Nocardioides albidus (KCTC 39607, CCTCC AB 2015297, THG-S11.7)

Name: Nocardioides albidus (KCTC 39607, CCTCC AB 2015297, THG-S11.7)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 141143

Type strain

Strain Designation THG-S11.7, THG-S11-7

Culture col. no. KCTC 39607 CCTCC AB 2015297 THG-S11.7 JCM 31749 THG-S11-7

NCBI tax ID(s) 1517589

Special Collections JCM KCTC Literature strains

History JCM <-- CCTCC AB 2015297 <-- T.-H. Yi; Kyung Hee Univ., South Korea; THG-S11.7. KCTC <- Tae-Hoo Yi, Kyung Hee univ.

Links

Nocardioides albidus THG-S11.7 is an aerobe, Gram-positive, coccus-shaped bacterium that forms circular colonies and was isolated from garden soil sample.

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

Name and taxonomic classification

SI-ID 27546

KCTC 39607

@ref 20215

Last LPSN update 2026-05-29 08:39:53

Domain Bacteria

Phylum Actinomycetota

Class Actinomycetes

Order Propionibacteriales

Family Nocardioidaceae

Genus Nocardioides

Species Nocardioides albidus

Full scientific name Nocardioides albidus Singh et al. 2016

Morphology

Cell morphology

@ref	Gram stain	Cell length	Cell width	Cell shape	Confidence
44062	positive	1.0-1.2 µm	1.0-1.2 µm	coccus-shaped
125438	positive				90.558
125439	positive				96.397

Colony morphology

@ref	Colony size	Colony color	Colony shape	Incubation period	Medium used
44062	1.0-3.0 mm	white	circular	3 days	Nutrient agar

Pigmentation

@ref	Production	Name
44062		flexirubin type pigments

Culture and growth conditions

Culture medium

@ref	Name	Growth
44062	Marine agar (MA)
44062	Nutrient agar (NA)
44062	Reasoner's 2A agar (R2A)
44062	LA
44062	MacConkey
44062	Trypticase Soy Agar (TSA)

Culture temp

@ref	Growth	Type	Temperature (°C)
44062	positive	growth	20-35
44062	positive	optimum	28
67770	positive	growth	28
67771	positive	growth	28

Culture pH

@ref	Ability	Type	PH
44062	positive	optimum	7
44062	positive	growth	6.0-7.5

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
44062	aerobe
67771	aerobe
125439	facultative anaerobe	97.208

Halophily

@ref	Salt	Growth	Tested relation	Concentration
44062	NaCl	positive	growth	0.5-3.0 %(w/v)
44062	NaCl	positive	optimum	2 %(w/v)

Observation

67770

Observationquinones: MK-8(H₄)

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
44062	17128 ChEBI	adipate	-	assimilation
44062	85146 ChEBI	carboxymethylcellulose	-	hydrolysis
44062		casein	-	hydrolysis
44062	17029 ChEBI	chitin	-	hydrolysis
44062	16947 ChEBI	citrate	-	assimilation
44062	17634 ChEBI	D-glucose	+	assimilation
44062	16899 ChEBI	D-mannitol	-	assimilation
44062	16024 ChEBI	D-mannose	-	assimilation
44062	27689 ChEBI	decanoate	-	assimilation
44062	16991 ChEBI	dna	-	hydrolysis
44062	4853 ChEBI	esculin	+	fermentation
44062	4853 ChEBI	esculin	+	hydrolysis
44062	5291 ChEBI	gelatin	-	hydrolysis
44062	24265 ChEBI	gluconate	+	assimilation
44062	17234 ChEBI	glucose	-	builds acid from
44062	30849 ChEBI	L-arabinose	-	assimilation
44062	17895 ChEBI	L-tyrosine	-	hydrolysis
44062	25115 ChEBI	malate	-	assimilation
44062	17306 ChEBI	maltose	-	assimilation
44062	506227 ChEBI	N-acetylglucosamine	+	assimilation
44062	17632 ChEBI	nitrate	-	reduction
44062	18401 ChEBI	phenylacetate	-	assimilation
44062	28017 ChEBI	starch	-	hydrolysis
44062	53426 ChEBI	tween 80	+	hydrolysis
44062	16199 ChEBI	urea	-	hydrolysis

