Nocardioides aurantiacus (DSM 12652, JCM 10917, NBRC 105375)

Name: Nocardioides aurantiacus (DSM 12652, JCM 10917, NBRC 105375)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 11084

Type strain

Culture col. no. DSM 12652 JCM 10917 NBRC 105375 BC 361 NCIMB 13748 1 more

NCBI tax ID(s) 86796

Special Collections DSMZ JCM CIP

History DSMZ <- C. Urcì; BC 361 CIP <- 2000, C Urzi, Sci. Fac., Messina, Italy: strain BC 361 JCM <-- DSM 12652 <-- C. Urzì BC361. CIP <- 2000, C. Urzi, Messina Univ., Messina, Italy: strain BC 361

Links

Nocardioides aurantiacus DSM 12652 is an obligate aerobe, Gram-positive, coccus-shaped bacterium that was isolated from marble statue.

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

Name and taxonomic classification

SI-ID 49334

CIP 106770,JCM 10917,DSM 12652,NCIMB 13748

@ref 20215

Last LPSN update 2026-05-29 08:27:29

Domain Bacteria

Phylum Actinomycetota

Class Actinomycetes

Order Propionibacteriales

Family Nocardioidaceae

Genus Nocardioides

Species Nocardioides aurantiacus

Full scientific name Nocardioides aurantiacus (Urzì et al. 2000) Wang et al. 2023

Synonyms (1)

Marmoricola aurantiacus

Morphology

Cell morphology

@ref	Gram stain	Cell shape	Confidence
116563	positive	coccus-shaped
125439	positive		99.488
125439			91.407
125438			91.5
125438	positive		90.188

Culture and growth conditions

Culture medium

@ref	Name	Medium link	Composition
4780	GYM STREPTOMYCES MEDIUM (DSMZ Medium 65)	Medium recipe at MediaDive	Name: GYM STREPTOMYCES MEDIUM (DSMZ Medium 65) Composition: Agar 18.0 g/l Malt extract 10.0 g/l Yeast extract 4.0 g/l Glucose 4.0 g/l CaCO3 2.0 g/l Distilled water
39566	MEDIUM 359 - for Marmoricola genus		Distilled water make up to (1000.000 ml);Sodium chloride (5.000 g);Agar(15.000 g);Glucose (10.000 g);Yeast extract (5.000 g);Malt extract (15.000 g);Starch maize (10.000 g);Calcium carbonate (2.000 g)
4780	TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535)	Medium recipe at MediaDive	Name: TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535) Composition: Trypticase soy broth 30.0 g/l Agar 15.0 g/l Distilled water
116563	CIP Medium 359	Medium recipe at CIP

Culture temp

@ref	Growth	Type	Temperature (°C)
4780	positive	growth	28
39566	positive	growth	25
67770	positive	growth	28
116563	positive	growth	22-30
116563	negative	growth	10
116563	negative	growth	37
116563	negative	growth	41
116563	negative	growth	45

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
116563	obligate aerobe
125438	aerobe	91.118
125439	obligate aerobe	98.194

Halophily

@ref	Salt	Growth	Tested relation	Concentration
116563	NaCl	positive	growth	2-6 %
116563	NaCl		growth	0 %
116563	NaCl		growth	10 %

Murein

@ref	Murein short key	Type
4780	A41.01	A3gamma LL-Dpm-Gly

Observation

67770

Observationquinones: MK-8(H₄)

