Nocardioides baekrokdamisoli (DSM 100725, KCTC 39748, NRRL B-65313)

Name: Nocardioides baekrokdamisoli (DSM 100725, KCTC 39748, NRRL B-65313)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 132635

Type strain

Strain Designation B2-12

Culture col. no. DSM 100725 KCTC 39748 NRRL B-65313 B2-12

NCBI tax ID(s) 1804624

Special Collections DSMZ KCTC Literature strains

History DSMZ <- J. S. Lee, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Republik of Korea; B2-12 KCTC <- Jung-Sook Lee, KRIBB

Links

Nocardioides baekrokdamisoli B2-12 is an aerobe, Gram-positive, coccus-shaped bacterium that forms circular colonies and was isolated from sediment soil of a crater lake.

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

Name and taxonomic classification

SI-ID 405510

KCTC 39748,DSM 100725

@ref 20215

Last LPSN update 2026-05-29 08:37:54

Domain Bacteria

Phylum Actinomycetota

Class Actinomycetes

Order Propionibacteriales

Family Nocardioidaceae

Genus Nocardioides

Species Nocardioides baekrokdamisoli

Full scientific name Nocardioides baekrokdamisoli Lee et al. 2016

Morphology

Cell morphology

@ref	Gram stain	Cell length	Cell width	Cell shape	Confidence
24903	positive	0.5-0.6 µm	0.4-0.5 µm	coccus-shaped
24903				rod-shaped
125438					90.9

Colony morphology

@ref	Colony color	Colony shape	Medium used
24903	creamy white	circular	R2A agar (Reasoner's 2A agar)

Culture and growth conditions

Culture medium

@ref	Name	Medium link	Composition
24424	1/10 R2A MEDIUM (DSMZ Medium 1578)	Medium recipe at MediaDive	Name: 1/10 R2A MEDIUM (DSMZ Medium 1578) Composition: Agar 15.0 g/l Casamino acids 0.05 g/l Starch 0.05 g/l Glucose 0.05 g/l Proteose peptone 0.05 g/l Yeast extract 0.05 g/l K2HPO4 0.03 g/l Na-pyruvate 0.03 g/l MgSO4 x 7 H2O 0.005 g/l Distilled water
24903	Reasoner's 2A agar (R2A)
24424	HETEROTROPHIC MEDIUM H3P (DSMZ Medium 428)	Medium recipe at MediaDive	Name: HETEROTROPHIC MEDIUM H3P (DSMZ Medium 428) Composition: Agar 19.802 g/l Na2HPO4 x 2 H2O 2.87129 g/l KH2PO4 2.27723 g/l D-Glucose 1.9802 g/l Na-lactate 0.990099 g/l Na-pyruvate 0.990099 g/l D-Mannitol 0.990099 g/l DL-Malate 0.990098 g/l Na-acetate 0.990098 g/l Yeast extract 0.990098 g/l NH4Cl 0.990098 g/l Disodium succinate 0.990098 g/l MgSO4 x 7 H2O 0.495049 g/l Ferric ammonium citrate 0.049505 g/l CaCl2 x 2 H2O 0.00990098 g/l NaVO3 x H2O 0.00495049 g/l Thiamine-HCl x 2 H2O 0.00247525 g/l Nicotinic acid 0.00247525 g/l Pyridoxine hydrochloride 0.00247525 g/l Calcium pantothenate 0.00247525 g/l H3BO3 0.00148515 g/l CoCl2 x 6 H2O 0.000990099 g/l Riboflavin 0.00049505 g/l ZnSO4 x 7 H2O 0.00049505 g/l MnCl2 x 4 H2O 0.000148515 g/l Na2MoO4 x 2 H2O 0.000148515 g/l NiCl2 x 6 H2O 9.90099e-05 g/l CuCl2 x 2 H2O 4.95049e-05 g/l Vitamin B12 4.95049e-05 g/l Folic acid 9.90099e-06 g/l Biotin 4.9505e-06 g/l Distilled water

Culture temp

@ref	Growth	Type	Temperature (°C)
24424	positive	growth	25
24903	positive	growth	15
24903	positive	growth	15.0-30.0
24903	positive	optimum	25
67771	positive	growth	25

