Nocardioides nitrophenolicus (DSM 15529, CIP 107017, JCM 10703)

Name: Nocardioides nitrophenolicus (DSM 15529, CIP 107017, JCM 10703)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 11110

Type strain

Culture col. no. DSM 15529 CIP 107017 JCM 10703 KCTC 0457BP NRRL B-24725 1 more

NCBI tax ID(s) 1303688 60489

Special Collections DSMZ JCM KCTC CIP

History JCM <-- Y.-H. Park NSP41. CIP <- 2001, JCM <- Y.-H. Park: strain NSP41

Links

Nocardioides nitrophenolicus DSM 15529 is an obligate aerobe, Gram-positive, motile bacterium of the family Nocardioidaceae.

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

Name and taxonomic classification

SI-ID 100824

DSM 15529,CIP 107017,JCM 10703

@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 nitrophenolicus

Full scientific name Nocardioides nitrophenolicus Yoon et al. 1999

Morphology

Cell morphology

@ref	Gram stain	Cell shape	Motility	Confidence
121314	positive	rod-shaped
125439	positive			99.553

Colony morphology

121314

Hemolysis ability0

Culture and growth conditions

Culture medium

@ref	Name	Medium link	Composition
5980	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
39638	MEDIUM 263 - for Clavibacter, Rathayibacter ratayi, Nocardiodes plantarum		Distilled water make up to (1000.000 ml);Sodium chloride (5.000 g);Agar(15.000 g);Glucose (5.000 g);Yeast extract (5.000 g);Trypticase peptone (10.000 g)
5980	TRYPTICASE SOY YEAST EXTRACT MEDIUM (DSMZ Medium 92)	Medium recipe at MediaDive	Name: TRYPTICASE SOY YEAST EXTRACT MEDIUM (DSMZ Medium 92) Composition: Trypticase soy broth 30.0 g/l Agar 15.0 g/l Yeast extract 3.0 g/l Distilled water
121314	CIP Medium 111	Medium recipe at CIP

Culture temp

@ref	Growth	Type	Temperature (°C)
5980	positive	growth	28
39638	positive	growth	30
67770	positive	growth	28
121314	positive	growth	25-41
121314	negative	growth	10
121314	negative	growth	45

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
121314	obligate aerobe
125439	obligate aerobe	98.399

Halophily

@ref	Salt	Growth	Tested relation	Concentration
121314	NaCl	positive	growth	0-4 %
121314	NaCl		growth	6 %
121314	NaCl		growth	8 %
121314	NaCl		growth	10 %

Observation

67770

Observationquinones: MK-8(H₄)

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
121314	16947 ChEBI	citrate	-	carbon source
121314	4853 ChEBI	esculin	+	hydrolysis
121314	606565 ChEBI	hippurate	+	hydrolysis
121314	17632 ChEBI	nitrate	-	reduction
121314	17632 ChEBI	nitrate	-	respiration
121314	16301 ChEBI	nitrite	-	reduction

Antibiotic resistance

@ref	Metabolite	Is sensitive	Is resistant
121314	0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)

Metabolite production

@ref	Chebi-ID	Metabolite	Production
121314	35581 ChEBI	indole

Metabolite tests

@ref	Chebi-ID	Metabolite	Voges-proskauer-test	Methylred-test
121314	15688 ChEBI	acetoin	-
121314	17234 ChEBI	glucose		-

Enzymes

@ref	Value	Activity	Ec
68382	acid phosphatase	+	3.1.3.2	from API zym
121314	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
121314	amylase	+
68382	beta-galactosidase	-	3.2.1.23	from API zym
121314	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
121314	caseinase	+	3.4.21.50
121314	catalase	-	1.11.1.6
68382	cystine arylamidase	-	3.4.11.3	from API zym
121314	DNase	+
68382	esterase (C 4)	+		from API zym
68382	esterase lipase (C 8)	+		from API zym
121314	gamma-glutamyltransferase	-	2.3.2.2
121314	gelatinase	-
68382	leucine arylamidase	+	3.4.11.1	from API zym
68382	lipase (C 14)	-		from API zym
121314	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
121314	ornithine decarboxylase	-	4.1.1.17
121314	oxidase	+
121314	phenylalanine ammonia-lyase	-	4.3.1.24
68382	trypsin	+	3.4.21.4	from API zym
121314	tryptophan deaminase	-
121314	tween esterase	-
121314	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
121314	-	+	+	+	-	+	+	-	+	-	+	+	-	-	-	+	-	-	-	-

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
121314	not determinedn.d.	+	+	+	+	-	-	-	+	-	+	+	-	-	-	-	-	-	-	-	+	-	+	-	+	-	-	+	+	+	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	+	+	-	-	-	-	-	-	-	-	-	-	+	-	+	+	-	+	+	-	-	-	-	-	+	-	+	-	-	-	-	+	+	-	-	-	-	-	-	-	+	-	+	+	-	+	+	-	+	+	-

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Engineered	#Waste	#Industrial wastewater

