Nocardioides pocheonensis (DSM 22773, KACC 14275, Gsoil 818)

Name: Nocardioides pocheonensis (DSM 22773, KACC 14275, Gsoil 818)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 132515

Type strain

Culture col. no. DSM 22773 KACC 14275 Gsoil 818 JCM 32749

NCBI tax ID(s) 661485

Special Collections DSMZ JCM Literature strains

Links

Nocardioides pocheonensis DSM 22773 is an aerobe, Gram-positive, rod-shaped prokaryote that forms circular colonies and was isolated from soil from a ginseng field.

Gram-positive rod-shaped colony-forming aerobe genome sequence 16S sequence

Name and taxonomic classification

SI-ID 406886

JCM 32749,DSM 22773

@ref 20215

Last LPSN update 2025-12-16 10:01:32

Domain Bacillati

Phylum Actinomycetota

Class Actinomycetes

Order Propionibacteriales

Family Nocardioidaceae

Genus Nocardioides

Species Nocardioides pocheonensis

Full scientific name Nocardioides pocheonensis (Lee et al. 2016) Wang et al. 2023

Synonyms (1)

Marmoricola pocheonensis

Morphology

Cell morphology

@ref	Gram stain	Cell length	Cell width	Cell shape	Motility
43654	positive	1-2 µm	0.3-0.4 µm	rod-shaped

Colony morphology

@ref	Colony size	Colony color	Colony shape	Incubation period	Medium used
43654	0.5-1 mm	Ivory	circular	3 days	R2A agar plates

Culture and growth conditions

Culture medium

@ref	Name	Growth
43654	Reasoner's 2A agar (R2A)
24304	R2A MEDIUM (DSMZ Medium 830)

Culture temp

@ref	Growth	Type	Temperature (°C)	Range
24304	positive	growth	28	mesophilic
43654	positive	growth	10-40
43654	positive	optimum	30	mesophilic
67770	positive	growth	28	mesophilic

Culture pH

@ref	Ability	Type	PH
43654	positive	optimum	7
43654	positive	growth	6-8

Physiology and metabolism

Oxygen tolerance

43654

Oxygen toleranceaerobe

Spore formation

43654

Spore formationno

Halophily

@ref	Salt	Growth	Tested relation	Concentration
43654	NaCl	positive	growth	0-2 %(w/v)
43654	NaCl	positive	optimum	0 %(w/v)

Observation

67770

Observationquinones: MK-8(H₄)

Metabolite utilization

@ref	Metabolite	Utilization activity	Kind of utilization tested
43654	2-oxogluconate	-	assimilation
43654	3-hydroxybenzoate	-	assimilation
43654	3-hydroxybutyrate	+	assimilation
43654	4-hydroxybenzoate	+	assimilation
43654	5-dehydro-D-gluconate	-	assimilation
43654	acetate	-	assimilation
43654	adipate	+	assimilation
43654	cellulose	-	hydrolysis
43654	citrate	-	assimilation
43654	D-glucose	+	assimilation
43654	D-mannitol	-	assimilation
43654	D-mannose	-	assimilation
43654	D-ribose	-	assimilation
43654	D-sorbitol	-	assimilation
43654	decanoate	-	assimilation
43654	dna	-	hydrolysis
43654	esculin	+	hydrolysis
43654	gelatin	-	hydrolysis
43654	gluconate	+	assimilation
43654	glucose	-	fermentation
43654	glycogen	+	assimilation
43654	itaconate	-	assimilation
43654	L-alanine 4-nitroanilide	-	assimilation
43654	L-arabinose	+	assimilation
43654	L-fucose	-	assimilation
43654	L-histidine	+	assimilation
43654	L-proline	+	assimilation
43654	L-rhamnose	-	assimilation
43654	L-serine	-	assimilation
43654	lactate	-	assimilation
43654	malate	-	assimilation
43654	malonate	-	assimilation
43654	maltose	-	assimilation
43654	melibiose	-	assimilation
43654	myo-inositol	+	assimilation
43654	N-acetylglucosamine	+	assimilation
43654	nitrate	+	reduction
43654	phenylacetate	-	assimilation
43654	propionate	-	assimilation
43654	salicin	-	assimilation
43654	skimmed milk	+	hydrolysis
43654	starch	-	hydrolysis
43654	suberic acid	-	assimilation
43654	sucrose	-	assimilation
43654	valerate	+	assimilation

