Name: Nocardioides daedukensis MDN22
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 11148

Type strain:

Species: Nocardioides daedukensis

Strain Designation: MDN22

Culture col. no.: DSM 23819, CCUG 57505, KCTC 19601

Strain history: <- CCUG <- <- J. H. Yoon, KRIBB, Taejon, South Korea

NCBI tax ID(s): 634462 (species)

SI-ID 397275

DSM 23819, CCUG 57505

Section

Nocardioides daedukensis MDN22 is an aerobe, Gram-positive, rod-shaped bacterium that was isolated from Soil around wastewater treatment plant.

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

Information on the name and the taxonomic classification. Name and taxonomic classification

	Last LPSN update	14-12-2023 (DD-MM-YYYY)
	Domain	"Bacteria"
	Phylum	*Actinomycetota*
	Class	*Actinomycetes*
	Order	*Propionibacteriales*
	Family	*Nocardioidaceae*
	Genus	*Nocardioides*
	Species	**Nocardioides daedukensis**
	Full Scientific Name (LPSN)	Nocardioides daedukensis Yoon et al. 2010

Information on morphological and physiological properties Morphology

[Ref.: #29539]	Gram stain	positive
[Ref.: #69480]	Gram stain	positive Confidence in %100

[Ref.: #29539]	Cell length	1.9 µm

[Ref.: #29539]	Cell width	0.6 µm

[Ref.: #29539]	Cell shape	rod-shaped

[Ref.: #29539]	Motility	no

[Ref.: #21372]	Colony color	Pearl gold (1036)
[Ref.: #21372]	Incubation period	10-14 days
[Ref.: #21372]	Cultivation medium used	ISP 2

[Ref.: #21372]	Colony color	Ocher brown (8001)
[Ref.: #21372]	Incubation period	10-14 days
[Ref.: #21372]	Cultivation medium used	ISP 7

[Ref.: #21372]	Colony color	Brown beige (1011)
[Ref.: #21372]	Incubation period	10-14 days
[Ref.: #21372]	Cultivation medium used	suter with tyrosine

[Ref.: #21372]	Colony color	Sand yellow (1002)
[Ref.: #21372]	Incubation period	10-14 days
[Ref.: #21372]	Cultivation medium used	suter without tyrosine

[Ref.: #21372]	Incubation period	10-14 days
[Ref.: #21372]	Cultivation medium used	ISP 3

[Ref.: #21372]	Incubation period	10-14 days
[Ref.: #21372]	Cultivation medium used	ISP 4

[Ref.: #21372]	Incubation period	10-14 days
[Ref.: #21372]	Cultivation medium used	ISP 5

[Ref.: #61351]	Incubation period	7 days

[Ref.: #29539]

Pigment production

yes

[Ref.: #21372]	Multicellular complex forming ability	no
[Ref.: #21372]	Medium Name (multicellularity)	ISP 2

[Ref.: #21372]	Multicellular complex forming ability	no
[Ref.: #21372]	Medium Name (multicellularity)	ISP 3

[Ref.: #21372]	Multicellular complex forming ability	no
[Ref.: #21372]	Medium Name (multicellularity)	ISP 4

[Ref.: #21372]	Multicellular complex forming ability	no
[Ref.: #21372]	Medium Name (multicellularity)	ISP 5

[Ref.: #21372]	Multicellular complex forming ability	no
[Ref.: #21372]	Medium Name (multicellularity)	ISP 7

[Ref.: #21372]	Multicellular complex forming ability	no
[Ref.: #21372]	Medium Name (multicellularity)	Suter with tyrosine

[Ref.: #21372]	Multicellular complex forming ability	no
[Ref.: #21372]	Medium Name (multicellularity)	Suter without tyrosine

Information on culture and growth conditions Culture and growth conditions

[Ref.: #17387]

Culture medium

TRYPTICASE SOY YEAST EXTRACT MEDIUM (DSMZ Medium 92)

[Ref.: #17387]

Culture medium growth

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Culture medium link

Medium recipe at MediaDive

[Ref.: #17387]

Culture medium composition

expand / minimize

[Ref.: #21372]

Culture medium

ISP 2

[Ref.: #21372]

Culture medium growth

[Ref.: #21372]

Culture medium composition

expand / minimize

[Ref.: #21372]

Culture medium

ISP 3

[Ref.: #21372]

Culture medium growth

[Ref.: #21372]

Culture medium composition

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[Ref.: #21372]

Culture medium

ISP 4

[Ref.: #21372]

Culture medium growth

[Ref.: #21372]

