Name: Nocardiopsis metallicus 114
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 11209

Type strain:

Species: Nocardiopsis metallicus

Strain Designation: 114

Culture col. no.: DSM 44598, CIP 107788, KBS 6, NRRL B-24159, JCM 12409, BCRC 16377, CGMCC 4.2089, NBRC 101841, VKM Ac-2522

Strain history: CIP <- 2002, DSMZ <- J. Haveland, BGR Hannover, Germany: strain KBS6

NCBI tax ID(s): 179819 (species)

SI-ID 100826

DSM 44598, NRRL B-24159, CIP 107788, BCRC 16377, CCRC 16377, JCM 12409, VKM Ac-2522, NBRC 101841, CGMCC 4.2089

Section

Nocardiopsis metallicus 114 is an obligate aerobe, spore-forming, mesophilic bacterium that was isolated from alkaline slag dump of metallurgical processing.

Gram-positive
spore-forming
mesophilic
obligate 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	*Streptosporangiales*
	Family	*Nocardiopsidaceae*
	Genus	*Nocardiopsis*
	Species	**Nocardiopsis metallicus**
	Full Scientific Name (LPSN)	Nocardiopsis metallicus Schippers et al. 2002

Information on morphological and physiological properties Morphology

[Ref.: #120918]	Gram stain	positive
[Ref.: #69480]	Gram stain	positive Confidence in %100

[Ref.: #120918]	Cell shape	filament-shaped

[Ref.: #120918]	Motility	no

Information on culture and growth conditions Culture and growth conditions

[Ref.: #11913]

Culture medium

TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535)

[Ref.: #11913]

Culture medium growth

[Ref.: #11913]

Culture medium link

Medium recipe at MediaDive

[Ref.: #11913]

Culture medium composition

expand / minimize

[Ref.: #39943]

Culture medium

MEDIUM 72- for trypto casein soja agar

[Ref.: #39943]

Culture medium growth

[Ref.: #39943]

Culture medium composition

expand / minimize

[Ref.: #11913]

Culture medium

GYM STREPTOMYCES MEDIUM (DSMZ Medium 65)

[Ref.: #11913]

Culture medium growth

[Ref.: #11913]

Culture medium link

Medium recipe at MediaDive

[Ref.: #11913]

Culture medium composition

expand / minimize

[Ref.: #11913]

Culture medium

GPHF-MEDIUM (DSMZ Medium 553)

[Ref.: #11913]

Culture medium growth

[Ref.: #11913]

Culture medium link

Medium recipe at MediaDive

[Ref.: #11913]

Culture medium composition

expand / minimize

[Ref.: #120918]

Culture medium

CIP Medium 72

[Ref.: #120918]

Culture medium growth

[Ref.: #120918]

Culture medium link

Medium recipe provided by DSMZ

	Kind of temperature		Temperature
[Ref.: #11913]		growth	28 °C
[Ref.: #39943]		growth	30 °C
[Ref.: #67770]		growth	28 °C
[Ref.: #120918]		growth	25-37 °C
[Ref.: #120918]	no	growth	10 °C
[Ref.: #120918]	no	growth	41 °C
[Ref.: #120918]	no	growth	45 °C

[Ref.: #11913]	Temperature range	mesophilic
[Ref.: #39943]	Temperature range	mesophilic
[Ref.: #67770]	Temperature range	mesophilic
[Ref.: #120918]	Temperature range	mesophilic
[Ref.: #120918]	Temperature range	psychrophilic
[Ref.: #120918]	Temperature range	thermophilic

Information on physiology and metabolism Physiology and metabolism

[Ref.: #120918]

Oxygen tolerance

obligate aerobe

[Ref.: #69481]	Ability of spore formation	yes Confidence in %100
[Ref.: #69480]	Ability of spore formation	yes Confidence in %99.446

	Salt	Tested relation		Salt conc.
[Ref.: #120918]	NaCl		growth	2-8	%
[Ref.: #120918]	NaCl	no	growth	0	%
[Ref.: #120918]	NaCl	no	growth	10	%