Culture pH

@ref	Ability	Type	PH
24903	positive	optimum	7
24903	positive	growth	6.0-8.0

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
24903	aerobe
67771	aerobe
125439	obligate aerobe	99.657

Spore formation

@ref	Spore formation	Confidence
24903
125439		95.39

Halophily

@ref	Salt	Growth	Tested relation	Concentration
24903	NaCl		optimum	0 %
24903	NaCl	positive	growth	<1.0 %(w/v)

Murein

@ref	Murein short key	Type
24903	A41.01	A3gamma LL-Dpm-Gly

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
24903	16808 ChEBI	2-dehydro-D-gluconate	-	builds acid from
24903	58143 ChEBI	5-dehydro-D-gluconate	-	builds acid from
24903	17128 ChEBI	adipate	-	assimilation
24903	27613 ChEBI	amygdalin	+	builds acid from
24903	22599 ChEBI	arabinose	-	assimilation
24903	18305 ChEBI	arbutin	+	builds acid from
24903	17057 ChEBI	cellobiose	+	builds acid from
24903	17108 ChEBI	D-arabinose	-	builds acid from
24903	18333 ChEBI	D-arabitol	-	builds acid from
24903	15824 ChEBI	D-fructose	+	builds acid from
24903	28847 ChEBI	D-fucose	-	builds acid from
24903	12936 ChEBI	D-galactose	+	builds acid from
24903	17634 ChEBI	D-glucose	-	assimilation
24903	17634 ChEBI	D-glucose	+	builds acid from
24903	62318 ChEBI	D-lyxose	-	builds acid from
24903	16899 ChEBI	D-mannitol	+	builds acid from
24903	16024 ChEBI	D-mannose	-	assimilation
24903	16024 ChEBI	D-mannose	+	builds acid from
24903	16988 ChEBI	D-ribose	+	builds acid from
24903	17924 ChEBI	D-sorbitol	-	builds acid from
24903	16443 ChEBI	D-tagatose	+	builds acid from
24903	16551 ChEBI	D-trehalose	+	builds acid from
24903	65327 ChEBI	D-xylose	-	builds acid from
24903	27689 ChEBI	decanoate	-	assimilation
24903	17113 ChEBI	erythritol	-	builds acid from
24903	4853 ChEBI	esculin	+	hydrolysis
24903		esculin ferric citrate	+	builds acid from
24903	16813 ChEBI	galactitol	-	builds acid from
24903	5291 ChEBI	gelatin	-	hydrolysis
24903	28066 ChEBI	gentiobiose	+	builds acid from
24903	24265 ChEBI	gluconate	-	builds acid from
24903	17234 ChEBI	glucose	-	fermentation
24903	17754 ChEBI	glycerol	+	builds acid from
24903	28087 ChEBI	glycogen	+	builds acid from
24903	15443 ChEBI	inulin	-	builds acid from
24903	30849 ChEBI	L-arabinose	+	builds acid from
24903	18403 ChEBI	L-arabitol	-	builds acid from
24903	18287 ChEBI	L-fucose	-	builds acid from
24903	62345 ChEBI	L-rhamnose	-	builds acid from
24903	17266 ChEBI	L-sorbose	-	builds acid from
24903	65328 ChEBI	L-xylose	+	builds acid from
24903	17716 ChEBI	lactose	-	builds acid from
24903	25115 ChEBI	malate	-	assimilation
24903	17306 ChEBI	maltose	-	assimilation
24903	17306 ChEBI	maltose	+	builds acid from
24903	29864 ChEBI	mannitol	-	assimilation
24903	6731 ChEBI	melezitose	-	builds acid from
24903	28053 ChEBI	melibiose	-	builds acid from
24903	320061 ChEBI	methyl alpha-D-glucopyranoside	-	builds acid from
24903	43943 ChEBI	methyl alpha-D-mannoside	-	builds acid from
24903	74863 ChEBI	methyl beta-D-xylopyranoside	-	builds acid from
24903	17268 ChEBI	myo-inositol	-	builds acid from
24903	506227 ChEBI	N-acetylglucosamine	-	assimilation
24903	506227 ChEBI	N-acetylglucosamine	+	builds acid from
24903	17632 ChEBI	nitrate	-	reduction
24903	18401 ChEBI	phenylacetate	-	assimilation
24903	32032 ChEBI	potassium gluconate	-	assimilation
24903	16634 ChEBI	raffinose	-	builds acid from
24903	15963 ChEBI	ribitol	-	builds acid from
24903	17814 ChEBI	salicin	+	builds acid from
24903	53258 ChEBI	sodium citrate	-	assimilation
24903	28017 ChEBI	starch	+	builds acid from
24903	17992 ChEBI	sucrose	+	builds acid from
24903	32528 ChEBI	turanose	-	builds acid from
24903	17151 ChEBI	xylitol	-	builds acid from