Culture medium composition

expand / minimize

[Ref.: #21372]

Culture medium

ISP 5

[Ref.: #21372]

Culture medium growth

[Ref.: #21372]

Culture medium composition

expand / minimize

[Ref.: #21372]

Culture medium

ISP 7

[Ref.: #21372]

Culture medium growth

[Ref.: #21372]

Culture medium composition

expand / minimize

[Ref.: #21372]

Culture medium

suter with tyrosine

[Ref.: #21372]

Culture medium growth

[Ref.: #21372]

Culture medium composition

expand / minimize

[Ref.: #21372]

Culture medium

suter without tyrosine

[Ref.: #21372]

Culture medium growth

[Ref.: #21372]

Culture medium composition

expand / minimize

[Ref.: #17387]

Culture medium

R2A MEDIUM (DSMZ Medium 830)

[Ref.: #17387]

Culture medium growth

[Ref.: #17387]

Culture medium link

Medium recipe at MediaDive

[Ref.: #17387]

Culture medium composition

expand / minimize

		Temperature
[Ref.: #17387]	growth	28 °C
[Ref.: #29539]	growth	04-37 °C
[Ref.: #29539]	optimum	30 °C
[Ref.: #61351]	growth	30 °C

[Ref.: #17387]	Temperature range	mesophilic
[Ref.: #29539]	Temperature range	mesophilic
[Ref.: #61351]	Temperature range	mesophilic

	pH	Kind of pH		pH
[Ref.: #29539]			optimum	7.5
[Ref.: #29539]			growth	06-10

Information on physiology and metabolism Physiology and metabolism

[Ref.: #29539]	Oxygen tolerance	aerobe
[Ref.: #61351]	Oxygen tolerance	aerobe

[Ref.: #29539]	Ability of spore formation	no
[Ref.: #69481]	Ability of spore formation	no Confidence in %94
[Ref.: #69480]	Ability of spore formation	no Confidence in %99.884

	Salt		Salt conc.
[Ref.: #21372]	NaCl	maximum	5	%
[Ref.: #29539]	NaCl	growth	0-9	%
[Ref.: #29539]	NaCl	optimum	0.25	%

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #21372]	arabinose ChEBI	-
[Ref.: #68375]	arabinose ChEBI	-	fermentation	* from API ID32STA
[Ref.: #68375]	arginine ChEBI	+	hydrolysis	* from API ID32STA
[Ref.: #68375]	cellobiose ChEBI	-	fermentation	* from API ID32STA
[Ref.: #21372]	cellulose ChEBI	+
[Ref.: #68375]	D-fructose ChEBI	+	fermentation	* from API ID32STA
[Ref.: #68375]	D-glucose ChEBI	+	fermentation	* from API ID32STA
[Ref.: #68379]	D-glucose ChEBI	-	fermentation	* from API Coryne
[Ref.: #68379]	D-mannitol ChEBI	-	fermentation	* from API Coryne, API ID32STA
[Ref.: #68375]	D-mannose ChEBI	+	fermentation	* from API ID32STA
[Ref.: #68379]	D-ribose ChEBI	-	fermentation	* from API Coryne, API ID32STA
[Ref.: #68379]	D-xylose ChEBI	-	fermentation	* from API Coryne
[Ref.: #29539]	esculin ChEBI	+	hydrolysis
[Ref.: #68379]	esculin ChEBI	+	hydrolysis	* from API Coryne
[Ref.: #68375]	esculin ChEBI	-	hydrolysis	* from API ID32STA
[Ref.: #21372]	fructose ChEBI	-
[Ref.: #68379]	gelatin ChEBI	+	hydrolysis	* from API Coryne
[Ref.: #21372]	glucose ChEBI	+
[Ref.: #68379]	glycogen ChEBI	-	fermentation	* from API Coryne
[Ref.: #68375]	lactose ChEBI	+	fermentation	* from API ID32STA
[Ref.: #68379]	lactose ChEBI	-	fermentation	* from API Coryne
[Ref.: #29539]	malate ChEBI	+	carbon source
[Ref.: #68375]	maltose ChEBI	+	fermentation	* from API ID32STA
[Ref.: #68379]	maltose ChEBI	-	fermentation	* from API Coryne
[Ref.: #21372]	mannose ChEBI	-
[Ref.: #21372]	myo-inositol ChEBI	-
[Ref.: #68375]	N-acetylglucosamine ChEBI	+	fermentation	* from API ID32STA
[Ref.: #29539]	nitrate ChEBI	+	reduction
[Ref.: #68375]	nitrate ChEBI	+	reduction	* from API ID32STA
[Ref.: #68379]	nitrate ChEBI	-	reduction	* from API Coryne
[Ref.: #68375]	ornithine ChEBI	-	degradation	* from API ID32STA
[Ref.: #21372]	raffinose ChEBI	-
[Ref.: #68375]	raffinose ChEBI	-	fermentation	* from API ID32STA
[Ref.: #21372]	rhamnose ChEBI	+
[Ref.: #21372]	sucrose ChEBI	-
[Ref.: #68379]	sucrose ChEBI	+	fermentation	* from API Coryne, API ID32STA
[Ref.: #29539]	trehalose ChEBI	+	carbon source
[Ref.: #68375]	trehalose ChEBI	-	fermentation	* from API ID32STA
[Ref.: #68375]	turanose ChEBI	+	fermentation	* from API ID32STA
[Ref.: #68375]	urea ChEBI	+	hydrolysis	* from API ID32STA
[Ref.: #21372]	xylose ChEBI	+
	Only first 10 entries are displayed. Click here to see all.