Metabolite production

@ref	Chebi-ID	Metabolite	Production
43654	35581 ChEBI	indole

Enzymes

@ref	Value	Activity	Ec
43654	acid phosphatase	+	3.1.3.2
43654	alkaline phosphatase	-	3.1.3.1
43654	alpha-chymotrypsin	-	3.4.21.1
43654	alpha-fucosidase	-	3.2.1.51
43654	alpha-galactosidase	-	3.2.1.22
43654	alpha-glucosidase	+	3.2.1.20
43654	alpha-mannosidase	-	3.2.1.24
43654	arginine dihydrolase	-	3.5.3.6
43654	beta-galactosidase	+	3.2.1.23
43654	beta-glucosidase	+	3.2.1.21
43654	beta-glucuronidase	-	3.2.1.31
43654	catalase	+	1.11.1.6
43654	cystine arylamidase	-	3.4.11.3
43654	cytochrome oxidase	-	1.9.3.1
43654	esterase (C 4)	+
43654	esterase Lipase (C 8)	+
43654	leucine arylamidase	-	3.4.11.1
43654	lipase (C 14)	-
43654	N-acetyl-beta-glucosaminidase	-	3.2.1.52
43654	naphthol-AS-BI-phosphohydrolase	+
43654	trypsin	-	3.4.21.4
43654	urease	-	3.5.1.5
43654	valine arylamidase	-

