Pedococcus dokdonensis (DSM 22329, CCUG 54521, KCTC 19248)

Name: Pedococcus dokdonensis (DSM 22329, CCUG 54521, KCTC 19248)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 6305

Type strain

Strain Designation DS-8

Culture col. no. DSM 22329 CCUG 54521 KCTC 19248 JCM 19120 DS-8

NCBI tax ID(s) 443156

Special Collections DSMZ CCUG JCM KCTC Literature strains

History <- CCUG <- J. H. Yoon, Korea Res. Inst. Biosci. & Biotechnol. (KRIBB), Taejon, South Korea; DS-8 CCUG 54521 <-- J.-H. Yoon DS-8. <- JH Yoon, KRIBB

Links

Pedococcus dokdonensis DS-8 is an aerobe, mesophilic, Gram-positive prokaryote that was isolated from Soil.

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

Name and taxonomic classification

SI-ID 404956

KCTC 19248,JCM 19120,DSM 22329,CCUG 54521

@ref 20215

Last LPSN update 2026-02-09 11:19:11

Domain Bacteria

Phylum Actinomycetota

Class Actinomycetes

Order Micrococcales

Family Intrasporangiaceae

Genus Pedococcus

Species Pedococcus dokdonensis

Full scientific name Pedococcus dokdonensis (Yoon et al. 2008) Nouioui et al. 2018

Synonyms (1)

Phycicoccus dokdonensis

Morphology

Cell morphology

@ref	Gram stain	Cell width	Cell shape	Confidence
32302	positive	0.5 µm	coccus-shaped
67771	positive
125438				91
125438	positive			91.372
125439	positive			98.9

Colony morphology

60211

Incubation period3-5 days

Pigmentation

32302

Productionyes

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
16285	TRYPTICASE SOY YEAST EXTRACT MEDIUM (DSMZ Medium 92)		Medium recipe at MediaDive	Name: TRYPTICASE SOY YEAST EXTRACT MEDIUM (DSMZ Medium 92) Composition: Trypticase soy broth 30.0 g/l Agar 15.0 g/l Yeast extract 3.0 g/l Distilled water
16285	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

Culture temp

@ref	Growth	Type	Temperature (°C)	Range
16285	positive	growth	28	mesophilic
32302	positive	growth	10-36
32302	positive	optimum	30	mesophilic
60211	positive	growth	30	mesophilic
67770	positive	growth	28	mesophilic
67771	positive	growth	30	mesophilic

Culture pH

@ref	Ability	Type	PH	PH range
32302	positive	optimum	7
32302	positive	growth	5-8.5	alkaliphile

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
32302	aerobe
60211	aerobe
67771	aerobe
125438	aerobe	92.97
125439	obligate aerobe	98.3

Spore formation

32302

Spore formationno

Halophily

@ref	Salt	Growth	Tested relation	Concentration
32302	NaCl	positive	growth	0-5 %
32302	NaCl	positive	optimum	0.75 %

Murein

@ref	Murein short key	Type
16285	A31	A1gamma m-Dpm-direct

Observation

@ref	Observation
67770	quinones: MK-8(H₄)
67771	quinones: MK-8(H4)

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
32302	17057 ChEBI	cellobiose	+	carbon source
32302	28757 ChEBI	fructose	+	carbon source
32302	28260 ChEBI	galactose	+	carbon source
32302	17716 ChEBI	lactose	+	carbon source