Metabolite production

@ref	Chebi-ID	Metabolite	Production
44062	35581 ChEBI	indole

Enzymes

@ref	Value	Activity	Ec
44062	acid phosphatase	+	3.1.3.2
44062	alkaline phosphatase	+	3.1.3.1
44062	alpha-chymotrypsin	-	3.4.21.1
44062	alpha-fucosidase	-	3.2.1.51
44062	alpha-galactosidase	-	3.2.1.22
44062	alpha-glucosidase	+	3.2.1.20
44062	alpha-mannosidase	-	3.2.1.24
44062	arginine dihydrolase	-	3.5.3.6
44062	beta-galactosidase	+	3.2.1.23
44062	beta-glucosidase	+	3.2.1.21
44062	beta-glucuronidase	-	3.2.1.31
44062	catalase	+	1.11.1.6
44062	cystine arylamidase	+	3.4.11.3
44062	cytochrome oxidase	+	1.9.3.1
44062	esterase (C 4)	+
44062	esterase Lipase (C 8)	+
44062	gelatinase	-
44062	leucine arylamidase	+	3.4.11.1
44062	lipase (C 14)	-
44062	N-acetyl-beta-glucosaminidase	-	3.2.1.52
44062	naphthol-AS-BI-phosphohydrolase	-
44062	trypsin	+	3.4.21.4
44062	urease	-	3.5.1.5
44062	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	palmitate biosynthesis	100	22 of 22
66794	ppGpp biosynthesis	100	4 of 4
66794	IAA biosynthesis	100	3 of 3
66794	methylglyoxal degradation	100	5 of 5
66794	resorcinol degradation	100	2 of 2
66794	valine metabolism	100	9 of 9
66794	phenylmercury acetate degradation	100	2 of 2
66794	cis-vaccenate biosynthesis	100	2 of 2
66794	vitamin K metabolism	100	5 of 5
66794	formaldehyde oxidation	100	3 of 3
66794	aerobactin biosynthesis	100	1 of 1
66794	taurine degradation	100	1 of 1
66794	ceramide biosynthesis	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	teichoic acid biosynthesis	100	1 of 1
66794	sulfopterin metabolism	100	4 of 4
66794	coenzyme A metabolism	100	4 of 4
66794	biotin biosynthesis	100	4 of 4
66794	cellulose degradation	100	5 of 5
66794	adipate degradation	100	2 of 2
66794	folate polyglutamylation	100	1 of 1
66794	phenylalanine metabolism	92.31	12 of 13
66794	urea cycle	92.31	12 of 13
66794	degradation of aromatic, nitrogen containing compounds	91.67	11 of 12
66794	threonine metabolism	90	9 of 10
66794	serine metabolism	88.89	8 of 9
66794	molybdenum cofactor biosynthesis	88.89	8 of 9
66794	NAD metabolism	88.89	16 of 18
66794	chorismate metabolism	88.89	8 of 9
66794	propanol degradation	85.71	6 of 7
66794	reductive acetyl coenzyme A pathway	85.71	6 of 7
66794	leucine metabolism	84.62	11 of 13
66794	purine metabolism	84.04	79 of 94
66794	glycolate and glyoxylate degradation	83.33	5 of 6
66794	pentose phosphate pathway	81.82	9 of 11
66794	Entner Doudoroff pathway	80	8 of 10
66794	glycogen metabolism	80	4 of 5
66794	factor 420 biosynthesis	80	4 of 5
66794	phenol degradation	80	16 of 20
66794	3-chlorocatechol degradation	80	4 of 5
66794	phenylacetate degradation (aerobic)	80	4 of 5
66794	flavin biosynthesis	80	12 of 15
66794	peptidoglycan biosynthesis	80	12 of 15
66794	propionate fermentation	80	8 of 10
66794	ethylmalonyl-CoA pathway	80	4 of 5
66794	4-hydroxyphenylacetate degradation	80	8 of 10
66794	tetrahydrofolate metabolism	78.57	11 of 14
66794	photosynthesis	78.57	11 of 14
66794	glutamate and glutamine metabolism	78.57	22 of 28
66794	heme metabolism	78.57	11 of 14
66794	citric acid cycle	78.57	11 of 14
66794	CO2 fixation in Crenarchaeota	77.78	7 of 9
66794	d-mannose degradation	77.78	7 of 9
66794	allantoin degradation	77.78	7 of 9
66794	pyrimidine metabolism	77.78	35 of 45
66794	vitamin B1 metabolism	76.92	10 of 13
66794	tryptophan metabolism	76.32	29 of 38
66794	histidine metabolism	75.86	22 of 29
66794	butanoate fermentation	75	3 of 4