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
68371	27613 ChEBI	amygdalin	-	builds acid from	from API 50CH acid
68371	17057 ChEBI	cellobiose	+	builds acid from	from API 50CH acid
116563	16947 ChEBI	citrate	-	carbon source
68371	17108 ChEBI	D-arabinose	-	builds acid from	from API 50CH acid
68371	18333 ChEBI	D-arabitol	-	builds acid from	from API 50CH acid
68371	28847 ChEBI	D-fucose	-	builds acid from	from API 50CH acid
68371	17634 ChEBI	D-glucose	+	builds acid from	from API 50CH acid
68371	62318 ChEBI	D-lyxose	-	builds acid from	from API 50CH acid
68371	16899 ChEBI	D-mannitol	-	builds acid from	from API 50CH acid
68371	16988 ChEBI	D-ribose	+	builds acid from	from API 50CH acid
68371	17924 ChEBI	D-sorbitol	-	builds acid from	from API 50CH acid
68371	16443 ChEBI	D-tagatose	-	builds acid from	from API 50CH acid
68371	65327 ChEBI	D-xylose	+	builds acid from	from API 50CH acid
68371	17113 ChEBI	erythritol	-	builds acid from	from API 50CH acid
116563	4853 ChEBI	esculin	+	hydrolysis
68371	4853 ChEBI	esculin	+	builds acid from	from API 50CH acid
68371	16813 ChEBI	galactitol	-	builds acid from	from API 50CH acid
68371	28066 ChEBI	gentiobiose	-	builds acid from	from API 50CH acid
68371	24265 ChEBI	gluconate	-	builds acid from	from API 50CH acid
68371	17754 ChEBI	glycerol	-	builds acid from	from API 50CH acid
68371	28087 ChEBI	glycogen	+	builds acid from	from API 50CH acid
116563	606565 ChEBI	hippurate	+	hydrolysis
68371	15443 ChEBI	inulin	-	builds acid from	from API 50CH acid
68371	30849 ChEBI	L-arabinose	+	builds acid from	from API 50CH acid
68371	18403 ChEBI	L-arabitol	-	builds acid from	from API 50CH acid
68371	18287 ChEBI	L-fucose	-	builds acid from	from API 50CH acid
68371	62345 ChEBI	L-rhamnose	-	builds acid from	from API 50CH acid
68371	17266 ChEBI	L-sorbose	-	builds acid from	from API 50CH acid
68371	65328 ChEBI	L-xylose	-	builds acid from	from API 50CH acid
68371	17306 ChEBI	maltose	+	builds acid from	from API 50CH acid
68371	6731 ChEBI	melezitose	-	builds acid from	from API 50CH acid
68371	28053 ChEBI	melibiose	-	builds acid from	from API 50CH acid
68371	43943 ChEBI	methyl alpha-D-mannoside	-	builds acid from	from API 50CH acid
68371	74863 ChEBI	methyl beta-D-xylopyranoside	-	builds acid from	from API 50CH acid
68371	17268 ChEBI	myo-inositol	-	builds acid from	from API 50CH acid
68371	59640 ChEBI	N-acetylglucosamine	-	builds acid from	from API 50CH acid
116563	17632 ChEBI	nitrate	-	reduction
116563	17632 ChEBI	nitrate	-	respiration
116563	16301 ChEBI	nitrite	-	reduction
68371	0 ChEBI	Potassium 2-ketogluconate	-	builds acid from	from API 50CH acid
68371	0 ChEBI	Potassium 5-ketogluconate	-	builds acid from	from API 50CH acid
68371	16634 ChEBI	raffinose	-	builds acid from	from API 50CH acid
68371	15963 ChEBI	ribitol	-	builds acid from	from API 50CH acid
68371	17814 ChEBI	salicin	+	builds acid from	from API 50CH acid
68371	28017 ChEBI	starch	+	builds acid from	from API 50CH acid
68371	17992 ChEBI	sucrose	+	builds acid from	from API 50CH acid
68371	27082 ChEBI	trehalose	-	builds acid from	from API 50CH acid
68371	32528 ChEBI	turanose	+	builds acid from	from API 50CH acid
68371	17151 ChEBI	xylitol	-	builds acid from	from API 50CH acid

Metabolite production

@ref	Chebi-ID	Metabolite	Production
116563	35581 ChEBI	indole

Metabolite tests

@ref	Chebi-ID	Metabolite	Voges-proskauer-test	Methylred-test
116563	15688 ChEBI	acetoin	-
116563	17234 ChEBI	glucose		-