	Antibiotica	Metabolite	Antibiotic resistance	Concentration
[Ref.: #68375]		novobiocin ChEBI	yes	1.8	µg	* from API ID32STA

	Metabolite production	Metabolite	Production
[Ref.: #68375]		acetoin ChEBI	yes	* from API ID32STA

	Physiological tests	Metabolite	Voges-Proskauer-test
[Ref.: #68375]		acetoin ChEBI	+	* from API ID32STA

	Enzyme	Enzyme activity	EC number
[Ref.: #68375]	alkaline phosphatase	+	3.1.3.1	* from API ID32STA
[Ref.: #68379]	alkaline phosphatase	-	3.1.3.1	* from API Coryne
[Ref.: #68382]	alpha-chymotrypsin	-	3.4.21.1	* from API zym
[Ref.: #68382]	alpha-fucosidase	-	3.2.1.51	* from API zym
[Ref.: #68382]	alpha-galactosidase	-	3.2.1.22	* from API zym
[Ref.: #68379]	alpha-glucosidase	-	3.2.1.20	* from API Coryne, API zym
[Ref.: #68382]	alpha-mannosidase	-	3.2.1.24	* from API zym
[Ref.: #68375]	arginine dihydrolase	+	3.5.3.6	* from API ID32STA
[Ref.: #68375]	beta-galactosidase	-	3.2.1.23	* from API ID32STA, API Coryne, API zym
[Ref.: #68379]	beta-glucosidase	+	3.2.1.21	* from API Coryne
[Ref.: #68375]	beta-glucosidase	-	3.2.1.21	* from API ID32STA, API zym
[Ref.: #68375]	beta-glucuronidase	-	3.2.1.31	* from API ID32STA, API Coryne, API zym
[Ref.: #68382]	cystine arylamidase	-	3.4.11.3	* from API zym
[Ref.: #29539]	cytochrome oxidase	+	1.9.3.1
[Ref.: #68382]	esterase (C 4)	-		* from API zym
[Ref.: #68382]	esterase lipase (C 8)	-		* from API zym
[Ref.: #68379]	gelatinase	+		* from API Coryne
[Ref.: #68375]	L-arginine arylamidase	-		* from API ID32STA
[Ref.: #68382]	leucine arylamidase	-	3.4.11.1	* from API zym
[Ref.: #68382]	lipase (C 14)	-		* from API zym
[Ref.: #68379]	N-acetyl-beta-glucosaminidase	-	3.2.1.52	* from API Coryne, API zym
[Ref.: #68382]	naphthol-AS-BI-phosphohydrolase	+		* from API zym
[Ref.: #68375]	ornithine decarboxylase	-	4.1.1.17	* from API ID32STA
[Ref.: #68379]	pyrazinamidase	+	3.5.1.B15	* from API Coryne
[Ref.: #68375]	pyrrolidonyl arylamidase	-	3.4.19.3	* from API ID32STA, API Coryne
[Ref.: #68382]	trypsin	-	3.4.21.4	* from API zym
[Ref.: #68375]	urease	+	3.5.1.5	* from API ID32STA
[Ref.: #68382]	valine arylamidase	-		* from API zym
	Only first 10 entries are displayed. Click here to see all.

API® Coryne:

Note that the displayed test results represent raw data and therefore may deviate!

