Pedococcus bigeumensis (DSM 19264, KCTC 19266, MSL-03)

Name: Pedococcus bigeumensis (DSM 19264, KCTC 19266, MSL-03)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 6306

Type strain

Strain Designation MSL-03

Culture col. no. DSM 19264 KCTC 19266 MSL-03 JCM 16023 MSL 03

NCBI tax ID(s) 433644

Special Collections DSMZ JCM KCTC Wink compendium Literature strains

History DSMZ <- Chang-Jin Kim; MSL-03 JCM <-- KCTC 19266 <-- C.-J. Kim MSL-03. KCTC <- CJ Kim, KRIBB

Links

Pedococcus bigeumensis MSL-03 is an aerobe, Gram-positive, coccus-shaped bacterium that was isolated from soil, farming field.

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

Name and taxonomic classification

SI-ID 398212

JCM 16023,KCTC 19266,DSM 19264

@ref 20215

Last LPSN update 2026-05-29 08:26:22

Domain Bacteria

Phylum Actinomycetota

Class Actinomycetes

Order Micrococcales

Family Intrasporangiaceae

Genus Pedococcus

Species Pedococcus bigeumensis

Full scientific name Pedococcus bigeumensis (Dastager et al. 2008) Nouioui et al. 2018

Synonyms (1)

Phycicoccus bigeumensis

Morphology

Cell morphology

@ref	Gram stain	Cell width	Cell shape	Confidence
32482	positive	0.4-0.5 µm	coccus-shaped
67771	positive
125439	positive			93.262

Colony morphology

@ref	Colony color	Incubation period	Medium used
19778	Ivory (1014)	10-14 days	ISP 2
19778	Ivory (1014)	10-14 days	ISP 3
19778	Ivory (1014)	10-14 days	ISP 4
19778	Ivory (1014)	10-14 days	ISP 5
19778	Ivory (1014)	10-14 days	ISP 6
19778	Ivory (1014)	10-14 days	ISP 7

Multicellular morphology

@ref	Forms multicellular complex	Medium name
19778		ISP 2
19778		ISP 3
19778		ISP 4
19778		ISP 5
19778		ISP 6
19778		ISP 7

Pigmentation

32482

Productionyes

Culture and growth conditions

Culture medium

@ref	Name	Medium link	Composition
7913	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
19778	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
19778	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:
19778	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
19778	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
19778	ISP 6		Name: ISP 6 (5318) Composition Peptone 15.0 g/l Proteose peptose 5.0 g/l Ferric ammonium citrate 0.5 g/l Sodium glycerophosphate 1.0 g/l Sodium thiosulfate 0.08 g/l Yeast extract 1.0 g/l Agar 15.0 g/l Sterilisation: 20 minutes at 121°C pH before sterilisation: Usage: Production of melanoid pigments Organisms: All Actinomycetes
19778	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

Culture temp

@ref	Growth	Type	Temperature (°C)
7913	positive	growth	28
19778	positive	optimum	28
32482	positive	growth	20-37
32482	positive	optimum	28
67770	positive	growth	28
67771	positive	growth	30

Culture pH

@ref	Ability	Type	PH	PH range
32482	positive	optimum	7.4
32482	positive	growth	07-12	alkaliphile

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
32482	aerobe
67771	aerobe
125439	obligate aerobe	96.1

Spore formation

@ref	Spore formation	Confidence
32482
125439		95.419

Halophily

@ref	Salt	Growth	Tested relation	Concentration
32482	NaCl	positive	growth	0-5 %
32482	NaCl	positive	optimum	0-5 %

Observation

@ref	Observation
32482	aggregates in chains
67770	quinones: MK-8(H₄)

