Name: Pedococcus ginsenosidimutans BXN5-13
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 6304

Type strain:

Species: Pedococcus ginsenosidimutans

Strain Designation: BXN5-13

Culture col. no.: DSM 21006, KCTC 19419, LMG 24462, JCM 18961

Strain history: <- ST Lee, KAIST

NCBI tax ID(s): 490570 (species)

SI-ID 323917

LMG 24462, DSM 21006, KCTC 19419, JCM 18961

Section

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

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

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	*Micrococcales*
	Family	*Intrasporangiaceae*
	Genus	*Pedococcus*
	Species	**Pedococcus ginsenosidimutans**
	Full Scientific Name (LPSN)	Pedococcus ginsenosidimutans (Wang et al. 2011) Nouioui et al. 2018

Synonym

Phycicoccus ginsenosidimutans

Information on morphological and physiological properties Morphology

[Ref.: #29835]	Gram stain	positive
[Ref.: #67771]	Gram stain	positive

[Ref.: #29835]	Cell width	0.5 µm

[Ref.: #29835]	Cell shape	coccus-shaped

[Ref.: #29835]	Motility	no

[Ref.: #21352]	Colony color	Brown beige (1011)
[Ref.: #21352]	Incubation period	10-14 days
[Ref.: #21352]	Cultivation medium used	ISP 2

[Ref.: #21352]	Colony color	Maize yellow (1006)
[Ref.: #21352]	Incubation period	10-14 days
[Ref.: #21352]	Cultivation medium used	ISP 3

[Ref.: #21352]	Incubation period	10-14 days
[Ref.: #21352]	Cultivation medium used	ISP 4

[Ref.: #21352]	Incubation period	10-14 days
[Ref.: #21352]	Cultivation medium used	ISP 5

[Ref.: #21352]	Incubation period	10-14 days
[Ref.: #21352]	Cultivation medium used	ISP 7

[Ref.: #21352]	Incubation period	10-14 days
[Ref.: #21352]	Cultivation medium used	suter with tyrosine

[Ref.: #21352]	Incubation period	10-14 days
[Ref.: #21352]	Cultivation medium used	suter without tyrosine

[Ref.: #29835]

Pigment production

yes

[Ref.: #21352]	Multicellular complex forming ability	no
[Ref.: #21352]	Medium Name (multicellularity)	ISP 2

[Ref.: #21352]	Multicellular complex forming ability	no
[Ref.: #21352]	Medium Name (multicellularity)	ISP 3

[Ref.: #21352]	Multicellular complex forming ability	no
[Ref.: #21352]	Medium Name (multicellularity)	ISP 4

[Ref.: #21352]	Multicellular complex forming ability	no
[Ref.: #21352]	Medium Name (multicellularity)	ISP 5

[Ref.: #21352]	Multicellular complex forming ability	no
[Ref.: #21352]	Medium Name (multicellularity)	ISP 7

[Ref.: #21352]	Multicellular complex forming ability	no
[Ref.: #21352]	Medium Name (multicellularity)	Suter with tyrosine

[Ref.: #21352]	Multicellular complex forming ability	no
[Ref.: #21352]	Medium Name (multicellularity)	Suter without tyrosine

Information on culture and growth conditions Culture and growth conditions

[Ref.: #9079]

Culture medium

R2A MEDIUM (DSMZ Medium 830)

[Ref.: #9079]

Culture medium growth

[Ref.: #9079]

Culture medium link

Medium recipe at MediaDive

[Ref.: #9079]

Culture medium composition

expand / minimize

[Ref.: #21352]

Culture medium

ISP 2

[Ref.: #21352]

Culture medium growth

[Ref.: #21352]

Culture medium composition

expand / minimize

[Ref.: #21352]

Culture medium

ISP 3

[Ref.: #21352]

Culture medium growth

[Ref.: #21352]

Culture medium composition

expand / minimize

[Ref.: #21352]

Culture medium

ISP 4

[Ref.: #21352]

Culture medium growth

[Ref.: #21352]

Culture medium composition

expand / minimize

[Ref.: #21352]

Culture medium

ISP 5

[Ref.: #21352]

Culture medium growth

[Ref.: #21352]

Culture medium composition

expand / minimize

[Ref.: #21352]

Culture medium

ISP 7

[Ref.: #21352]

Culture medium growth

[Ref.: #21352]

Culture medium composition

expand / minimize

[Ref.: #21352]

Culture medium

suter with tyrosine

[Ref.: #21352]

Culture medium growth

[Ref.: #21352]

Culture medium composition

expand / minimize

[Ref.: #21352]

Culture medium

suter without tyrosine

[Ref.: #21352]

Culture medium growth

[Ref.: #21352]

Culture medium composition

expand / minimize

		Temperature
[Ref.: #9079]	growth	28 °C
[Ref.: #29835]	growth	10-37 °C
[Ref.: #29835]	optimum	30 °C
[Ref.: #67770]	growth	28 °C
[Ref.: #67771]	growth	30 °C

