Nocardioides oleivorans (DSM 16090, NCIMB 14004, BAS 3)

Name: Nocardioides oleivorans (DSM 16090, NCIMB 14004, BAS 3)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 11112

Type strain

Culture col. no. DSM 16090 NCIMB 14004 BAS 3 IAM 15341 CIP 108901 2 more

NCBI tax ID(s) 273676

Special Collections DSMZ JCM CIP Literature strains

History <- A. Schippers <- K. Bosecker, BAS3 2005, DSMZ NCIMB 14004 <-- A. Schippers BAS3 <-- K. Bosecker. CIP <- 2005, DSMZ

Links

Nocardioides oleivorans DSM 16090 is an aerobe, Gram-positive, rod-shaped bacterium that was isolated from Oil sample.

Gram-positive rod-shaped aerobe genome sequence 16S sequence Bacteria

Name and taxonomic classification

SI-ID 305282

DSM 16090,NCIMB 14004,JCM 14342,CIP 108901,IAM 15341

@ref 20215

Last LPSN update 2026-02-09 11:20:27

Domain Bacteria

Phylum Actinomycetota

Class Actinomycetes

Order Propionibacteriales

Family Nocardioidaceae

Genus Nocardioides

Species Nocardioides oleivorans

Full scientific name Nocardioides oleivorans Schippers et al. 2005

Morphology

Cell morphology

@ref	Gram stain	Cell length	Cell width	Cell shape	Confidence
31420	positive	1.1 µm	0.3 µm	rod-shaped
121410	positive			rod-shaped
125439	positive				98.8

Pigmentation

31420

Productionyes

Culture and growth conditions

Culture medium

@ref	Name	Medium link	Composition
38362	MEDIUM 57 - for Streptomyces, Nocardioides, Lentzea albidocapillata and Streptoverticillium reticulum		Distilled water make up to (1000.000 ml);Agar (15.000 g);Glucose (4.000g);Yeast extract (4.000 g);Malt extract (10.000 g);Calcium carbonate (2.000 g)
6286	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
6286	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
121410	CIP Medium 57	Medium recipe at CIP

Culture temp

@ref	Growth	Type	Temperature (°C)
6286	positive	growth	28
31420	positive	growth	25-30
31420	positive	optimum	30
38362	positive	growth	30
67770	positive	growth	28
121410	positive	growth	10-41
121410	negative	growth	45

Culture pH

@ref	Ability	Type	PH
31420	positive	optimum	7.15
31420	positive	growth	7-7.3

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
31420	aerobe
121410	obligate aerobe
125438	aerobe	90.319
125439	obligate aerobe	98.7

Spore formation

31420

Spore formationno

Halophily

@ref	Salt	Growth	Tested relation	Concentration
31420	NaCl	positive	growth	2 %
31420	NaCl	positive	optimum	2 %
121410	NaCl	positive	growth	0-4 %
121410	NaCl		growth	6 %
121410	NaCl		growth	8 %
121410	NaCl		growth	10 %

Murein

@ref	Murein short key	Type
6286	A41.01	A3gamma LL-Dpm-Gly

Observation

@ref	Observation
31420	aggregates in clumps
67770	quinones: MK-8(H₄)