	API ID	Reduction of nitrateNIT	PyrazinamidasePYZ	Pyrrolidonyl arylamidasePYRA	Alkaline phosphatasePAL	beta-Glucuronidasebeta GUR	beta-Galactosidasebeta GAL	alpha-Glucosidasealpha GLU	N-Acetyl-beta-Glucosidasebeta NAG	Esculin hydrolysis/beta-GlucosidaseESC	Urease/urea hydrolysisURE	Gelatinase/gelatin hydrolysisGEL	Control fermentationControl	Fermentation of D-glucoseGLU	Fermentation of D-riboseRIB	Fermentation of D-xyloseXYL	Fermentation of D-mannitolMAN	Fermentation of maltoseMAL	Fermentation of lactoseLAC	Fermentation of sucroseSAC	Fermentation of glycogenGLYG	CatalaseCAT
[Ref.: #21372]	501	-	+	-	-	-	-	-	-	+	+/-	+	not determinedn.d.	-	-	-	-	-	-	+	-	not determinedn.d.

API® ID32STA:

Note that the displayed test results represent raw data and therefore may deviate!

	API ID	Urease/urea hydrolysisURE	Arginine dihydrolaseADH (Arg)	Ornithine decarboxylaseODC	Esculin hydrolysisESC	Fermentation of D-glucoseGLU	Fermentation of D-fructoseFRU	Fermentation of D-mannoseMNE	Fermentation of maltoseMAL	Fermentation of lactoseLAC	Fermentation of trehaloseTRE	Fermentation of D-mannitolMAN	Fermentation of raffinoseRAF	Fermentation of D-riboseRIB	Fermentation of cellobioseCEL	Reduction of nitrateNIT	Acetoin production (Voges Proskauer test)VP	beta-Galactosidasebeta GAL	L-arginine arylamidaseArgA	Alkaline phosphatasePAL	Pyrrolidonyl arylamidasePyrA	Novobiocin resistanceNOVO	Fermentation of sucroseSAC	Fermentation of N-acetyl-glucosamineNAG	Fermentation of turanoseTUR	Fermentation of arabinoseARA	beta-Glucuronidasebeta GUR
[Ref.: #17387]	6222	+	+	-	-	+	+	+	+	+	-	-	-	-	-	+	+	-	-	+	-	+	+	+	+	-	-

API® zym:

Note that the displayed test results represent raw data and therefore may deviate!

	API ID	Control	2-naphthyl phosphateAlkaline phosphatase	2-naphthyl butyrateEsterase (C 4)	2-naphtyl caprylateEsterase Lipase (C 8)	2-naphthyl myristateLipase (C 14)	L-leucyl-2-naphthylamideLeucine arylamidase	L-valyl-2-naphthylamideValine arylamidase	L-cystyl-2-naphthylamideCystine arylamidase	N-benzoyl-DL-arginine-2-naphthylamideTrypsin	N-glutaryl-phenylalanine-2-naphthylamidealpha- Chymotrypsin	2-naphthyl phosphateAcid phosphatase	Naphthol-AS-BI-phosphateNaphthol-AS-BI-phosphohydrolase	6-Br-2-naphthyl-alphaD-galactpyranosidealpha- Galactosidase	2-naphthyl-betaD-galactpyranosidebeta- Galactosidase	Naphthol-AS-BI-betaD-glucuronidebeta- Glucuronidase	2-naphthyl-alphaD-glucopyranosidealpha- Glucosidase	6-Br-2-naphthyl-betaD-glucopyranosidebeta- Glucosidase	1-naphthyl-N-acetyl-betaD-glucosaminideN-acetyl-beta- glucosaminidase	6-Br-2-naphthyl-alphaD-mannopyranosidealpha- Mannosidase	2-naphthyl-alphaL-fucopyranosidealpha- Fucosidase
[Ref.: #21372]	1013	not determinedn.d.	+/-	-	-	-	-	-	-	-	-	+/-	+	-	-	-	-	-	-	-	-

Information on isolation source, the sampling and environmental conditions Isolation, sampling and environmental information

[Ref.: #17387]	Sample type/isolated from	Soil around wastewater treatment plant
[Ref.: #17387]	Geographic location (country and/or sea, region)	Taejon
[Ref.: #17387]	Country	Republic of Korea
[Ref.: #17387]	Country ISO 3 Code	KOR
[Ref.: #17387]	Continent	Asia

[Ref.: #61351]	Sample type/isolated from	Soil around wastewater treatment plant
[Ref.: #61351]	Sampling date	2006-01-01
[Ref.: #61351]	Geographic location (country and/or sea, region)	Taejon
[Ref.: #61351]	Country	Republic of Korea
[Ref.: #61351]	Country ISO 3 Code	KOR
[Ref.: #61351]	Continent	Asia
* marker position based on {}

Isolation sources categories

#Engineered	#Waste	#Water treatment plant
#Environmental	#Terrestrial	#Soil

What are isolation sources categories?