[Ref.: #9079]	Temperature range	mesophilic
[Ref.: #29835]	Temperature range	mesophilic
[Ref.: #67770]	Temperature range	mesophilic
[Ref.: #67771]	Temperature range	mesophilic

	pH	Kind of pH		pH
[Ref.: #29835]			optimum	7
[Ref.: #29835]			growth	05-10

Information on physiology and metabolism Physiology and metabolism

[Ref.: #29835]	Oxygen tolerance	aerobe
[Ref.: #67771]	Oxygen tolerance	aerobe

[Ref.: #29835]

Ability of spore formation

	Salt		Salt conc.
[Ref.: #21352]	NaCl	growth	0	%
[Ref.: #29835]	NaCl	growth	0-5	%
[Ref.: #29835]	NaCl	optimum	0-2	%

[Ref.: #67770]

Observation

quinones: MK-8(H₄)

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #21352]	arabinose ChEBI	-
[Ref.: #21352]	cellulose ChEBI	-
[Ref.: #68379]	D-glucose ChEBI	-	fermentation	* from API Coryne
[Ref.: #68379]	D-mannitol ChEBI	-	fermentation	* from API Coryne
[Ref.: #68379]	D-ribose ChEBI	-	fermentation	* from API Coryne
[Ref.: #68379]	D-xylose ChEBI	-	fermentation	* from API Coryne
[Ref.: #68379]	esculin ChEBI	+	hydrolysis	* from API Coryne
[Ref.: #21352]	fructose ChEBI	-
[Ref.: #68379]	gelatin ChEBI	-	hydrolysis	* from API Coryne
[Ref.: #21352]	glucose ChEBI	-
[Ref.: #29835]	glucose ChEBI	+	carbon source
[Ref.: #68379]	glycogen ChEBI	-	fermentation	* from API Coryne
[Ref.: #68379]	lactose ChEBI	-	fermentation	* from API Coryne
[Ref.: #29835]	malate ChEBI	+	carbon source
[Ref.: #68379]	maltose ChEBI	-	fermentation	* from API Coryne
[Ref.: #29835]	mannitol ChEBI	+	carbon source
[Ref.: #21352]	mannose ChEBI	-
[Ref.: #21352]	myo-inositol ChEBI	-
[Ref.: #29835]	nitrate ChEBI	+	reduction
[Ref.: #68379]	nitrate ChEBI	-	reduction	* from API Coryne
[Ref.: #21352]	raffinose ChEBI	-
[Ref.: #21352]	rhamnose ChEBI	-
[Ref.: #21352]	sucrose ChEBI	-
[Ref.: #68379]	urea ChEBI	-	hydrolysis	* from API Coryne
[Ref.: #21352]	xylose ChEBI	-
	Only first 10 entries are displayed. Click here to see all.

	Enzyme	Enzyme activity	EC number
[Ref.: #68382]	acid phosphatase	+	3.1.3.2	* from API zym
[Ref.: #68382]	alkaline phosphatase	+	3.1.3.1	* from API zym, API Coryne
[Ref.: #68382]	alpha-chymotrypsin	-	3.4.21.1	* from API zym
[Ref.: #68382]	alpha-fucosidase	-	3.2.1.51	* from API zym
[Ref.: #68382]	alpha-galactosidase	+	3.2.1.22	* from API zym
[Ref.: #68382]	alpha-glucosidase	+	3.2.1.20	* from API zym
[Ref.: #68382]	alpha-mannosidase	+	3.2.1.24	* from API zym
[Ref.: #68382]	beta-galactosidase	+	3.2.1.23	* from API zym, API Coryne
[Ref.: #68379]	beta-glucosidase	+	3.2.1.21	* from API Coryne
[Ref.: #68382]	beta-glucosidase	-	3.2.1.21	* from API zym
[Ref.: #68382]	beta-glucuronidase	-	3.2.1.31	* from API zym, API Coryne
[Ref.: #29835]	catalase	+	1.11.1.6
[Ref.: #29835]	cytochrome oxidase	+	1.9.3.1
[Ref.: #68382]	esterase (C 4)	+		* from API zym
[Ref.: #68382]	esterase lipase (C 8)	+		* from API zym
[Ref.: #68379]	gelatinase	-		* from API Coryne
[Ref.: #68382]	leucine arylamidase	+	3.4.11.1	* from API zym
[Ref.: #68382]	lipase (C 14)	-		* from API zym
[Ref.: #68382]	N-acetyl-beta-glucosaminidase	-	3.2.1.52	* from API zym
[Ref.: #68382]	naphthol-AS-BI-phosphohydrolase	+		* from API zym
[Ref.: #68379]	pyrazinamidase	-	3.5.1.B15	* from API Coryne
[Ref.: #68379]	pyrrolidonyl arylamidase	-	3.4.19.3	* from API Coryne
[Ref.: #68382]	trypsin	-	3.4.21.4	* from API zym
[Ref.: #29835]	urease	+	3.5.1.5
[Ref.: #68379]	urease	-	3.5.1.5	* from API Coryne
	Only first 10 entries are displayed. Click here to see all.