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
31420	30089 ChEBI	acetate	+	carbon source
31420	16449 ChEBI	alanine	+	carbon source
68371	27613 ChEBI	amygdalin	-	builds acid from	from API 50CH acid
68371	18305 ChEBI	arbutin	-	builds acid from	from API 50CH acid
31420	35391 ChEBI	aspartate	+	carbon source
31420	17057 ChEBI	cellobiose	+	carbon source
68371	17057 ChEBI	cellobiose	-	builds acid from	from API 50CH acid
121410	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	15824 ChEBI	D-fructose	-	builds acid from	from API 50CH acid
68371	28847 ChEBI	D-fucose	-	builds acid from	from API 50CH acid
68371	12936 ChEBI	D-galactose	-	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	16024 ChEBI	D-mannose	-	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
121410	4853 ChEBI	esculin	+	hydrolysis
68371	4853 ChEBI	esculin	+	builds acid from	from API 50CH acid
31420	28757 ChEBI	fructose	+	carbon source
68371	16813 ChEBI	galactitol	-	builds acid from	from API 50CH acid
31420	28260 ChEBI	galactose	+	carbon source
68371	28066 ChEBI	gentiobiose	-	builds acid from	from API 50CH acid
31420	24265 ChEBI	gluconate	+	carbon source
68371	24265 ChEBI	gluconate	-	builds acid from	from API 50CH acid
31420	17234 ChEBI	glucose	+	carbon source
68371	17754 ChEBI	glycerol	-	builds acid from	from API 50CH acid
68371	28087 ChEBI	glycogen	-	builds acid from	from API 50CH acid
121410	606565 ChEBI	hippurate	+	hydrolysis
31420	27570 ChEBI	histidine	+	carbon source
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
31420	24996 ChEBI	lactate	+	carbon source
68371	17716 ChEBI	lactose	-	builds acid from	from API 50CH acid
31420	25017 ChEBI	leucine	+	carbon source
31420	25115 ChEBI	malate	+	carbon source
31420	17306 ChEBI	maltose	+	carbon source
68371	17306 ChEBI	maltose	-	builds acid from	from API 50CH acid
31420	29864 ChEBI	mannitol	+	carbon source
31420	37684 ChEBI	mannose	+	carbon source
68371	6731 ChEBI	melezitose	-	builds acid from	from API 50CH acid
31420	28053 ChEBI	melibiose	+	carbon source
68371	28053 ChEBI	melibiose	-	builds acid from	from API 50CH acid
68371	320061 ChEBI	methyl alpha-D-glucopyranoside	-	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
121410	17632 ChEBI	nitrate	-	reduction
121410	17632 ChEBI	nitrate	-	respiration
121410	16301 ChEBI	nitrite	-	reduction
31420	18401 ChEBI	phenylacetate	+	carbon source
68371		Potassium 2-ketogluconate	-	builds acid from	from API 50CH acid
68371		Potassium 5-ketogluconate	-	builds acid from	from API 50CH acid
31420	26271 ChEBI	proline	+	carbon source
31420	17272 ChEBI	propionate	+	carbon source
31420	17148 ChEBI	putrescine	+	carbon source
31420	15361 ChEBI	pyruvate	+	carbon source
68371	16634 ChEBI	raffinose	-	builds acid from	from API 50CH acid
31420	26546 ChEBI	rhamnose	+	carbon source
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
31420	17992 ChEBI	sucrose	+	carbon source
68371	17992 ChEBI	sucrose	-	builds acid from	from API 50CH acid
31420	27082 ChEBI	trehalose	+	carbon source
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
121410	35581 ChEBI	indole

Metabolite tests

@ref	Chebi-ID	Metabolite	Voges-proskauer-test	Methylred-test
121410	15688 ChEBI	acetoin	-
121410	17234 ChEBI	glucose		-

Enzymes

@ref	Value	Activity	Ec
68382	acid phosphatase	+	3.1.3.2	from API zym
121410	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
121410	amylase	-
68382	beta-galactosidase	+	3.2.1.23	from API zym
121410	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
121410	caseinase	+	3.4.21.50
121410	catalase	+	1.11.1.6
68382	cystine arylamidase	+	3.4.11.3	from API zym
121410	DNase	+
68382	esterase (C 4)	+		from API zym
68382	esterase lipase (C 8)	+		from API zym
121410	gamma-glutamyltransferase	+	2.3.2.2
121410	gelatinase	+
121410	lecithinase	-
68382	leucine arylamidase	+	3.4.11.1	from API zym
121410	lipase	-
68382	lipase (C 14)	+		from API zym
121410	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
121410	ornithine decarboxylase	-	4.1.1.17
121410	oxidase	-
121410	phenylalanine ammonia-lyase	+	4.3.1.24
121410	protease	+
68382	trypsin	-	3.4.21.4	from API zym
121410	tryptophan deaminase	-
121410	tween esterase	+
121410	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
121410	-	+	+	+	+	+	+	+	-	-	+	+	+	+	-	+	+	-	-	-

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
121410	not determinedn.d.	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	+	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Engineered	#Industrial	#Oil reservoir

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent
6286	Oil sample	Gifhorn	Germany	DEU	Europe
67770	Crude oil sample from the oilfield Oerrel of the Gifhorn Trough		Germany	DEU	Europe
121410	Crude oil		Germany	DEU	Europe

Taxonmaps

69479

Global distribution of 16S sequence AJ698724 (>99% sequence identity) for Nocardioides oleivorans from Microbeatlas