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #120918]	citrate ChEBI	-	carbon source
[Ref.: #120918]	esculin ChEBI	-	hydrolysis
[Ref.: #120918]	hippurate ChEBI	+	hydrolysis
[Ref.: #120918]	nitrate ChEBI	-	reduction
[Ref.: #120918]	nitrate ChEBI	-	respiration
[Ref.: #120918]	nitrite ChEBI	-	reduction

	Antibiotica	Metabolite	Antibiotic sensitivity	Antibiotic resistance
[Ref.: #120918]		0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)	no	yes

	Metabolite production	Metabolite	Production
[Ref.: #120918]		indole ChEBI	no

	Physiological tests	Metabolite	Voges-Proskauer-test	Methylred-test
[Ref.: #120918]		acetoin ChEBI	-
[Ref.: #120918]		glucose ChEBI		-

	Enzyme	Enzyme activity	EC number
[Ref.: #68382]	acid phosphatase	+	3.1.3.2	* from API zym
[Ref.: #120918]	alcohol dehydrogenase	-	1.1.1.1
[Ref.: #68382]	alkaline phosphatase	+	3.1.3.1	* from API zym
[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.: #68382]	alpha-glucosidase	+	3.2.1.20	* from API zym
[Ref.: #68382]	alpha-mannosidase	-	3.2.1.24	* from API zym
[Ref.: #120918]	amylase	+
[Ref.: #120918]	beta-galactosidase	+	3.2.1.23
[Ref.: #68382]	beta-galactosidase	-	3.2.1.23	* from API zym
[Ref.: #68382]	beta-glucosidase	-	3.2.1.21	* from API zym
[Ref.: #68382]	beta-glucuronidase	-	3.2.1.31	* from API zym
[Ref.: #120918]	caseinase	+	3.4.21.50
[Ref.: #120918]	catalase	+	1.11.1.6
[Ref.: #68382]	cystine arylamidase	-	3.4.11.3	* from API zym
[Ref.: #120918]	DNase	+
[Ref.: #68382]	esterase (C 4)	+		* from API zym
[Ref.: #68382]	esterase lipase (C 8)	+		* from API zym
[Ref.: #120918]	gamma-glutamyltransferase	-	2.3.2.2
[Ref.: #120918]	gelatinase	+
[Ref.: #120918]	lecithinase	-
[Ref.: #68382]	leucine arylamidase	+	3.4.11.1	* from API zym
[Ref.: #120918]	lipase	-
[Ref.: #68382]	lipase (C 14)	-		* from API zym
[Ref.: #120918]	lysine decarboxylase	-	4.1.1.18
[Ref.: #68382]	N-acetyl-beta-glucosaminidase	-	3.2.1.52	* from API zym
[Ref.: #68382]	naphthol-AS-BI-phosphohydrolase	+		* from API zym
[Ref.: #120918]	ornithine decarboxylase	-	4.1.1.17
[Ref.: #120918]	oxidase	-
[Ref.: #120918]	phenylalanine ammonia-lyase	-	4.3.1.24
[Ref.: #120918]	protease	+
[Ref.: #68382]	trypsin	-	3.4.21.4	* from API zym
[Ref.: #120918]	tryptophan deaminase	-
[Ref.: #120918]	tween esterase	-
[Ref.: #120918]	urease	+	3.5.1.5
[Ref.: #68382]	valine arylamidase	-		* from API zym
	Only first 10 entries are displayed. Click here to see all.

API® Biotype100:

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

	API ID	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
[Ref.: #120918]	2431	not determinedn.d.	+	+	+	+	+	-	-	+	-	+	+	+	-	-	-	+	+	-	+	+	+	+	-	+	-	-	-	-	-	-	-	+	-	+	-	+	-	-	-	-	-	-	-	-	-	-	-	-	+	+	+	-	-	+	-	-	-	-	-	-	+	+	+	+	-	-	-	-	-	-	-	-	+	-	-	+	-	-	-	+	+	-	-	-	-	-	-	-	+	+	+	+	-	+	+	+	-	+	+

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.: #120918]	10648	-	+	+	+	-	+	-	-	-	+	+	+	-	-	-	+	-	-	-	-

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

[Ref.: #11913]	Sample type/isolated from	alkaline slag dump of metallurgical processing
[Ref.: #11913]	Country	Germany
[Ref.: #11913]	Country ISO 3 Code	DEU
[Ref.: #11913]	Continent	Europe