Metabolite production

@ref	Chebi-ID	Metabolite	Production
24903	35581 ChEBI	indole

Enzymes

@ref	Value	Activity	Ec
24903	acid phosphatase	+	3.1.3.2
24903	alkaline phosphatase	-	3.1.3.1
24903	alpha-chymotrypsin	-	3.4.21.1
24903	alpha-fucosidase	-	3.2.1.51
24903	alpha-galactosidase	-	3.2.1.22
24903	alpha-glucosidase	-	3.2.1.20
24903	alpha-mannosidase	-	3.2.1.24
24903	arginine dihydrolase	-	3.5.3.6
24903	beta-galactosidase	-	3.2.1.23
24903	beta-glucosidase	-	3.2.1.21
24903	beta-glucuronidase	-	3.2.1.31
24903	catalase	-	1.11.1.6
24903	cystine arylamidase	-	3.4.11.3
24903	cytochrome oxidase	-	1.9.3.1
24903	esterase (C 4)	+
24903	esterase lipase (C 8)	+
24903	leucine arylamidase	+	3.4.11.1
24903	lipase (C 14)	-
24903	N-acetyl-beta-glucosaminidase	-	3.2.1.52
24903	naphthol-AS-BI-phosphohydrolase	+
24903	trypsin	-	3.4.21.4
24903	urease	-	3.5.1.5
24903	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	adipate degradation	100	2 of 2
66794	vitamin K metabolism	100	5 of 5
66794	palmitate biosynthesis	100	22 of 22
66794	biotin biosynthesis	100	4 of 4
66794	formaldehyde oxidation	100	3 of 3
66794	coenzyme A metabolism	100	4 of 4
66794	cis-vaccenate biosynthesis	100	2 of 2
66794	UDP-GlcNAc biosynthesis	100	3 of 3
66794	folate polyglutamylation	100	1 of 1
66794	ppGpp biosynthesis	100	4 of 4
66794	CDP-diacylglycerol biosynthesis	100	2 of 2
66794	teichoic acid biosynthesis	100	1 of 1
66794	methylglyoxal degradation	100	5 of 5
66794	pentose phosphate pathway	90.91	10 of 11
66794	Entner Doudoroff pathway	90	9 of 10
66794	chorismate metabolism	88.89	8 of 9
66794	valine metabolism	88.89	8 of 9
66794	isoleucine metabolism	87.5	7 of 8
66794	peptidoglycan biosynthesis	86.67	13 of 15
66794	reductive acetyl coenzyme A pathway	85.71	6 of 7
66794	phenylalanine metabolism	84.62	11 of 13
66794	vitamin B12 metabolism	82.35	28 of 34
66794	threonine metabolism	80	8 of 10
66794	propionate fermentation	80	8 of 10
66794	factor 420 biosynthesis	80	4 of 5
66794	phenylacetate degradation (aerobic)	80	4 of 5
66794	flavin biosynthesis	80	12 of 15
66794	ethylmalonyl-CoA pathway	80	4 of 5
66794	photosynthesis	78.57	11 of 14
66794	glutamate and glutamine metabolism	78.57	22 of 28
66794	tetrahydrofolate metabolism	78.57	11 of 14
66794	heme metabolism	78.57	11 of 14
66794	CO2 fixation in Crenarchaeota	77.78	7 of 9
66794	NAD metabolism	77.78	14 of 18
66794	serine metabolism	77.78	7 of 9
66794	d-mannose degradation	77.78	7 of 9
66794	molybdenum cofactor biosynthesis	77.78	7 of 9
66794	acetate fermentation	75	3 of 4
66794	arginine metabolism	75	18 of 24
66794	glycogen biosynthesis	75	3 of 4
66794	sulfopterin metabolism	75	3 of 4
66794	gluconeogenesis	75	6 of 8
66794	proline metabolism	72.73	8 of 11
66794	histidine metabolism	72.41	21 of 29
66794	alanine metabolism	72.41	21 of 29
66794	cardiolipin biosynthesis	71.43	5 of 7
66794	propanol degradation	71.43	5 of 7
66794	citric acid cycle	71.43	10 of 14
66794	purine metabolism	71.28	67 of 94
66794	urea cycle	69.23	9 of 13
66794	leucine metabolism	69.23	9 of 13
66794	pyrimidine metabolism	68.89	31 of 45
66794	non-pathway related	68.42	26 of 38