Aquatic Samples	27
Soil Samples	322
Animal Samples	139
Plant Samples	214
Total Samples	702

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
6286	1	Risk group (German classification) According to TRBA 466
121410	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	ASM413725v1 assembly for Nocardioides oleivorans CGMCC 4.6882	contig	GCA_004137255	273676.3	2867494351	273676	77.11

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
6286	Nocardioides oleivorans partial 16S rRNA gene, type strain DSM 16090T	AJ698724	1479		273676
124043	Nocardioides oleivorans partial 16S rRNA gene, isolate strain #17 (MBG-DUTH)/DSM 16090 (ELTE)	OU548671	830		273676

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Nocardioides oleivorans CGMCC 4.6882
NCBI: GCA_004137255

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	no	80.80	no
125439	motility	BacteriaNetⓘ	no	60.40	no
125439	gram_stain	BacteriaNetⓘ	positive	98.80	no
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	98.70	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Nocardioides oleivorans strain CGMCC 4.6882
PATRIC: 273676.3

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	yes	89.06	yes
125438	anaerobic	anaerobicⓘ	no	97.75	yes
125438	spore-forming	spore-formingⓘ	no	54.44	no
125438	aerobic	aerobicⓘ	yes	90.32	yes
125438	thermophilic	thermophileⓘ	no	97.99	no
125438	flagellated	motile2+ⓘ	no	78.00	no

Literature

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Nocardioides baculatus sp. nov., a novel actinomycete isolated from the rhizosphere of Tagetes patula.	Chhetri G, Kim I, Kang M, Kim J, So Y, Seo T	Int J Syst Evol Microbiol	10.1099/ijsem.0.005012	2021
Phylogeny	Nocardioides zhouii sp. nov., isolated from the Hailuogou Glacier in China.	Zhang GQ, Liu Q, Liu HC, Zhou YG, Xin YH	Int J Syst Evol Microbiol	10.1099/ijsem.0.003471	2019
Phylogeny	Nocardioides sonneratiae sp. nov., an endophytic actinomycete isolated from a branch of Sonneratia apetala.	Li F, Tuo L, Su ZW, Wei XQ, Zhang XY, Gao CH, Huang RM	Int J Syst Evol Microbiol	10.1099/ijsem.0.001979	2017
Phylogeny	Nocardioides cavernae sp. nov., an actinobacterium isolated from a karst cave.	Han MX, Fang BZ, Tian Y, Zhang WQ, Jiao JY, Liu L, Zhang ZT, Xiao M, Wei DQ, Li WJ	Int J Syst Evol Microbiol	10.1099/ijsem.0.001676	2017
Phylogeny	Nocardioides flavus sp. nov., isolated from marine sediment.	Wang S, Zhou Y, Zhang G	Int J Syst Evol Microbiol	10.1099/ijsem.0.001507	2016
Phylogeny	Nocardioides hwasunensis sp. nov.	Lee SD, Lee DW, Kim JS	Int J Syst Evol Microbiol	10.1099/ijs.0.65015-0	2008
Phylogeny	Nocardioides furvisabuli sp. nov., isolated from black sand.	Lee SD	Int J Syst Evol Microbiol	10.1099/ijs.0.64444-0	2007
Phylogeny	Nocardioides oleivorans sp. nov., a novel crude-oil-degrading bacterium.	Schippers A, Schumann P, Sproer C	Int J Syst Evol Microbiol	10.1099/ijs.0.63500-0	2005

References

#6286	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 16090
#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 )
#27727	IJSEM 1501 2005 ( DOI 10.1099/ijs.0.63500-0 , PubMed 16014472 )
#31420	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 #27727
#38362	; 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 .
#121410	Collection of Institut Pasteur ; Curators of the CIP; CIP 108901
#124043	Isabel Schober, Julia Koblitz: Data extracted from sequence databases, automatically matched based on designation and taxonomy .
#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 oleivorans (DSM 16090, NCIMB 14004, BAS 3)

Name and taxonomic classification

Morphology

Cell morphology

Pigmentation

Culture and growth conditions

Culture medium

Culture temp

Culture pH

Physiology and metabolism

Oxygen tolerance

Spore formation

Halophily

Murein

Observation

Metabolite utilization

Metabolite production

Metabolite tests

Enzymes

API zym

API 50CHac

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_004137255

16S sequences

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

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