Name: Nocardioides rubriscoriae Sco-A25
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 130492

Type strain:

Species: Nocardioides rubriscoriae

Strain Designation: Sco-A25

Culture col. no.: DSM 23986, KCTC 19805, NBRC 107916

Strain history: <- SD Lee, Cheju Univ.

NCBI tax ID(s): 642762 (species)

SI-ID 399824

DSM 23986

Section

Nocardioides rubriscoriae Sco-A25 is an aerobe, mesophilic, Gram-positive bacterium that was isolated from red-coloured layer of scoria from a parasitic volcano.

Gram-positive
aerobe
mesophilic
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 rubriscoriae**
	Full Scientific Name (LPSN)	Nocardioides rubriscoriae corrig. Lee and Lee 2014

Synonym

Nocardioides rubroscoriae

Information on morphological and physiological properties Morphology

[Ref.: #67771]	Gram stain	positive
[Ref.: #69480]	Gram stain	positive Confidence in %99.999

Information on culture and growth conditions Culture and growth conditions

[Ref.: #21695]

Culture medium

GYM STREPTOMYCES MEDIUM (DSMZ Medium 65)

[Ref.: #21695]

Culture medium growth

[Ref.: #21695]

Culture medium link

Medium recipe at MediaDive

[Ref.: #21695]

Culture medium composition

expand / minimize

	Temperatures	Kind of temperature		Temperature
[Ref.: #21695]			growth	28 °C
[Ref.: #67771]			growth	30 °C

[Ref.: #21695]	Temperature range	mesophilic
[Ref.: #67771]	Temperature range	mesophilic

Information on physiology and metabolism Physiology and metabolism

[Ref.: #67771]

Oxygen tolerance

aerobe

[Ref.: #69480]

Ability of spore formation

no Confidence in %99.973

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

[Ref.: #21695]	Sample type/isolated from	red-coloured layer of scoria (volcanic ash) from a parasitic volcano
[Ref.: #21695]	Geographic location (country and/or sea, region)	Jeju
[Ref.: #21695]	Country	Republic of Korea
[Ref.: #21695]	Country ISO 3 Code	KOR
[Ref.: #21695]	Continent	Asia

[Ref.: #67771]	Sample type/isolated from	From volcanic ash (scoria)
[Ref.: #67771]	Geographic location (country and/or sea, region)	Jeju
[Ref.: #67771]	Country	Republic of Korea
[Ref.: #67771]	Country ISO 3 Code	KOR
[Ref.: #67771]	Continent	Asia
* marker position based on {}

Isolation sources categories

#Environmental	#Terrestrial	#Dust
#Environmental	#Terrestrial	#Volcanic

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence FN386714 (>99% sequence identity) for Nocardioides rubriscoriae from Microbeatlas

Aquatic Samples	9
Soil Samples	13
Animal Samples	17
Plant Samples	19
Total Samples	58

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

[Ref.: #21695]

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.: #21695]	Nocardioides rubriscoriae partial 16S rRNA gene, type strain Sco-A25T	FN386714	1415	ENA	642762 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Nocardioides rubriscoriae DSM 23986	GCA_008087085	contig	GenBank	642762 tax ID	*
[Ref.: #66792]	Nocardioides rubriscoriae strain DSM 23986	642762.3	wgs	PATRIC	642762 tax ID	*
[Ref.: #66792]	Nocardioides rubriscoriae DSM 23986	2899979250	draft	JGI IMG/M	642762 tax ID	*

[Ref.: #21695]

GC-content

71.6 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: Nocardioides rubriscoriae strain DSM 23986 PATRIC: 642762.3
[Ref.: #69481]	spore-forming	no	57	no

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Nocardioides rubriscoriae strain DSM 23986 PATRIC: 642762.3
[Ref.: #69480]	gram-positive	yes	90.515	yes
[Ref.: #69480]	anaerobic	no	98.238	no
[Ref.: #69480]	halophile	no	96.871	no
[Ref.: #69480]	spore-forming	no	77.011	no
[Ref.: #69480]	glucose-util	yes	86.698	no
[Ref.: #69480]	thermophile	no	97.918	yes
[Ref.: #69480]	flagellated	no	94.175	no
[Ref.: #69480]	aerobic	yes	89.415	yes
[Ref.: #69480]	motile	no	76.41	no
[Ref.: #69480]	glucose-ferment	no	88.033	no

Availability in culture collections External links

[Ref.: #21695]

Culture collection no.

DSM 23986, KCTC 19805, NBRC 107916

[Ref.: #89016]

SI-ID 399824

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Nocardioides dongxiaopingii sp. nov., isolated from leaves of Lamiophlomis rotata on the Qinghai-Tibet Plateau.	Zhang S, Wang X, Yang J, Lu S, Lai XH, Jin D, Huang Y, Zhu W, Li J, Pu J, Huang Y, Tian Z, Dong K, Zhang G, Lei W, Wang S, Xu J	Int J Syst Evol Microbiol	10.1099/ijsem.0.004161	2020	*
Phylogeny	Nocardioides litoris sp. nov., isolated from the Taean seashore.	Lee DW, Lee AH, Lee H, Kim JJ, Khim JS, Yim UH, Kim BS	Int J Syst Evol Microbiol	10.1099/ijsem.0.001954	2017	*
Phylogeny	Nocardioides rubroscoriae sp. nov., isolated from volcanic ash.	Lee SD, Lee DW	Antonie Van Leeuwenhoek	10.1007/s10482-014-0161-0	2014	*

References

#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 )

#21695

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 23986

#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) .

#67771 Korean Collection for Type Cultures (KCTC) ; Curators of the KCTC;

#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 )

#89016

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-ID399824.1 )

* These data were automatically processed and therefore are not curated

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Nocardioides rubriscoriae strain DSM 23986

Nocardioides rubriscoriae strain DSM 23986

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