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
32482	22599 ChEBI	arabinose	+	carbon source
32482	17057 ChEBI	cellobiose	+	carbon source
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
32482	28757 ChEBI	fructose	+	carbon source
68379	5291 ChEBI	gelatin	+	hydrolysis	from API Coryne
32482	17234 ChEBI	glucose	+	carbon source
68379	28087 ChEBI	glycogen	-	fermentation	from API Coryne
32482	17716 ChEBI	lactose	+	carbon source
68379	17716 ChEBI	lactose	-	fermentation	from API Coryne
68379	17306 ChEBI	maltose	-	fermentation	from API Coryne
32482	29864 ChEBI	mannitol	+	carbon source
32482	37684 ChEBI	mannose	+	carbon source
32482	28053 ChEBI	melibiose	+	carbon source
32482	17632 ChEBI	nitrate	+	reduction
68379	17632 ChEBI	nitrate	-	reduction	from API Coryne
32482	16634 ChEBI	raffinose	+	carbon source
32482	26546 ChEBI	rhamnose	+	carbon source
68379	17992 ChEBI	sucrose	+	fermentation	from API Coryne
32482	27082 ChEBI	trehalose	+	carbon source
68379	16199 ChEBI	urea	-	hydrolysis	from API Coryne

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
68379	alpha-glucosidase	+	3.2.1.20	from API Coryne
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
68382	cystine arylamidase	-	3.4.11.3	from API zym
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
68379	N-acetyl-beta-glucosaminidase	-	3.2.1.52	from API Coryne
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
68379	urease	-	3.5.1.5	from API Coryne
68382	valine arylamidase	+		from API zym

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
19778	-	-	-	+	-	+	+	-	+	-	+	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
19778	not determinedn.d.	+	+	+	-	+	+	-	-	+	+	+	+	+	+	+	+	+	+	-

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Engineered	#Agriculture	#Field
#Environmental	#Terrestrial	#Soil

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent
7913	soil, farming field	Bigeum Island	Republic of Korea	KOR	Asia
67770	Soil	Bigeum Island	Republic of Korea	KOR	Asia
67771	From farming field	Bikeum island	Republic of Korea	KOR	Asia

Taxonmaps

69479

Global distribution of 16S sequence EF466128 (>99% sequence identity) for Pedococcus from Microbeatlas

Aquatic Samples	473
Soil Samples	3476
Animal Samples	999
Plant Samples	606
Total Samples	5554

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
7913	1	Risk group (German classification) According to TRBA 466
19778	1	Risk group (German classification) According to TRBA 466

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	NCBI tax ID	Score
124043	ASM3953179v1 assembly for Pedococcus bigeumensis JCM 16023	contig	GCA_039531795	433644	72.92

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
7913	Phycicoccus sp. MSL 03 16S ribosomal RNA gene, partial sequence	EF466128	1488		433644

GC content

@ref	GC-content (mol%)	Method
7913	73.4	high performance liquid chromatography (HPLC)
32482	73.4

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: ASM3953179v1 assembly for Pedococcus bigeumensis JCM 16023
NCBI: GCA_039531795

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	96.10	no
125439	gram_stain	BacteriaNetⓘ	positive	93.26	no
125439	motility	BacteriaNetⓘ	no	65.03	no
125439	spore_formation	BacteriaNetⓘ	no	95.42	no

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 cremeus sp. nov., isolated from forest soil, and emended description of the genus Phycicoccus.	Zhang JY, Liu XY, Liu SJ	Int J Syst Evol Microbiol	10.1099/ijs.0.020842-0	2010
Phylogeny	Phycicoccus bigeumensis sp. nov., a mesophilic actinobacterium isolated from Bigeum Island, Korea.	Dastager SG, Lee JC, Ju YJ, Park DJ, Kim CJ	Int J Syst Evol Microbiol	10.1099/ijs.0.65563-0	2008

References

#7913	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 19264
#19778	Wink, J.: Compendium of Actinobacteria. HZI-Helmholtz-Centre for Infection Research, Braunschweig .
#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 )
#28702	IJSEM 2425 2008 ( DOI 10.1099/ijs.0.65563-0 , PubMed 18842868 )
#32482	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 #28702
#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 .
#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 )

Content

About us

Pedococcus bigeumensis (DSM 19264, KCTC 19266, MSL-03)

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_039531795

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

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