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent
39638			Republic of Korea	KOR	Asia
5980	Industrial wastewater		Republic of Korea	KOR	Asia
67770	Industrial wastewater		Republic of Korea	KOR	Asia
121314	Environment, Industrial wastewater	Taejon	Republic of Korea	KOR	Asia

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
5980	1	Risk group (German classification) According to TRBA 466
121314	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
66792	ASM1690751v1 assembly for Nocardioides nitrophenolicus DSM 15529	contig	GCA_016907515	60489.4	2893560988	60489	76.73
66792	ASM131360v1 assembly for Nocardioides nitrophenolicus JCM 10703	contig	GCA_001313605	1303688.4	2734481954	1303688	0

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
20218	Nocardioides sp. NSP 41 16S-23S internal transcribed spacer, complete sequence	AF017507	328		60489
5980	Nocardioides nitrophenolicus strain NSP 41 16S ribosomal RNA gene, partial sequence	AF005024	1475		60489

GC content

@ref	GC-content (mol%)	Method
5980	71.4	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: ASM1690751v1 assembly for Nocardioides nitrophenolicus DSM 15529
NCBI: GCA_016907515

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	98.40	no
125439	motility	BacteriaNetⓘ	no	86.90	no
125439	gram_stain	BacteriaNetⓘ	positive	99.55	no
125439	spore_formation	BacteriaNetⓘ	yes	62.72	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Nocardioides nitrophenolicus JCM 10703
PATRIC: 1303688.4

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	yes	80.97	no
125438	anaerobic	anaerobicⓘ	no	89.35	yes
125438	spore-forming	spore-formingⓘ	no	77.96	no
125438	aerobic	aerobicⓘ	yes	75.96	yes
125438	thermophilic	thermophileⓘ	no	96.52	yes
125438	flagellated	motile2+ⓘ	no	79.50	no

Literature

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Nocardioides gilvus sp. nov., isolated from Namtso Lake.	Zhang HX, Wang K, Xu ZX, Chen GJ, Du ZJ.	Antonie Van Leeuwenhoek	10.1007/s10482-016-0735-0	2016
Phylogeny	Nocardioides pakistanensis sp. nov., isolated from a hot water spring of Tatta Pani in Pakistan.	Amin A, Ahmed I, Habib N, Abbas S, Xiao M, Hozzein WN, Li WJ.	Antonie Van Leeuwenhoek	10.1007/s10482-016-0711-8	2016
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 panacisoli sp. nov., isolated from the soil of a ginseng field.	Cho CH, Lee JS, An DS, Whon TW, Kim SG	Int J Syst Evol Microbiol	10.1099/ijs.0.012690-0	2009
Phylogeny	Nocardioides caeni sp. nov., isolated from wastewater.	Yoon JH, Kang SJ, Park S, Kim W, Oh TK	Int J Syst Evol Microbiol	10.1099/ijs.0.010124-0	2009
Phylogeny	Nocardioides humi sp. nov., a beta-glucosidase-producing bacterium isolated from soil of a ginseng field.	Kim MK, Srinivasan S, Park MJ, Sathiyaraj G, Kim YJ, Yang DC	Int J Syst Evol Microbiol	10.1099/ijs.0.008821-0	2009
Phylogeny	Nocardioides nitrophenolicus sp. nov., a p-nitrophenol-degrading bacterium.	Yoon JH, Cho YG, Lee ST, Suzuki K, Nakase T, Park YH	Int J Syst Bacteriol	10.1099/00207713-49-2-675	1999
Phylogeny	Nocardioides carbamazepini sp. nov., an ibuprofen degrader isolated from a biofilm bacterial community enriched on carbamazepine.	Benedek T, Papai M, Gharieb K, Bedics A, Tancsics A, Toth E, Daood H, Maroti G, Wirth R, Menashe O, Boka K, Kriszt B	Syst Appl Microbiol	10.1016/j.syapm.2022.126339	2022

References

#5980	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 15529
#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 )
#20218	Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P.: StrainInfo introduces electronic passports for microorganisms.. Syst Appl Microbiol. 37: 42 - 50 2014 ( DOI 10.1016/j.syapm.2013.11.002 , PubMed 24321274 )
#39638	; Curators of the CIP;
#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) .
#67770	Japan Collection of Microorganism (JCM) ; Curators of the JCM;
#68382	Automatically annotated from API zym .
#121314	Collection of Institut Pasteur ; Curators of the CIP; CIP 107017
#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 nitrophenolicus (DSM 15529, CIP 107017, JCM 10703)

Name and taxonomic classification

Morphology

Cell morphology

Colony morphology

Culture and growth conditions

Culture medium

Culture temp

Physiology and metabolism

Oxygen tolerance

Halophily

Observation

Metabolite utilization

Antibiotic resistance

Metabolite production

Metabolite tests

Enzymes

API zym

API biotype100

Isolation, sampling and environmental information

Isolation source categories

Isolation

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_016907515

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

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