66794	dTDPLrhamnose biosynthesis	75	6 of 8
66794	acetate fermentation	75	3 of 4
66794	isoleucine metabolism	75	6 of 8
66794	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	75	6 of 8
66794	ketogluconate metabolism	75	6 of 8
66794	vitamin B12 metabolism	73.53	25 of 34
66794	alanine metabolism	72.41	21 of 29
66794	cardiolipin biosynthesis	71.43	5 of 7
66794	glutathione metabolism	71.43	10 of 14
66794	arginine metabolism	70.83	17 of 24
66794	glycolysis	70.59	12 of 17
66794	acetoin degradation	66.67	2 of 3
66794	L-lactaldehyde degradation	66.67	2 of 3
66794	methane metabolism	66.67	2 of 3
66794	cysteine metabolism	66.67	12 of 18
66794	methionine metabolism	65.38	17 of 26
66794	lipid metabolism	64.52	20 of 31
66794	proline metabolism	63.64	7 of 11
66794	d-xylose degradation	63.64	7 of 11
66794	non-pathway related	63.16	24 of 38
66794	gluconeogenesis	62.5	5 of 8
66794	androgen and estrogen metabolism	62.5	10 of 16
66794	carnitine metabolism	62.5	5 of 8
66794	C4 and CAM-carbon fixation	62.5	5 of 8
66794	oxidative phosphorylation	61.54	56 of 91
66794	gallate degradation	60	3 of 5
66794	lipoate biosynthesis	60	3 of 5
66794	arachidonate biosynthesis	60	3 of 5
66794	3-phenylpropionate degradation	60	9 of 15
66794	isoprenoid biosynthesis	57.69	15 of 26
66794	tyrosine metabolism	57.14	8 of 14
66794	ubiquinone biosynthesis	57.14	4 of 7
66794	degradation of sugar alcohols	56.25	9 of 16
66794	aspartate and asparagine metabolism	55.56	5 of 9
66794	metabolism of disaccharids	54.55	6 of 11
66794	bile acid biosynthesis, neutral pathway	52.94	9 of 17
66794	pantothenate biosynthesis	50	3 of 6
66794	mannosylglycerate biosynthesis	50	1 of 2
66794	aminopropanol phosphate biosynthesis	50	1 of 2
66794	cyclohexanol degradation	50	2 of 4
66794	toluene degradation	50	2 of 4
66794	glycine metabolism	50	5 of 10
66794	myo-inositol biosynthesis	50	5 of 10
66794	ethanol fermentation	50	1 of 2
66794	vitamin E metabolism	50	2 of 4
66794	CMP-KDO biosynthesis	50	2 of 4
66794	lysine metabolism	47.62	20 of 42
66794	cholesterol biosynthesis	45.45	5 of 11
66794	vitamin B6 metabolism	45.45	5 of 11
66794	4-hydroxymandelate degradation	44.44	4 of 9
66794	lipid A biosynthesis	44.44	4 of 9
66794	nitrate assimilation	44.44	4 of 9
66794	benzoyl-CoA degradation	42.86	3 of 7
66794	ascorbate metabolism	40.91	9 of 22
66794	glycine betaine biosynthesis	40	2 of 5
66794	coenzyme M biosynthesis	40	4 of 10
66794	phosphatidylethanolamine bioynthesis	38.46	5 of 13
66794	degradation of pentoses	35.71	10 of 28
66794	polyamine pathway	34.78	8 of 23
66794	cyanate degradation	33.33	1 of 3
66794	degradation of hexoses	33.33	6 of 18
66794	sulfoquinovose degradation	33.33	1 of 3
66794	1,4-dihydroxy-6-naphthoate biosynthesis	33.33	2 of 6
66794	(5R)-carbapenem carboxylate biosynthesis	33.33	1 of 3
66794	selenocysteine biosynthesis	33.33	2 of 6
66794	sphingosine metabolism	33.33	2 of 6
66794	acetyl CoA biosynthesis	33.33	1 of 3
66794	phenylpropanoid biosynthesis	30.77	4 of 13
66794	sulfate reduction	30.77	4 of 13
66794	arachidonic acid metabolism	27.78	5 of 18
66794	dolichyl-diphosphooligosaccharide biosynthesis	27.27	3 of 11
66794	catecholamine biosynthesis	25	1 of 4
66794	lactate fermentation	25	1 of 4
66794	alginate biosynthesis	25	1 of 4
66794	glycogen biosynthesis	25	1 of 4
66794	degradation of sugar acids	24	6 of 25
66794	carotenoid biosynthesis	22.73	5 of 22
66794	daunorubicin biosynthesis	22.22	2 of 9