API® Coryne:

Note that the displayed test results represent raw data and therefore may deviate!

	API ID	Reduction of nitrateNIT	PyrazinamidasePYZ	Pyrrolidonyl arylamidasePYRA	Alkaline phosphatasePAL	beta-Glucuronidasebeta GUR	beta-Galactosidasebeta GAL	alpha-Glucosidasealpha GLU	N-Acetyl-beta-Glucosidasebeta NAG	Esculin hydrolysis/beta-GlucosidaseESC	Urease/urea hydrolysisURE	Gelatinase/gelatin hydrolysisGEL	Control fermentationControl	Fermentation of D-glucoseGLU	Fermentation of D-riboseRIB	Fermentation of D-xyloseXYL	Fermentation of D-mannitolMAN	Fermentation of maltoseMAL	Fermentation of lactoseLAC	Fermentation of sucroseSAC	Fermentation of glycogenGLYG	CatalaseCAT
[Ref.: #21352]	481	-	-	-	+	-	+	+/-	+/-	+	-	-	not determinedn.d.	-	-	-	-	-	-	+/-	-	not determinedn.d.

API® zym:

Note that the displayed test results represent raw data and therefore may deviate!

	API ID	Control	2-naphthyl phosphateAlkaline phosphatase	2-naphthyl butyrateEsterase (C 4)	2-naphtyl caprylateEsterase Lipase (C 8)	2-naphthyl myristateLipase (C 14)	L-leucyl-2-naphthylamideLeucine arylamidase	L-valyl-2-naphthylamideValine arylamidase	L-cystyl-2-naphthylamideCystine arylamidase	N-benzoyl-DL-arginine-2-naphthylamideTrypsin	N-glutaryl-phenylalanine-2-naphthylamidealpha- Chymotrypsin	2-naphthyl phosphateAcid phosphatase	Naphthol-AS-BI-phosphateNaphthol-AS-BI-phosphohydrolase	6-Br-2-naphthyl-alphaD-galactpyranosidealpha- Galactosidase	2-naphthyl-betaD-galactpyranosidebeta- Galactosidase	Naphthol-AS-BI-betaD-glucuronidebeta- Glucuronidase	2-naphthyl-alphaD-glucopyranosidealpha- Glucosidase	6-Br-2-naphthyl-betaD-glucopyranosidebeta- Glucosidase	1-naphthyl-N-acetyl-betaD-glucosaminideN-acetyl-beta- glucosaminidase	6-Br-2-naphthyl-alphaD-mannopyranosidealpha- Mannosidase	2-naphthyl-alphaL-fucopyranosidealpha- Fucosidase
[Ref.: #21352]	993	not determinedn.d.	+	+	+	-	+	+/-	+/-	-	-	+	+	+	+	-	+	-	-	+	-

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

[Ref.: #9079]	Sample type/isolated from	soil of a ginseng field
[Ref.: #9079]	Geographic location (country and/or sea, region)	Jilin district, Baekdu Mountain
[Ref.: #9079]	Country	China
[Ref.: #9079]	Country ISO 3 Code	CHN
[Ref.: #9079]	Continent	Asia

[Ref.: #67770]	Sample type/isolated from	Soil of a ginseng field of Baekdu Mountain
[Ref.: #67770]	Geographic location (country and/or sea, region)	Jinlin District
[Ref.: #67770]	Country	China
[Ref.: #67770]	Country ISO 3 Code	CHN
[Ref.: #67770]	Continent	Asia

[Ref.: #67771]	Sample type/isolated from	From soil of ginseng field
[Ref.: #67771]	Geographic location (country and/or sea, region)	Baekdu Mountain in Jilin district
[Ref.: #67771]	Country	Republic of Korea
[Ref.: #67771]	Country ISO 3 Code	KOR
[Ref.: #67771]	Continent	Asia
* marker position based on {}

Isolation sources categories

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

What are isolation sources categories?

[Ref.: #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

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

[Ref.: #9079]

Biosafety level

Risk group (German classification)
According to TRBA 466

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.: #9079]	Phycicoccus ginsenosidimutans strain BXN5-13 16S ribosomal RNA gene, partial sequence	EU332824	1405	ENA	490570 tax ID

[Ref.: #9079]	GC-content	70.8 mol%	high performance liquid chromatography (HPLC)
[Ref.: #29835]	GC-content	70.8 mol%

Availability in culture collections External links

[Ref.: #9079]

Culture collection no.

DSM 21006, KCTC 19419, LMG 24462, JCM 18961

[Ref.: #75779]

SI-ID 323917

Literature:

Topic	Title	Authors	Journal	DOI	Year
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 .

#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 (see below)

#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 .

#75779

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-ID323917.1 )

#26211

IJSEM 524 2011 ( DOI 10.1099/ijs.0.022137-0 , PubMed 20382795 )

* These data were automatically processed and therefore are not curated

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