Nocardioides scoriae (DSM 22127, KCTC 19597, Sco-D01)

Name: Nocardioides scoriae (DSM 22127, KCTC 19597, Sco-D01)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 11088

Type strain

Strain Designation Sco-D01

Culture col. no. DSM 22127 KCTC 19597 Sco-D01 JCM 17444

NCBI tax ID(s) 642780

Special Collections DSMZ JCM KCTC Wink compendium

Links

Nocardioides scoriae Sco-D01 is a mesophilic prokaryote that was isolated from volcanic ash.

mesophilic genome sequence 16S sequence

Name and taxonomic classification

SI-ID 396522

JCM 17444,KCTC 19597,DSM 22127

@ref 20215

Last LPSN update 2025-12-16 09:49:30

Domain Bacillati

Phylum Actinomycetota

Class Actinomycetes

Order Propionibacteriales

Family Nocardioidaceae

Genus Nocardioides

Species Nocardioides scoriae

Full scientific name Nocardioides scoriae (Lee and Lee 2010) Wang et al. 2023

Synonyms (1)

Marmoricola scoriae

Morphology

Cell morphology

@ref	Gram stain	Confidence
125438	positive	90.274
125439	positive	98.4

Colony morphology

@ref	Colony color	Incubation period	Medium used
19799	Maize yellow	10-14 days	ISP 2
19799	Beige	10-14 days	ISP 3
19799	Beige	10-14 days	ISP 4
19799	Light ivory	10-14 days	ISP 5
19799	Sand yellow	10-14 days	ISP 6
19799	Oxide red	10-14 days	ISP 7

Multicellular morphology

@ref	Forms multicellular complex	Medium name
19799		ISP 2
19799		ISP 3
19799		ISP 4
19799		ISP 5
19799		ISP 6
19799		ISP 7

Culture and growth conditions

Culture medium

@ref	Name	Medium link	Composition
16147	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
19799	ISP 2		Name: ISP 2 / Yeast Malt Agar (5265); 5265 Composition Malt extract 10.0 g/l Yeast extract 4.0 g/l Glucose 4.0 g/l Agar 15.0 g/l Preparation: Sterilisation: 20 minutes at 121°C pH before sterilisation: 7.0 Usage: Maintenance and Taxonomy Organisms: All Actinomycetes
19799	ISP 3		Name: ISP 3; 5315 Composition Dog oat flakes 20.0 g/l Trace element solution (5314) 2.5 ml/l Agar 18.0 g/l Preparation: Oat flakes are cooked for 20 minutes, trace element solution and agar are added (in the case of non rolled oat flakes the suspension has to bee filtrated). Sterilisation: 20 minutes at 121°C pH before sterilisation: 7.8 Usage: Maintenance and taxonomy (e.g. SEM As liquid medium for metabolite production) Organisms: All Actinomycetes Trace element solution 5314 Name: Trace element solution 5314; 5314 Composition CaCl2 x H2O 3.0 g/l Fe-III-citrate 1.0 g/l MnSO4 0.2 g/l ZnCl2 0.1 g/l CuSO4 x 5 H2O 0.025 g/l Sodium tetra borate 0.2 g/l CoCl2 x 6 H2O 0.004 g/l Sodium molybdate 0.01 g/l Preparation: Use double destillated water. Sterilisation: 20 minutes at 121°C pH before sterilisation: Usage: Trace element solution for different media Organisms:
19799	ISP 4		Name: ISP 4; DSM 547 Solution I: Difco soluble starch, 10.0 g. Make a paste of the starch with a small amount of cold distilled water and bring to a volume of 500 ml. Solution II: CaCO3 2.0 g K2HPO4 (anhydrous) 1.0 g MgSO4 x 7 H2O 1.0 g NaCl 1.0 g (NH4)2SO4 2.0 g Distilled water 500.0 ml Trace salt solution (see below) 1.0 ml The pH should be between 7.0 and 7.4. Do not adjust if it is within this range. Mix solutions I and II together. Add 20.0 g agar. Liquify agar by steaming at 100°C for 10 to 20 min. Trace element solution: FeSO4 x 7 H2O 0.1 g MnCl2 x 4 H2O 0.1 g ZnSO4 x 7 H2O 0.1 g Distilled water 100.0 ml
19799	ISP 5		Name: ISP 5 (5323) Composition L-Asparagine 1.0 g/l Glycerol 10.0 g/l K2HPO4 1.0 g/l Salt solution (see preparation) 1.0 ml/l Agar 20.0 g/l Preparation: Salt solution 1.0 g FeSO4 x 7 H2O 1.0 g MnCl2 x 4 H2O 1.0 g ZNSO4 x 7 H2O in 100 ml water Sterilisation: 20 minutes at 121°C pH before sterilisation: 7.2 Usage: Maintenance and taxonomy Organisms: All Actinomycetes
19799	ISP 6		Name: ISP 6 (5318) Composition Peptone 15.0 g/l Proteose peptose 5.0 g/l Ferric ammonium citrate 0.5 g/l Sodium glycerophosphate 1.0 g/l Sodium thiosulfate 0.08 g/l Yeast extract 1.0 g/l Agar 15.0 g/l Sterilisation: 20 minutes at 121°C pH before sterilisation: Usage: Production of melanoid pigments Organisms: All Actinomycetes
19799	ISP 7		Name: ISP 7 (5322) Composition Glycerol 15.0 g/l L-Tyrosine 0.5 g/l L-Asparagine 1.0 g/l K2HPO4 0.5 g/l NaCl 0.5 g/l FeSO4 x 7 H2O 0.01 g/l Trace element solution 5343 1.0 ml/l Agar 20.0 Sterilisation: 20 minutes at 121°C pH before sterilisation: 7.3 Usage: Production of melanoid pigments Organisms: All Actinomycetes
16147	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