Fatty acid profile

Metadata FA analysis

@ref

44062

Fatty acid	Percentage
C16:0 iso	44.4
C15:0 iso	16.6
C16:0	10
C17:0 anteiso	6.7
C14:0 iso	4.8
C17:1ω6c	4.1
C18:1ω9c	3
C18:0 iso	2.9
C17:0 iso	2.4
10-methyl C17:0	1.2
C17:1ω8c	1.1
C10:0	1

Isolation, sampling and environmental information

Isolation source categories

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

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent	Enrichment culture	Enrichment culture duration	Enrichment culture temperature
44062	garden soil sample	Michuhol library garden, Incheon	Republic of Korea	KOR	Asia	NA agar	7 days	28
67770	Garden soil	Incheon	Republic of Korea	KOR	Asia
67771	From garden soil in Incheon		Republic of Korea	KOR	Asia

Taxonmaps

69479

Global distribution of 16S sequence KM073954 (>99% sequence identity) for Nocardioides albidus from Microbeatlas

Aquatic Samples	5
Soil Samples	17
Animal Samples	4
Plant Samples	10
Total Samples	36

Interaction and safety

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
67770	ASM633500v1 assembly for Nocardioides albidus CCTCC AB 2015297	scaffold	GCA_006335005	1517589.3	2902201542	1517589	27

16S sequences

@ref	Description	Accession	Database
44062	Nocardioides albidus 16S ribosomal RNA gene, partial sequence	KM073954

GC content

@ref	GC-content (mol%)	Method
44062	72.2	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: ASM633500v1 assembly for Nocardioides albidus CCTCC AB 2015297
NCBI: GCA_006335005

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	gram_stain	BacteriaNetⓘ	positive	96.40	no
125439	oxygen_tolerance	BacteriaNetⓘ	facultative anaerobe	97.21	no
125439	motility	BacteriaNetⓘ	no	73.36	no
125439	spore_formation	BacteriaNetⓘ	yes	49.64	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Nocardioides albidus strain CCTCC AB 2015297
PATRIC: 1517589.3

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	yes	90.56	no
125438	anaerobic	anaerobicⓘ	no	97.80	yes
125438	spore-forming	spore-formingⓘ	no	63.06	no
125438	aerobic	aerobicⓘ	yes	87.93	yes
125438	thermophilic	thermophileⓘ	no	93.81	yes
125438	flagellated	motile2+ⓘ	no	59.10	no

Literature

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Nocardioides vastitatis sp. nov., isolated from Taklamakan desert soil.	Liu SW, Xue CM, Li FN, Sun CH	Int J Syst Evol Microbiol	10.1099/ijsem.0.003718	2020
Phylogeny	Nocardioides albidus sp. nov., an actinobacterium isolated from garden soil.	Singh H, Du J, Trinh H, Won K, Yang JE, Yin C, Kook M, Yi TH	Int J Syst Evol Microbiol	10.1099/ijsem.0.000730	2015

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 )
#44062	Hina Singh, Juan Du, Huan Trinh, KyungHwa Won, Jung-Eun Yang, ChangShik Yin, MooChang Kook and Tae-Hoo Yi: Nocardioides albidus sp. nov., an actinobacterium isolated from garden soil. IJSEM 66: 371 - 378 2016 ( DOI 10.1099/ijsem.0.000730 , PubMed 26530636 )
#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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Nocardioides albidus (KCTC 39607, CCTCC AB 2015297, THG-S11.7)

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

Halophily

Observation

Metabolite utilization

Metabolite production

Enzymes

Pathway annotation

Fatty acid profile

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Sequence information

Genome sequences

Genome browser: GCA_006335005

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

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