Enzymes

@ref	Value	Activity	Ec
68382	acid phosphatase	+	3.1.3.2	from API zym
116563	alcohol dehydrogenase	-	1.1.1.1
68382	alkaline phosphatase	+	3.1.3.1	from API zym
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
68382	alpha-mannosidase	-	3.2.1.24	from API zym
116563	amylase	+
68382	beta-galactosidase	-	3.2.1.23	from API zym
116563	beta-galactosidase	+	3.2.1.23
68382	beta-glucosidase	+	3.2.1.21	from API zym
68382	beta-glucuronidase	-	3.2.1.31	from API zym
116563	caseinase	+	3.4.21.50
116563	catalase	+	1.11.1.6
68382	cystine arylamidase	+	3.4.11.3	from API zym
116563	DNase	-
68382	esterase (C 4)	+		from API zym
68382	esterase lipase (C 8)	+		from API zym
116563	gamma-glutamyltransferase	+	2.3.2.2
116563	gelatinase	+/-
68382	leucine arylamidase	+	3.4.11.1	from API zym
68382	lipase (C 14)	-		from API zym
116563	lysine decarboxylase	-	4.1.1.18
68382	N-acetyl-beta-glucosaminidase	-	3.2.1.52	from API zym
68382	naphthol-AS-BI-phosphohydrolase	+		from API zym
116563	ornithine decarboxylase	-	4.1.1.17
116563	oxidase	-
116563	phenylalanine ammonia-lyase	+	4.3.1.24
68382	trypsin	+	3.4.21.4	from API zym
116563	tryptophan deaminase	-
116563	tween esterase	-
116563	urease	-	3.5.1.5
68382	valine arylamidase	+		from API zym

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
116563	-	+	+	+	-	+	+	+	+	-	+	+	-	-	-	+	+	-	-	-

API 50CHac

@ref	ControlQ	GLY	ERY	DARA	LARA	RIB	DXYL	LXYL	ADO	MDX	GAL	GLU	FRU	MNE	SBE	RHA	DUL	INO	MAN	SOR	MDM	MDG	NAG	AMY	ARB	ESC	SAL	CEL	MAL	LAC	MEL	SAC	TRE	INU	MLZ	RAF	AMD	GLYG	XLT	GEN	TUR	LYX	TAG	DFUC	LFUC	DARL	LARL	GNT	2KG	5KG
116563	not determinedn.d.	-	-	-	+	+	+	-	-	-	+/-	+	+/-	+/-	-	-	-	-	-	-	-	+/-	-	-	+/-	+	+	+	+	+/-	-	+	-	-	-	-	+	+	-	-	+	-	-	-	-	-	-	-	-	-