Culture temp

@ref	Growth	Type	Temperature (°C)	Range
16147	positive	growth	28	mesophilic
19799	positive	optimum	28	mesophilic
67770	positive	growth	28	mesophilic

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
125438	aerobe	92.237
125439	obligate aerobe	99.1

Observation

67770

Observationquinones: MK-8(H₄)

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity
19799	22599 ChEBI	arabinose	+/-
19799	62968 ChEBI	cellulose	+/-
19799	28757 ChEBI	fructose	+/-
19799	17234 ChEBI	glucose	+/-
19799	29864 ChEBI	mannitol	+/-
19799	17268 ChEBI	myo-inositol	+/-
19799	16634 ChEBI	raffinose	+/-
19799	26546 ChEBI	rhamnose	+/-
19799	17992 ChEBI	sucrose	+/-
19799	18222 ChEBI	xylose	+/-

Enzymes

@ref	Value	Activity	Ec
68382	acid phosphatase	+	3.1.3.2	from API zym
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
68382	beta-galactosidase	-	3.2.1.23	from API zym
68382	beta-glucosidase	+	3.2.1.21	from API zym
68382	beta-glucuronidase	-	3.2.1.31	from API zym
68382	cystine arylamidase	+	3.4.11.3	from API zym
68382	esterase (C 4)	-		from API zym
68382	esterase lipase (C 8)	+		from API zym
68382	leucine arylamidase	+	3.4.11.1	from API zym
68382	lipase (C 14)	+		from API zym
68382	N-acetyl-beta-glucosaminidase	-	3.2.1.52	from API zym
68382	naphthol-AS-BI-phosphohydrolase	+		from API zym
68382	trypsin	+	3.4.21.4	from API zym
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
19799	not determinedn.d.	+	-	+	+	+	+	+	+	-	+	+	-	-	-	+	+	-	-	-

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Environmental	#Terrestrial	#Dust
#Environmental	#Terrestrial	#Volcanic

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent
16147	volcanic ash	Jeju Island, Oreum (a parasitic volcano)	Republic of Korea	KOR	Asia
67770	Volcanic ash	Jeju	Republic of Korea	KOR	Asia

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
16147	1	Risk group (German 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	IMG-taxon 2634166904 annotated assembly for Nocardioides scoriae DSM 22127	chromosome	GCA_900104965	642780.3	2634166904	642780	86.76

Genome browser: GCA_900104965

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
16147	Marmoricola scoriae partial 16S rRNA gene, type strain Sco-D01T	FN386750	1425		642780

GC content

@ref	GC-content (mol%)	Method
16147	72.0	high performance liquid chromatography (HPLC)
67770	72	high performance liquid chromatography (HPLC)
67770	73.5	genome sequence analysis

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Marmoricola scoriae DSM 22127
IMG: 2634166904

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	no	81.20	no
125439	motility	BacteriaNetⓘ	no	62.70	no
125439	gram_stain	BacteriaNetⓘ	positive	98.40	no
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	99.10	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Marmoricola scoriae strain DSM 22127
PATRIC: 642780.3

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	yes	90.27	no
125438	anaerobic	anaerobicⓘ	no	98.89	no
125438	aerobic	aerobicⓘ	yes	92.24	no
125438	spore-forming	spore-formingⓘ	no	59.53	no
125438	thermophilic	thermophileⓘ	no	96.59	yes
125438	flagellated	motile2+ⓘ	no	71.50	no

Literature

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Nocardioides echinoideorum sp. nov., isolated from sea urchins (Tripneustes gratilla).	Lin SY, Wen CZ, Hameed A, Liu YC, Hsu YH, Shen FT, Lai WA, Young CC	Int J Syst Evol Microbiol	10.1099/ijs.0.000206	2015
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

References

#16147	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 22127
#19799	Wink, J.: Compendium of Actinobacteria. HZI-Helmholtz-Centre for Infection Research, Braunschweig .
#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 )
#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 .
#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 scoriae (DSM 22127, KCTC 19597, Sco-D01)

Name and taxonomic classification

Morphology

Cell morphology

Colony morphology

Multicellular morphology

Culture and growth conditions

Culture medium

Culture temp

Physiology and metabolism

Oxygen tolerance

Observation

Metabolite utilization

Enzymes

API zym

Isolation, sampling and environmental information

Isolation source categories

Isolation

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_900104965

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

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