Enzymes

@ref	Value	Activity	Ec
32302	cytochrome oxidase	+	1.9.3.1

Pathway annotation

Computationally determined by

@ref	pathway	enzyme coverage	annotated reactions
66794	coenzyme A metabolism	100	4 of 4
66794	acetate fermentation	100	4 of 4
66794	threonine metabolism	100	10 of 10
66794	allantoin degradation	100	9 of 9
66794	formaldehyde oxidation	100	3 of 3
66794	starch degradation	100	10 of 10
66794	cardiolipin biosynthesis	100	7 of 7
66794	vitamin K metabolism	100	5 of 5
66794	cis-vaccenate biosynthesis	100	2 of 2
66794	phenylacetate degradation (aerobic)	100	5 of 5
66794	glycolate and glyoxylate degradation	100	6 of 6
66794	teichoic acid biosynthesis	100	1 of 1
66794	denitrification	100	2 of 2
66794	anapleurotic synthesis of oxalacetate	100	1 of 1
66794	ppGpp biosynthesis	100	4 of 4
66794	folate polyglutamylation	100	1 of 1
66794	suberin monomers biosynthesis	100	2 of 2
66794	adipate degradation	100	2 of 2
66794	UDP-GlcNAc biosynthesis	100	3 of 3
66794	palmitate biosynthesis	100	22 of 22
66794	CDP-diacylglycerol biosynthesis	100	2 of 2
66794	myo-inositol biosynthesis	90	9 of 10
66794	chorismate metabolism	88.89	8 of 9
66794	serine metabolism	88.89	8 of 9
66794	valine metabolism	88.89	8 of 9
66794	molybdenum cofactor biosynthesis	88.89	8 of 9
66794	isoleucine metabolism	87.5	7 of 8
66794	reductive acetyl coenzyme A pathway	85.71	6 of 7
66794	purine metabolism	82.98	78 of 94
66794	pentose phosphate pathway	81.82	9 of 11
66794	metabolism of disaccharids	81.82	9 of 11
66794	peptidoglycan biosynthesis	80	12 of 15
66794	flavin biosynthesis	80	12 of 15
66794	Entner Doudoroff pathway	80	8 of 10
66794	methylglyoxal degradation	80	4 of 5
66794	ethylmalonyl-CoA pathway	80	4 of 5
66794	cellulose degradation	80	4 of 5
66794	pyrimidine metabolism	80	36 of 45
66794	glycogen metabolism	80	4 of 5
66794	factor 420 biosynthesis	80	4 of 5
66794	photosynthesis	78.57	11 of 14
66794	heme metabolism	78.57	11 of 14
66794	NAD metabolism	77.78	14 of 18
66794	d-mannose degradation	77.78	7 of 9
66794	phenylalanine metabolism	76.92	10 of 13
66794	urea cycle	76.92	10 of 13
66794	leucine metabolism	76.92	10 of 13
66794	glycolysis	76.47	13 of 17
66794	dTDPLrhamnose biosynthesis	75	6 of 8
66794	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	75	6 of 8
66794	sulfopterin metabolism	75	3 of 4
66794	glycogen biosynthesis	75	3 of 4
66794	gluconeogenesis	75	6 of 8
66794	alanine metabolism	72.41	21 of 29
66794	glutamate and glutamine metabolism	71.43	20 of 28
66794	non-pathway related	68.42	26 of 38
66794	acetyl CoA biosynthesis	66.67	2 of 3
66794	cyanate degradation	66.67	2 of 3
66794	L-lactaldehyde degradation	66.67	2 of 3
66794	acetoin degradation	66.67	2 of 3
66794	CO2 fixation in Crenarchaeota	66.67	6 of 9
66794	sulfoquinovose degradation	66.67	2 of 3
66794	selenocysteine biosynthesis	66.67	4 of 6
66794	octane oxidation	66.67	2 of 3
66794	histidine metabolism	65.52	19 of 29
66794	lysine metabolism	64.29	27 of 42
66794	glutathione metabolism	64.29	9 of 14
66794	tetrahydrofolate metabolism	64.29	9 of 14
66794	proline metabolism	63.64	7 of 11
66794	d-xylose degradation	63.64	7 of 11
66794	tryptophan metabolism	63.16	24 of 38
66794	degradation of sugar alcohols	62.5	10 of 16
66794	ketogluconate metabolism	62.5	5 of 8
66794	arginine metabolism	62.5	15 of 24
66794	C4 and CAM-carbon fixation	62.5	5 of 8
66794	methionine metabolism	61.54	16 of 26
66794	oxidative phosphorylation	61.54	56 of 91
66794	lipid metabolism	61.29	19 of 31
66794	cysteine metabolism	61.11	11 of 18
66794	lipoate biosynthesis	60	3 of 5
66794	degradation of aromatic, nitrogen containing compounds	58.33	7 of 12
66794	isoprenoid biosynthesis	57.69	15 of 26
66794	propanol degradation	57.14	4 of 7
66794	citric acid cycle	57.14	8 of 14
66794	ubiquinone biosynthesis	57.14	4 of 7
66794	tyrosine metabolism	57.14	8 of 14
66794	nitrate assimilation	55.56	5 of 9
66794	aspartate and asparagine metabolism	55.56	5 of 9
66794	mannosylglycerate biosynthesis	50	1 of 2
66794	CMP-KDO biosynthesis	50	2 of 4
66794	biotin biosynthesis	50	2 of 4
66794	butanoate fermentation	50	2 of 4
66794	ethanol fermentation	50	1 of 2
66794	coenzyme M biosynthesis	50	5 of 10
66794	pantothenate biosynthesis	50	3 of 6
66794	phenylmercury acetate degradation	50	1 of 2
66794	propionate fermentation	50	5 of 10
66794	kanosamine biosynthesis II	50	1 of 2
66794	bile acid biosynthesis, neutral pathway	47.06	8 of 17
66794	sulfate reduction	46.15	6 of 13
66794	vitamin B6 metabolism	45.45	5 of 11
66794	lipid A biosynthesis	44.44	4 of 9
66794	androgen and estrogen metabolism	43.75	7 of 16
66794	degradation of pentoses	42.86	12 of 28
66794	metabolism of amino sugars and derivatives	40	2 of 5
66794	arachidonate biosynthesis	40	2 of 5
66794	glycine metabolism	40	4 of 10
66794	phenol degradation	40	8 of 20
66794	gallate degradation	40	2 of 5
66794	D-cycloserine biosynthesis	40	2 of 5
66794	3-chlorocatechol degradation	40	2 of 5
66794	polyamine pathway	39.13	9 of 23
66794	arachidonic acid metabolism	38.89	7 of 18
66794	vitamin B1 metabolism	38.46	5 of 13
66794	phosphatidylethanolamine bioynthesis	38.46	5 of 13
66794	carnitine metabolism	37.5	3 of 8
66794	(5R)-carbapenem carboxylate biosynthesis	33.33	1 of 3
66794	IAA biosynthesis	33.33	1 of 3
66794	enterobactin biosynthesis	33.33	1 of 3
66794	sphingosine metabolism	33.33	2 of 6
66794	3-phenylpropionate degradation	33.33	5 of 15
66794	ascorbate metabolism	31.82	7 of 22
66794	phenylpropanoid biosynthesis	30.77	4 of 13
66794	benzoyl-CoA degradation	28.57	2 of 7
66794	degradation of sugar acids	28	7 of 25
66794	degradation of hexoses	27.78	5 of 18
66794	cholesterol biosynthesis	27.27	3 of 11
66794	dolichyl-diphosphooligosaccharide biosynthesis	27.27	3 of 11
66794	vitamin B12 metabolism	26.47	9 of 34
66794	alginate biosynthesis	25	1 of 4
66794	toluene degradation	25	1 of 4
66794	cyclohexanol degradation	25	1 of 4
66794	catecholamine biosynthesis	25	1 of 4
66794	lactate fermentation	25	1 of 4
66794	carotenoid biosynthesis	22.73	5 of 22
66794	4-hydroxymandelate degradation	22.22	2 of 9
66794	chlorophyll metabolism	22.22	4 of 18