66794	IAA biosynthesis	66.67	2 of 3
66794	L-lactaldehyde degradation	66.67	2 of 3
66794	acetoin degradation	66.67	2 of 3
66794	aspartate and asparagine metabolism	66.67	6 of 9
66794	allantoin degradation	66.67	6 of 9
66794	glycolysis	64.71	11 of 17
66794	d-xylose degradation	63.64	7 of 11
66794	dTDPLrhamnose biosynthesis	62.5	5 of 8
66794	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	62.5	5 of 8
66794	androgen and estrogen metabolism	62.5	10 of 16
66794	methionine metabolism	61.54	16 of 26
66794	lipid metabolism	61.29	19 of 31
66794	cysteine metabolism	61.11	11 of 18
66794	gallate degradation	60	3 of 5
66794	glycogen metabolism	60	3 of 5
66794	cellulose degradation	60	3 of 5
66794	lipoate biosynthesis	60	3 of 5
66794	ubiquinone biosynthesis	57.14	4 of 7
66794	tyrosine metabolism	57.14	8 of 14
66794	degradation of sugar alcohols	56.25	9 of 16
66794	nitrate assimilation	55.56	5 of 9
66794	tryptophan metabolism	55.26	21 of 38
66794	oxidative phosphorylation	54.95	50 of 91
66794	metabolism of disaccharids	54.55	6 of 11
66794	isoprenoid biosynthesis	53.85	14 of 26
66794	lysine metabolism	52.38	22 of 42
66794	suberin monomers biosynthesis	50	1 of 2
66794	pantothenate biosynthesis	50	3 of 6
66794	cyclohexanol degradation	50	2 of 4
66794	toluene degradation	50	2 of 4
66794	ribulose monophosphate pathway	50	1 of 2
66794	C4 and CAM-carbon fixation	50	4 of 8
66794	butanoate fermentation	50	2 of 4
66794	ethanol fermentation	50	1 of 2
66794	ketogluconate metabolism	50	4 of 8
66794	sphingosine metabolism	50	3 of 6
66794	aminopropanol phosphate biosynthesis	50	1 of 2
66794	degradation of aromatic, nitrogen containing compounds	50	6 of 12
66794	glutathione metabolism	50	7 of 14
66794	sulfate reduction	46.15	6 of 13
66794	phenol degradation	45	9 of 20
66794	lipid A biosynthesis	44.44	4 of 9
66794	aclacinomycin biosynthesis	42.86	3 of 7
66794	bile acid biosynthesis, neutral pathway	41.18	7 of 17
66794	glycine metabolism	40	4 of 10
66794	glycine betaine biosynthesis	40	2 of 5
66794	3-phenylpropionate degradation	40	6 of 15
66794	arachidonate biosynthesis	40	2 of 5
66794	4-hydroxyphenylacetate degradation	40	4 of 10
66794	bacilysin biosynthesis	40	2 of 5
66794	vitamin B1 metabolism	38.46	5 of 13
66794	carnitine metabolism	37.5	3 of 8
66794	ascorbate metabolism	36.36	8 of 22
66794	acetyl CoA biosynthesis	33.33	1 of 3
66794	4-hydroxymandelate degradation	33.33	3 of 9
66794	enterobactin biosynthesis	33.33	1 of 3
66794	selenocysteine biosynthesis	33.33	2 of 6
66794	cyanate degradation	33.33	1 of 3
66794	arachidonic acid metabolism	33.33	6 of 18
66794	(5R)-carbapenem carboxylate biosynthesis	33.33	1 of 3
66794	phosphatidylethanolamine bioynthesis	30.77	4 of 13
66794	myo-inositol biosynthesis	30	3 of 10
66794	starch degradation	30	3 of 10
66794	benzoyl-CoA degradation	28.57	2 of 7
66794	degradation of hexoses	27.78	5 of 18
66794	dolichyl-diphosphooligosaccharide biosynthesis	27.27	3 of 11
66794	degradation of pentoses	25	7 of 28
66794	lactate fermentation	25	1 of 4
66794	vitamin E metabolism	25	1 of 4
66794	CMP-KDO biosynthesis	25	1 of 4
66794	catecholamine biosynthesis	25	1 of 4