[Ref.: #67770]	Sample type/isolated from	Alkaline slag dump associated with metallurgical processing
[Ref.: #67770]	Country	Germany
[Ref.: #67770]	Country ISO 3 Code	DEU
[Ref.: #67770]	Continent	Europe

[Ref.: #120918]	Sample type/isolated from	Alkaline slag dump of metallurgical processing
[Ref.: #120918]	Country	Germany
[Ref.: #120918]	Country ISO 3 Code	DEU
[Ref.: #120918]	Continent	Europe
* marker position based on {}

Isolation sources categories

#Engineered	#Industrial	-
#Condition	#Alkaline	-

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence AJ420769 (>99% sequence identity) for Nocardiopsis from Microbeatlas

Aquatic Samples	1
Soil Samples	2
Animal Samples	23
Plant Samples
Total Samples	26

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

[Ref.: #11913]	Biosafety level	1	Risk group (German classification) According to TRBA 466
[Ref.: #120918]	Biosafety level	1	Risk group (French classification)

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.: #11913]	Nocardiopsis metallicus partial 16S rRNA gene, strain R2A	AJ420769	1488	ENA	179819 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Nocardiopsis metallicus DSM 44598	GCA_014201115	contig	GenBank	179819 tax ID	*
[Ref.: #66792]	Nocardiopsis metallicus strain DSM 44598	179819.3	wgs	PATRIC	179819 tax ID	*
[Ref.: #66792]	Nocardiopsis metallicus DSM 44598	2856454764	draft	JGI IMG/M	179819 tax ID	*

[Ref.: #11913]	GC-content	70.8 mol%
[Ref.: #67770]	GC-content	70.8 mol%	high performance liquid chromatography (HPLC)

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: Nocardiopsis metallicus strain DSM 44598 PATRIC: 179819.3
[Ref.: #69481]	spore-forming	yes	100	no

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Nocardiopsis metallicus strain DSM 44598 PATRIC: 179819.3
[Ref.: #69480]	motile	no	92.9	no
[Ref.: #69480]	gram-positive	yes	93.707	no
[Ref.: #69480]	anaerobic	no	99.213	no
[Ref.: #69480]	aerobic	yes	94.017	no
[Ref.: #69480]	halophile	yes	59.267	no
[Ref.: #69480]	spore-forming	yes	94.07	no
[Ref.: #69480]	glucose-util	yes	87.194	no
[Ref.: #69480]	flagellated	no	97.845	no
[Ref.: #69480]	thermophile	no	98.797	yes
[Ref.: #69480]	glucose-ferment	no	93.134	no

Availability in culture collections External links

[Ref.: #11913]

Culture collection no.

DSM 44598, CIP 107788, KBS 6, NRRL B-24159, JCM 12409, BCRC 16377, CGMCC 4.2089, NBRC 101841, VKM Ac-2522

[Ref.: #80454]

SI-ID 100826

Literature:

Topic	Title	Authors	Journal	DOI	Year
Enzymology	New structures and composition of cell wall teichoic acids from Nocardiopsis synnemataformans, Nocardiopsis halotolerans, Nocardiopsis composta and Nocardiopsis metallicus: a chemotaxonomic value.	Tul'skaya EM, Shashkov AS, Streshinskaya GM, Potekhina NV, Evtushenko LI	Antonie Van Leeuwenhoek	10.1007/s10482-014-0280-7	2014	*
Phylogeny	Nocardiopsis metallicus sp. nov., a metal-leaching actinomycete isolated from an alkaline slag dump.	Schippers A, Bosecker K, Willscher S, Sproer C, Schumann P, Kroppenstedt RM	Int J Syst Evol Microbiol	10.1099/00207713-52-6-2291	2002	*

References

#11913

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 44598

#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 )

#39943 ; 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 .

#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 .

#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 )

#80454

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-ID100826.1 )

#120918 Collection of Institut Pasteur ; Curators of the CIP; CIP 107788
* These data were automatically processed and therefore are not curated

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Nocardiopsis metallicus strain DSM 44598

Nocardiopsis metallicus strain DSM 44598

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