Information on possible application of the strain and its possible interaction with e.g. potential hosts Safety information

[Ref.: #17387]

Biosafety level

Risk group (German classification)
According to TRBA 466

Information on genomic background e.g. entries in nucleic sequence databass Sequence information

16S Sequence information:

	Sequence accession description	Seq. accession number	Sequence length (bp)	Sequence database	Associated NCBI tax ID
[Ref.: #17387]	Nocardioides daedukensis strain MDN22 16S ribosomal RNA gene, partial sequence	FJ842646	1475	ENA	634462 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Nocardioides daedukensis DSM 23819	GCA_013408415	contig	GenBank	634462 tax ID	*
[Ref.: #66792]	Nocardioides daedukensis strain DSM 23819	634462.3	wgs	PATRIC	634462 tax ID	*
[Ref.: #66792]	Nocardioides daedukensis DSM 23819	2844615251	draft	JGI IMG/M	634462 tax ID	*

[Ref.: #17387]	GC-content	68.7 mol%	high performance liquid chromatography (HPLC)
[Ref.: #29539]	GC-content	68.7 mol%

Data predicted using genome information as a basis Genome-based predictions

	Trait	Prediction	Confidence in %	In training data
	Predictions from GenomeNet Sporulation v. 1 based on: Nocardioides daedukensis strain DSM 23819 PATRIC: 634462.3
[Ref.: #69481]	spore-forming	no	94	no

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Nocardioides daedukensis strain DSM 23819 PATRIC: 634462.3
[Ref.: #69480]	gram-positive	yes	92.928	yes
[Ref.: #69480]	anaerobic	no	98.437	yes
[Ref.: #69480]	halophile	no	93.994	no
[Ref.: #69480]	spore-forming	no	84.283	yes
[Ref.: #69480]	glucose-util	yes	85.017	yes
[Ref.: #69480]	thermophile	no	98.964	yes
[Ref.: #69480]	flagellated	no	94.57	no
[Ref.: #69480]	aerobic	yes	93.711	yes
[Ref.: #69480]	motile	no	76.799	yes
[Ref.: #69480]	glucose-ferment	no	88.714	no

Availability in culture collections External links

[Ref.: #17387]

Culture collection no.

DSM 23819, CCUG 57505, KCTC 19601

[Ref.: #80397]

SI-ID 397275

Literature:

Topic	Title	Authors	Journal	DOI	Year
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 pacificus sp. nov., isolated from deep sub-seafloor sediment.	Fan X, Qiao Y, Gao X, Zhang XH	Int J Syst Evol Microbiol	10.1099/ijs.0.059873-0	2014	*
Phylogeny	Nocardioides daejeonensis sp. nov., a denitrifying bacterium isolated from sludge in a sewage-disposal plant.	Woo SG, Srinivasan S, Yang J, Jung YA, Kim MK, Lee M	Int J Syst Evol Microbiol	10.1099/ijs.0.033308-0	2011	*
Phylogeny	Nocardioides daedukensis sp. nov., a halotolerant bacterium isolated from soil.	Yoon JH, Park S, Kang SJ, Lee JS, Lee KC, Oh TK	Int J Syst Evol Microbiol	10.1099/ijs.0.015354-0	2009	*

References

#17387

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 23819

#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 )

#21372

Wink, J.: Compendium of Actinobacteria. HZI-Helmholtz-Centre for Infection Research, Braunschweig .

#29539

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 #25936 (see below)

#61351 Culture Collection University of Gothenburg (CCUG) ; Curators of the CCUG; CCUG 57505

#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) .

#68375

Automatically annotated from API ID32STA .

#68379

Automatically annotated from API Coryne .

#68382

Automatically annotated from API zym .

#69480

Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann: Predictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) .

#69481

Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch: Predictions based on the model GenomeNet Sporulation v. 1 . ( DOI 10.21203/rs.3.rs-2527258/v1 )

#80397

Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.: StrainInfo: A central database for resolving microbial strain identifiers . ( DOI 10.60712/SI-ID397275.1 )

#25936

IJSEM 1334 2010 ( DOI 10.1099/ijs.0.015354-0 , PubMed 19667373 )

* These data were automatically processed and therefore are not curated

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Nocardioides daedukensis strain DSM 23819

Nocardioides daedukensis strain DSM 23819

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Change proposal