API biotype100

@ref	ControlQ	D-glucose as carbon sourceGLU	D-fructose as carbon sourceFRU	D-galactose as carbon sourceGAL	D-trehalose as carbon sourceTRE	D-mannose as carbon sourceMNE	L-sorbose as carbon sourceSBE	D-melibiose as carbon sourceMEL	sucrose as carbon sourceSAC	D-raffinose as carbon sourceRAF	maltotriose as carbon sourceMTE	maltose as carbon sourceMAL	lactose as carbon sourceLAC	lactulose as carbon sourceLTE	1-O-methyl-beta-galactopyranoside as carbon sourceMbGa	1-O-methyl-alpha-galactopyranoside as carbon sourceMaGa	D-cellobiose as carbon sourceCEL	gentiobiose as carbon sourceGEN	1-O-methyl-beta-D-glucopyranoside as carbon sourceMbGu	esculin as carbon sourceESC	D-ribose as carbon sourceRIB	L-arabinose as carbon sourceARA	D-xylose as carbon sourceXYL	palatinose as carbon sourcePLE	L-rhamnose as carbon sourceRHA	L-fucose as carbon sourceFUC	D-melezitose as carbon sourceMLZ	D-arabitol as carbon sourceDARL	L-arabitol as carbon sourceLARL	xylitol as carbon sourceXLT	dulcitol as carbon sourceDUL	D-tagatose as carbon sourceTAG	glycerol as carbon sourceGLY	myo-inositol as carbon sourceINO	D-mannitol as carbon sourceMAN	maltitol as carbon sourceMTL	D-turanose as carbon sourceTUR	D-sorbitol as carbon sourceSOR	adonitol as carbon sourceADO	hydroxyquinoline-beta-glucuronide as carbon sourceHBG	D-lyxose as carbon sourceLYX	i-erythritol as carbon sourceERY	1-O-methyl-alpha-D-glucoside as carbon sourceMDG	3-O-methyl-D-glucose as carbon source3MDG	D-saccharate as carbon sourceSAT	mucate as carbon sourceMUC	L-tartrate as carbon sourceLTAT	D-tartrate as carbon sourceDTAT	meso-tartrate as carbon sourceMTAT	D-malate as carbon sourceDMLT	L-malate as carbon sourceLMLT	cis-aconitate as carbon sourceCATE	trans-aconitate as carbon sourceTATE	tricarballylate as carbon sourceTTE	citrate as carbon sourceCIT	D-glucuronate as carbon sourceGRT	D-galacturonate as carbon sourceGAT	2-ketogluconate as carbon source2KG	5-ketogluconate as carbon source5KG	tryptophan as carbon sourceTRY	N-acetyl-D-glucosamine as carbon sourceNAG	D-gluconate as carbon sourceGNT	phenylacetate as carbon sourcePAC	protocatechuate as carbon sourcePAT	4-hydroxybenzoate as carbon sourcepOBE	quinate as carbon sourceQAT	gentisate as carbon sourceGTE	3-hydroxybenzoate as carbon sourcemOBE	benzoate as carbon sourceBAT	3-phenylpropionate as carbon sourcePPAT	m-coumarate as carbon sourceCMT	trigonelline as carbon sourceTGE	betaine as carbon sourceBET	putrescine as carbon sourcePCE	4-aminobutyrate as carbon sourceABT	histamine as carbon sourceHIN	DL-lactate as carbon sourceLAT	caprate as carbon sourceCAP	caprylate as carbon sourceCYT	L-histidine as carbon sourceHIS	succinate as carbon sourceSUC	fumarate as carbon sourceFUM	glutarate as carbon sourceGRE	DL-glycerate as carbon sourceGYT	5-aminovalerate as carbon sourceAVT	ethanolamine as carbon sourceETN	tryptamine as carbon sourceTTN	D-glucosamine as carbon sourceGLN	itaconate as carbon sourceITA	3-hydroxybutyrate as carbon source3OBU	L-aspartate as carbon sourceAPT	L-glutamate as carbon sourceGTT	L-proline as carbon sourcePRO	D-alanine as carbon sourceDALA	L-alanine as carbon sourceLALA	L-serine as carbon sourceSER	malonate as carbon sourceMNT	propionate as carbon sourcePROP	L-tyrosine as carbon sourceTYR	2-ketoglutarate as carbon source2KT
116563	not determinedn.d.	+	+	+	+	+	-	-	+	-	+	+	+	+	-	-	+	+	-	+	-	+	+	+	-	-	-	+	-	+	-	-	+	-	+	+	+	+	-	-	-	-	-	-	-	-	-	-	-	-	+	-	-	-	-	-	-	+	-	-	-	+	-	-	+	+	-	-	-	-	-	-	-	-	-	-	+	-	-	-	+	+	-	-	-	-	-	+	-	+	-	-	-	-	-	-	-	-	-	-

Isolation, sampling and environmental information

Isolation source categories

Cat1
#Engineered

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent	Isolation date
4780	marble statue	München	Germany	DEU	Europe
67770	Marble statue (Wagmüller's monument) in the old Nordfriedhof cemetery	Munich	Germany	DEU	Europe
116563	Marble statue	München	Germany	DEU	Europe	1991