Pathway annotation

Computationally determined by

@ref	pathway	enzyme coverage	annotated reactions
66794	anapleurotic synthesis of oxalacetate	100	1 of 1
66794	octane oxidation	100	3 of 3
66794	enterobactin biosynthesis	100	3 of 3
66794	acetate fermentation	100	4 of 4
66794	palmitate biosynthesis	100	22 of 22
66794	ppGpp biosynthesis	100	4 of 4
66794	cis-vaccenate biosynthesis	100	2 of 2
66794	valine metabolism	100	9 of 9
66794	methylglyoxal degradation	100	5 of 5
66794	starch degradation	100	10 of 10
66794	threonine metabolism	100	10 of 10
66794	Entner Doudoroff pathway	100	10 of 10
66794	taurine degradation	100	1 of 1
66794	suberin monomers biosynthesis	100	2 of 2
66794	UDP-GlcNAc biosynthesis	100	3 of 3
66794	CDP-diacylglycerol biosynthesis	100	2 of 2
66794	sulfopterin metabolism	100	4 of 4
66794	coenzyme A metabolism	100	4 of 4
66794	formaldehyde oxidation	100	3 of 3
66794	phenylacetate degradation (aerobic)	100	5 of 5
66794	kanosamine biosynthesis II	100	2 of 2
66794	biotin biosynthesis	100	4 of 4
66794	folate polyglutamylation	100	1 of 1
66794	cellulose degradation	100	5 of 5
66794	adipate degradation	100	2 of 2
66794	pentose phosphate pathway	90.91	10 of 11
66794	alanine metabolism	89.66	26 of 29
66794	serine metabolism	88.89	8 of 9
66794	CO2 fixation in Crenarchaeota	88.89	8 of 9
66794	4-hydroxymandelate degradation	88.89	8 of 9
66794	gluconeogenesis	87.5	7 of 8
66794	C4 and CAM-carbon fixation	87.5	7 of 8
66794	propanol degradation	85.71	6 of 7
66794	photosynthesis	85.71	12 of 14
66794	reductive acetyl coenzyme A pathway	85.71	6 of 7
66794	phenylalanine metabolism	84.62	11 of 13
66794	leucine metabolism	84.62	11 of 13
66794	NAD metabolism	83.33	15 of 18
66794	glycolate and glyoxylate degradation	83.33	5 of 6
66794	flavin biosynthesis	80	12 of 15
66794	propionate fermentation	80	8 of 10
66794	glycine betaine biosynthesis	80	4 of 5
66794	ethylmalonyl-CoA pathway	80	4 of 5
66794	glycogen metabolism	80	4 of 5
66794	factor 420 biosynthesis	80	4 of 5
66794	peptidoglycan biosynthesis	80	12 of 15
66794	vitamin K metabolism	80	4 of 5
66794	gallate degradation	80	4 of 5
66794	vitamin B12 metabolism	79.41	27 of 34
66794	glutamate and glutamine metabolism	78.57	22 of 28
66794	citric acid cycle	78.57	11 of 14
66794	heme metabolism	78.57	11 of 14
66794	chorismate metabolism	77.78	7 of 9
66794	d-mannose degradation	77.78	7 of 9
66794	lipid metabolism	77.42	24 of 31
66794	urea cycle	76.92	10 of 13
66794	purine metabolism	75.53	71 of 94
66794	butanoate fermentation	75	3 of 4
66794	isoleucine metabolism	75	6 of 8
66794	glycogen biosynthesis	75	3 of 4
66794	dTDPLrhamnose biosynthesis	75	6 of 8
66794	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	75	6 of 8
66794	ketogluconate metabolism	75	6 of 8
66794	degradation of aromatic, nitrogen containing compounds	75	9 of 12
66794	metabolism of disaccharids	72.73	8 of 11
66794	proline metabolism	72.73	8 of 11
66794	glutathione metabolism	71.43	10 of 14
66794	cardiolipin biosynthesis	71.43	5 of 7
66794	lysine metabolism	71.43	30 of 42
66794	tetrahydrofolate metabolism	71.43	10 of 14
66794	glycolysis	70.59	12 of 17
66794	myo-inositol biosynthesis	70	7 of 10
66794	vitamin B1 metabolism	69.23	9 of 13
66794	pyrimidine metabolism	68.89	31 of 45
66794	non-pathway related	68.42	26 of 38
66794	tryptophan metabolism	68.42	26 of 38
66794	aspartate and asparagine metabolism	66.67	6 of 9
66794	molybdenum cofactor biosynthesis	66.67	6 of 9
66794	L-lactaldehyde degradation	66.67	2 of 3
66794	acetoin degradation	66.67	2 of 3
66794	cyanate degradation	66.67	2 of 3
66794	IAA biosynthesis	66.67	2 of 3
66794	3-phenylpropionate degradation	66.67	10 of 15
66794	cysteine metabolism	66.67	12 of 18
66794	degradation of pentoses	64.29	18 of 28
66794	d-xylose degradation	63.64	7 of 11
66794	oxidative phosphorylation	62.64	57 of 91
66794	degradation of sugar alcohols	62.5	10 of 16
66794	androgen and estrogen metabolism	62.5	10 of 16
66794	histidine metabolism	62.07	18 of 29
66794	phosphatidylethanolamine bioynthesis	61.54	8 of 13
66794	arachidonate biosynthesis	60	3 of 5
66794	lipoate biosynthesis	60	3 of 5
66794	3-chlorocatechol degradation	60	3 of 5
66794	degradation of sugar acids	60	15 of 25
66794	isoprenoid biosynthesis	57.69	15 of 26
66794	ubiquinone biosynthesis	57.14	4 of 7
66794	tyrosine metabolism	57.14	8 of 14
66794	polyamine pathway	56.52	13 of 23
66794	phenol degradation	55	11 of 20
66794	arginine metabolism	54.17	13 of 24
66794	sulfate reduction	53.85	7 of 13
66794	lactate fermentation	50	2 of 4
66794	methionine metabolism	50	13 of 26
66794	mannosylglycerate biosynthesis	50	1 of 2
66794	cyclohexanol degradation	50	2 of 4
66794	aminopropanol phosphate biosynthesis	50	1 of 2
66794	toluene degradation	50	2 of 4
66794	ethanol fermentation	50	1 of 2
66794	glycine metabolism	50	5 of 10
66794	ribulose monophosphate pathway	50	1 of 2
66794	carnitine metabolism	50	4 of 8
66794	CMP-KDO biosynthesis	50	2 of 4
66794	coenzyme M biosynthesis	50	5 of 10
66794	phenylmercury acetate degradation	50	1 of 2
66794	bile acid biosynthesis, neutral pathway	47.06	8 of 17
66794	vitamin B6 metabolism	45.45	5 of 11
66794	cholesterol biosynthesis	45.45	5 of 11
66794	ascorbate metabolism	45.45	10 of 22
66794	nitrate assimilation	44.44	4 of 9
66794	degradation of hexoses	44.44	8 of 18
66794	carotenoid biosynthesis	40.91	9 of 22
66794	4-hydroxyphenylacetate degradation	40	4 of 10
66794	O-antigen biosynthesis	40	2 of 5
66794	hydrogen production	40	2 of 5
66794	methane metabolism	33.33	1 of 3
66794	chlorophyll metabolism	33.33	6 of 18
66794	acetyl CoA biosynthesis	33.33	1 of 3
66794	sphingosine metabolism	33.33	2 of 6
66794	(5R)-carbapenem carboxylate biosynthesis	33.33	1 of 3
66794	pantothenate biosynthesis	33.33	2 of 6
66794	lipid A biosynthesis	33.33	3 of 9
66794	selenocysteine biosynthesis	33.33	2 of 6
66794	benzoyl-CoA degradation	28.57	2 of 7
66794	aclacinomycin biosynthesis	28.57	2 of 7
66794	arachidonic acid metabolism	27.78	5 of 18
66794	dolichyl-diphosphooligosaccharide biosynthesis	27.27	3 of 11
66794	alginate biosynthesis	25	1 of 4
66794	vitamin E metabolism	25	1 of 4