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Environmental	#Aquatic	#Lake (large)
#Environmental	#Aquatic	#Sediment
#Environmental	#Terrestrial	#Soil

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent	Enrichment culture	Enrichment culture duration	Enrichment culture temperature
24424	sediment soil of a crater lake	Jeju island, Hallasan volcano, Baekrodam lake	Republic of Korea	KOR	Asia
24903						R2A agar (Reasoner's 2A agar) (BD)	28 days	25
67771	From soil	Jeju	Republic of Korea	KOR	Asia

Taxonmaps

69479

Global distribution of 16S sequence LC127008 (>99% sequence identity) for Nocardioides baekrokdamisoli from Microbeatlas

Aquatic Samples	2
Soil Samples	114
Animal Samples	20
Plant Samples	18
Total Samples	154

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
24424	1	Risk group (German classification)

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
66792	ASM394532v1 assembly for Nocardioides baekrokdamisoli KCTC 39748	complete	GCA_003945325	1804624.3	2843215260	1804624	92.17

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
24424	Nocardioides baekrokdamisoli gene for 16S rRNA, partial sequence	LC127008	1437		1804624

GC content

@ref	GC-content (mol%)	Method
24903	67	high performance liquid chromatography (HPLC)
24424	67.0	high performance liquid chromatography (HPLC)

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: ASM394532v1 assembly for Nocardioides baekrokdamisoli KCTC 39748
BV-BRC: 1804624.3

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	99.66	no
125439	motility	BacteriaNetⓘ	yes	41.50	no
125439	gram_stain	BacteriaNetⓘ	positive	77.73	no
125439	spore_formation	BacteriaNetⓘ	no	95.39	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Nocardioides baekrokdamisoli KCTC 39748
NCBI: GCA_003945325.1

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	yes	89.95	no
125438	anaerobic	anaerobicⓘ	no	93.88	no
125438	aerobic	aerobicⓘ	yes	81.32	yes
125438	spore-forming	spore-formingⓘ	no	72.57	yes
125438	thermophilic	thermophileⓘ	no	94.97	yes
125438	flagellated	motile2+ⓘ	no	90.90	yes

Literature

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Nocardioides baekrokdamisoli sp. nov., isolated from soil of a crater lake.	Lee KC, Kim KK, Kim JS, Kim DS, Ko SH, Yang SH, Shin YK, Lee JS	Int J Syst Evol Microbiol	10.1099/ijsem.0.001340	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 )
#24424	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 100725
#24903	K. C. K. Lee, Kwang Kyu,Kim, Jong-Shik,Kim, Dae-Shin,Ko, Suk-Hyung,Yang, Seung-Hoon,Shin, Yong Kook,Lee, Jung-Sook: Nocardioides baekrokdamisoli sp. nov., isolated from soil of a crater lake. IJSEM 66: 4231 - 4235 2016 ( DOI 10.1099/ijsem.0.001340 , PubMed 27470265 )
#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 )
#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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Nocardioides baekrokdamisoli (DSM 100725, KCTC 39748, NRRL B-65313)

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

Murein

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_003945325

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

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