growth	0-5 %
29835	NaCl	positive	optimum	0-2 %

Observation

67770

Observationquinones: MK-8(H₄)

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
21352	22599 ChEBI	arabinose	-
21352	62968 ChEBI	cellulose	-
68379	17634 ChEBI	D-glucose	-	fermentation	from API Coryne
68379	16899 ChEBI	D-mannitol	-	fermentation	from API Coryne
68379	16988 ChEBI	D-ribose	-	fermentation	from API Coryne
68379	65327 ChEBI	D-xylose	-	fermentation	from API Coryne
68379	4853 ChEBI	esculin	+	hydrolysis	from API Coryne
21352	28757 ChEBI	fructose	-
68379	5291 ChEBI	gelatin	-	hydrolysis	from API Coryne
21352	17234 ChEBI	glucose	-
29835	17234 ChEBI	glucose	+	carbon source
68379	28087 ChEBI	glycogen	-	fermentation	from API Coryne
68379	17716 ChEBI	lactose	-	fermentation	from API Coryne
29835	25115 ChEBI	malate	+	carbon source
68379	17306 ChEBI	maltose	-	fermentation	from API Coryne
29835	29864 ChEBI	mannitol	+	carbon source
21352	37684 ChEBI	mannose	-
21352	17268 ChEBI	myo-inositol	-
29835	17632 ChEBI	nitrate	+	reduction
68379	17632 ChEBI	nitrate	-	reduction	from API Coryne
21352	16634 ChEBI	raffinose	-
21352	26546 ChEBI	rhamnose	-
21352	17992 ChEBI	sucrose	-
68379	16199 ChEBI	urea	-	hydrolysis	from API Coryne
21352	18222 ChEBI	xylose	-

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
68379	alkaline phosphatase	+	3.1.3.1	from API Coryne
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
68382	beta-galactosidase	+	3.2.1.23	from API zym
68379	beta-galactosidase	+	3.2.1.23	from API Coryne
68382	beta-glucosidase	-	3.2.1.21	from API zym
68379	beta-glucosidase	+	3.2.1.21	from API Coryne
68382	beta-glucuronidase	-	3.2.1.31	from API zym
68379	beta-glucuronidase	-	3.2.1.31	from API Coryne
29835	catalase	+	1.11.1.6
29835	cytochrome oxidase	+	1.9.3.1
68382	esterase (C 4)	+		from API zym
68382	esterase lipase (C 8)	+		from API zym
68379	gelatinase	-		from API Coryne
68382	leucine arylamidase	+	3.4.11.1	from API zym
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
68379	pyrazinamidase	-	3.5.1.B15	from API Coryne
68379	pyrrolidonyl arylamidase	-	3.4.19.3	from API Coryne
68382	trypsin	-	3.4.21.4	from API zym
29835	urease	+	3.5.1.5
68379	urease	-	3.5.1.5	from API Coryne

API coryne

@ref	Reduction of nitrateNIT	PYZ	PYRA	PAL	beta GUR	beta GAL	alpha GLU	beta NAG	ESC	URE	GEL	Control fermentationControl	GLU	RIB	XYL	MAN	MAL	LAC	SAC	GLYG	CAT
21352	-	-	-	+	-	+	+/-	+/-	+	-	-	not determinedn.d.	-	-	-	-	-	-	+/-	-	not determinedn.d.

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
21352	not determinedn.d.	+	+	+	-	+	+/-	+/-	-	-	+	+	+	+	-	+	-	-	+	-

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Engineered	#Agriculture	#Field
#Environmental	#Terrestrial	#Soil
#Host	#Plants	#Herbaceous plants (Grass,Crops)

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent
9079	soil of a ginseng field	Jilin district, Baekdu Mountain	China	CHN	Asia
67770	Soil of a ginseng field of Baekdu Mountain	Jinlin District	China	CHN	Asia
67771	From soil of ginseng field	Baekdu Mountain in Jilin district	Republic of Korea	KOR	Asia

Taxonmaps

69479

Global distribution of 16S sequence EU332824 (>99% sequence identity) for Intrasporangiaceae from Microbeatlas

Aquatic Samples	17
Soil Samples	148
Animal Samples	133
Plant Samples	46
Total Samples	344

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
9079	1	Risk group (German classification) According to TRBA 466

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	NCBI tax ID	Score
124043	ASM3954439v1 assembly for Pedococcus ginsenosidimutans JCM 18961	contig	GCA_039544395	490570	68.94

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
9079	Phycicoccus ginsenosidimutans strain BXN5-13 16S ribosomal RNA gene, partial sequence	EU332824	1405		490570

GC content

@ref	GC-content (mol%)	Method
9079	70.8	high performance liquid chromatography (HPLC)
29835	70.8

Genome-based predictions

Literature

Topic	Title	Authors	Journal	DOI	Year
Genetics	Genome-Based Taxonomic Classification of the Phylum Actinobacteria.	Nouioui I, Carro L, Garcia-Lopez M, Meier-Kolthoff JP, Woyke T, Kyrpides NC, Pukall R, Klenk HP, Goodfellow M, Goker M.	Front Microbiol	10.3389/fmicb.2018.02007	2018
Phylogeny	Phycicoccus ginsengisoli sp. nov., isolated from cultivated ginseng soil.	Kang JP, Kim YJ, Nguyen NL, Hoang VA, Farh ME, Joo SC, Quan LH, Yang DC	Int J Syst Evol Microbiol	10.1099/ijsem.0.001515	2016
Phylogeny	Phycicoccus ginsenosidimutans sp. nov., isolated from soil of a ginseng field.	Wang L, An DS, Jin FX, Lee ST, Im WT, Bae HM	Int J Syst Evol Microbiol	10.1099/ijs.0.022137-0	2010

References

#9079	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 21006
#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 )
#21352	Wink, J.: Compendium of Actinobacteria. HZI-Helmholtz-Centre for Infection Research, Braunschweig .
#26211	IJSEM 524 2011 ( DOI 10.1099/ijs.0.022137-0 , PubMed 20382795 )
#29835	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 #26211
#67770	Japan Collection of Microorganism (JCM) ; Curators of the JCM;
#67771	Korean Collection for Type Cultures (KCTC) ; Curators of the KCTC;
#68379	Automatically annotated from API Coryne .
#68382	Automatically annotated from API zym .
#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 .
#124043	Isabel Schober, Julia Koblitz: Data extracted from sequence databases, automatically matched based on designation and taxonomy .
#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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Pedococcus ginsenosidimutans (DSM 21006, KCTC 19419, LMG 24462)

Name and taxonomic classification

Morphology

Cell morphology

Colony morphology

Multicellular morphology

Pigmentation

Culture and growth conditions

Culture medium

Culture temp

Culture pH

Physiology and metabolism

Oxygen tolerance

Spore formation

Halophily

Observation

Metabolite utilization

Enzymes

API coryne

API zym

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_039544395

16S sequences

GC content

Genome-based predictions

Literature

Literature

References

BacDive

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