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Environmental	#Terrestrial	#Soil

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent	Latitude	Longitude	Sampling date
16285	Soil	Dokdo (37° 14' 12'' N 131° 52' 07'' E)	Republic of Korea	KOR	Asia	37.2367	131.869 37.2367/131.869
60211	Soil	Dokdo	Republic of Korea	KOR	Asia			2004-05-01
67770	Soil
67771	From soil	Dokdo	Republic of Korea	KOR	Asia

Taxonmaps

69479

Global distribution of 16S sequence EF555583 (>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
16285	1	Risk group (German classification) According to TRBA 466

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
66792	IMG-taxon 2634166372 annotated assembly for Pedococcus dokdonensis DSM 22329	chromosome	GCA_900104525	443156.3	2634166372	443156	85.23

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
16285	Phycicoccus dokdonensis strain DS-8 16S ribosomal RNA gene, partial sequence	EF555583	1481		443156

GC content

@ref	GC-content (mol%)	Method
16285	70.7	high performance liquid chromatography (HPLC)
32302	70.7

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Phycicoccus dokdonensis DSM 22329
IMG: 2634166372

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	no	72.90	no
125439	motility	BacteriaNetⓘ	no	69.80	no
125439	gram_stain	BacteriaNetⓘ	positive	98.90	no
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	98.30	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Phycicoccus dokdonensis strain DSM 22329
PATRIC: 443156.3

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	yes	91.37	yes
125438	anaerobic	anaerobicⓘ	no	98.14	yes
125438	spore-forming	spore-formingⓘ	no	66.38	yes
125438	aerobic	aerobicⓘ	yes	92.97	no
125438	thermophilic	thermophileⓘ	no	96.50	yes
125438	flagellated	motile2+ⓘ	no	91.00	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
Phylogeny	Phycicoccus aerophilus sp. nov., isolated from air.	Weon HY, Yoo SH, Kim BY, Schumann P, Kroppenstedt RM, Hong SK, Kwon SW	Int J Syst Evol Microbiol	10.1099/ijs.0.65202-0	2008
Phylogeny	Phycicoccus dokdonensis sp. nov., isolated from soil.	Yoon JH, Lee SY, Kang SJ, Oh TK	Int J Syst Evol Microbiol	10.1099/ijs.0.65284-0	2008

References

#16285	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 22329
#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 )
#28541	IJSEM 597 2008 ( DOI 10.1099/ijs.0.65284-0 , PubMed 18319462 )
#32302	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 #28541
#60211	Culture Collection University of Gothenburg (CCUG) ; Curators of the CCUG; CCUG 54521
#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) .
#66794	Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg: BRENDA, the ELIXIR core data resource in 2021: new developments and updates. Nucleic Acids Res. 49: D498 - D508 2020 ( DOI 10.1093/nar/gkaa1025 , PubMed 33211880 )
#67770	Japan Collection of Microorganism (JCM) ; Curators of the JCM;
#67771	Korean Collection for Type Cultures (KCTC) ; Curators of the KCTC;
#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 .
#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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Pedococcus dokdonensis (DSM 22329, CCUG 54521, KCTC 19248)

Name and taxonomic classification

Morphology

Cell morphology

Colony morphology

Pigmentation

Culture and growth conditions

Culture medium

Culture temp

Culture pH

Physiology and metabolism

Oxygen tolerance

Spore formation

Halophily

Murein

Observation

Metabolite utilization

Enzymes

Pathway annotation

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_900104525

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

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