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
24304	soil from a ginseng field	Pocheon Province	Republic of Korea	KOR	Asia
43654	Soil of a ginseng field	Pocheon Province	Republic of Korea	KOR	Asia
67770	Ginseng field in Pocheon Province		Republic of Korea	KOR	Asia

Taxonmaps

69479

Global distribution of 16S sequence GQ339906 (>99% sequence identity) for Marmoricola pocheonensis from Microbeatlas

Aquatic Samples	8
Soil Samples	226
Animal Samples	22
Plant Samples	20
Total Samples	276

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
24304	1	Risk group (German classification)

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
67770	ASM372553v1 assembly for Nocardioides pocheonensis Gsoil 818	scaffold	GCA_003725535	661485.3	2862970826	661485	53.27

Genome browser: GCA_003725535

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
24304	Nocardioides pocheonensis strain Gsoil 818 16S ribosomal RNA gene, partial sequence	GQ339906	1457		661485

GC content

@ref	GC-content (mol%)	Method
43654	70	high performance liquid chromatography (HPLC)
24304	70.0	high performance liquid chromatography (HPLC)

Genome-based predictions

Predictions

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Marmoricola pocheonensis Gsoil 818
NCBI: GCA_003725535.1

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	yes	89.81	yes
125438	anaerobic	anaerobicⓘ	no	95.56	yes
125438	aerobic	aerobicⓘ	yes	88.35	yes
125438	spore-forming	spore-formingⓘ	no	60.10	yes
125438	thermophilic	thermophileⓘ	no	95.49	no
125438	flagellated	motile2+ⓘ	no	58.50	no

Literature

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Agromyces silvae sp. nov., Rathayibacter soli sp. nov., and Nocardioides terrisoli sp. nov., Isolated from Soil.	Lee H, Chaudhary DK, Kim DU.	J Microbiol Biotechnol	10.4014/jmb.2404.04007	2024
Phylogeny	Marmoricola caldifontis sp. nov., a novel actinobacterium isolated from a hot spring.	Habib N, Khan IU, Xiao M, Li S, Saqib M, Xian WD, Butt S, Li WJ	Int J Syst Evol Microbiol	10.1099/ijsem.0.004016	2020
Phylogeny	Marmoricola mangrovicus sp. nov., an endophytic actinobacterium isolated from Kandelia candel.	Li FN, Jiang ZK, Liu SW, Tuo L, Lee SM, Sun CH	Int J Syst Evol Microbiol	10.1099/ijsem.0.003326	2019
Phylogeny	Marmoricola ginsengisoli sp. nov. and Marmoricola pocheonensis sp. nov. isolated from a ginseng-cultivating field.	Lee HY, Liu Q, Kang MS, Kim SK, Lee SY, Im WT	Int J Syst Evol Microbiol	10.1099/ijsem.0.000977	2016

References

#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 )
#24304	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 22773
#43654	Hye-Yeon Lee, Qingmei Liu, Myung-Suk Kang, Soo-Ki Kim, Soon-Youl Lee, Wan-Taek Im: Marmoricola ginsengisoli sp. nov. and Marmoricola pocheonensis sp. nov. isolated from a ginseng-cultivating field. IJSEM 66: 1996 - 2001 2016 ( DOI 10.1099/ijsem.0.000977 , PubMed 26883120 )
#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;
#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 )
#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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Nocardioides pocheonensis (DSM 22773, KACC 14275, Gsoil 818)

Name and taxonomic classification

Morphology

Cell morphology

Colony morphology

Culture and growth conditions

Culture medium

Culture temp

Culture pH

Physiology and metabolism

Oxygen tolerance

Spore formation

Halophily

Observation

Metabolite utilization

Metabolite production

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_003725535

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

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