Taxonmaps

69479

Global distribution of 16S sequence Y18629 (>99% sequence identity) for Marmoricola aurantiacus from Microbeatlas

Aquatic Samples	77
Soil Samples	215
Animal Samples	557
Plant Samples	97
Total Samples	946

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
4780	1	Risk group (German classification) According to TRBA 466
116563	1	Risk group (French classification) According to TRBA 466

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
67770	ASM375250v1 assembly for Nocardioides aurantiacus DSM 12652	contig	GCA_003752505	86796.3	2781126051	86796	78.32

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
4780	Marmoricola aurantiacus 16S rRNA gene, partial	Y18629	1497		86796

GC content

@ref	GC-content (mol%)	Method
4780	72	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: ASM375250v1 assembly for Nocardioides aurantiacus DSM 12652
NCBI: GCA_003752505

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	98.19	no
125439	motility	BacteriaNetⓘ	no	91.41	no
125439	gram_stain	BacteriaNetⓘ	positive	99.49	no
125439	spore_formation	BacteriaNetⓘ	yes	41.62	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Marmoricola aurantiacus strain DSM 12652
PATRIC: 86796.3

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	yes	90.19	no
125438	anaerobic	anaerobicⓘ	no	98.85	yes
125438	aerobic	aerobicⓘ	yes	91.12	yes
125438	spore-forming	spore-formingⓘ	no	62.39	no
125438	thermophilic	thermophileⓘ	no	96.99	yes
125438	flagellated	motile2+ⓘ	no	91.50	no

Literature

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Marmoricola solisilvae sp. nov. and Marmoricola terrae sp. nov., isolated from soil and emended description of the genus Marmoricola.	Kim SJ, Lim JM, Hamada M, Ahn JH, Weon HY, Suzuki KI, Ahn TY, Kwon SW	Int J Syst Evol Microbiol	10.1099/ijs.0.000184	2015
Phylogeny	Marmoricola korecus sp. nov.	Lee SD, Lee DW, Ko YH	Int J Syst Evol Microbiol	10.1099/ijs.0.025460-0	2010
Phylogeny	Marmoricola scoriae sp. nov., isolated from volcanic ash.	Lee DW, Lee SD	Int J Syst Evol Microbiol	10.1099/ijs.0.018242-0	2009
Phylogeny	Marmoricola bigeumensis sp. nov., a member of the family Nocardioidaceae.	Dastager SG, Lee JC, Ju YJ, Park DJ, Kim CJ	Int J Syst Evol Microbiol	10.1099/ijs.0.65576-0	2008
Phylogeny	Marmoricola aequoreus sp. nov., a novel actinobacterium isolated from marine sediment.	Lee SD	Int J Syst Evol Microbiol	10.1099/ijs.0.64696-0	2007
Phylogeny	Marmoricola aurantiacus gen. nov., sp. nov., a coccoid member of the family Nocardioidaceae isolated from a marble statue.	Urzi C, Salamone P, Schumann P, Stackebrandt E	Int J Syst Evol Microbiol	10.1099/00207713-50-2-529	2000

References

#4780	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 12652
#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 )
#39566	; Curators of the CIP;
#67770	Japan Collection of Microorganism (JCM) ; Curators of the JCM;
#68371	Automatically annotated from API 50CH acid .
#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 .
#116563	Collection of Institut Pasteur ; Curators of the CIP; CIP 106770
#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 )

Content

About us

Nocardioides aurantiacus (DSM 12652, JCM 10917, NBRC 105375)

Name and taxonomic classification

Morphology

Cell morphology

Culture and growth conditions

Culture medium

Culture temp

Physiology and metabolism

Oxygen tolerance

Halophily

Murein

Observation

Metabolite utilization

Metabolite production

Metabolite tests

Enzymes

API zym

API 50CHac

API biotype100

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_003752505

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

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