Nocardioides rubriscoriae (DSM 23986, KCTC 19805, NBRC 107916)

Name: Nocardioides rubriscoriae (DSM 23986, KCTC 19805, NBRC 107916)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 130492

Type strain

Strain Designation Sco-A25

Culture col. no. DSM 23986 KCTC 19805 NBRC 107916 Sco-A25

NCBI tax ID(s) 642762

Special Collections DSMZ KCTC

History <- S. D. Lee, Jeju National Univ., Rep. of Korea; Sco-A25 <- D. W. Lee <- SD Lee, Cheju Univ.

Links

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

Gram-positive aerobe genome sequence 16S sequence Bacteria

Name and taxonomic classification

SI-ID 399824

KCTC 19805,NBRC 107916,DSM 23986

@ref 20215

Last LPSN update 2026-02-09 11:31:14

Domain Bacteria

Phylum Actinomycetota

Class Actinomycetes

Order Propionibacteriales

Family Nocardioidaceae

Genus Nocardioides

Species Nocardioides rubriscoriae

Full scientific name Nocardioides rubriscoriae corrig. Lee and Lee 2014

Synonyms (1)

Nocardioides rubroscoriae

Morphology

Cell morphology

@ref	Gram stain	Confidence
67771	positive
125439	positive	99.4

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
21695	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

Culture temp

@ref	Growth	Type	Temperature (°C)
21695	positive	growth	28
67771	positive	growth	30

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
67771	aerobe
125439	obligate aerobe	95.6

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
21695	red-coloured layer of scoria (volcanic ash) from a parasitic volcano	Jeju	Republic of Korea	KOR	Asia
67771	From volcanic ash (scoria)	Jeju	Republic of Korea	KOR	Asia

Taxonmaps

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

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
21695	1	Risk group (German classification)

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
66792	ASM808708v1 assembly for Nocardioides rubriscoriae DSM 23986	contig	GCA_008087085	642762.3	2899979250	642762	72.82

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
21695	Nocardioides rubriscoriae partial 16S rRNA gene, type strain Sco-A25T	FN386714	1415		642762

GC content

@ref	GC-content (mol%)	Method
21695	71.6	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: Nocardioides rubriscoriae DSM 23986
NCBI: GCA_008087085

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	no	69.40	no
125439	motility	BacteriaNetⓘ	no	75.80	no
125439	gram_stain	BacteriaNetⓘ	positive	99.40	no
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	95.60	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Nocardioides rubriscoriae strain DSM 23986
PATRIC: 642762.3

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	yes	88.74	yes
125438	anaerobic	anaerobicⓘ	no	96.23	no
125438	aerobic	aerobicⓘ	yes	87.91	no
125438	spore-forming	spore-formingⓘ	no	56.33	no
125438	thermophilic	thermophileⓘ	no	93.71	no
125438	flagellated	motile2+ⓘ	no	64.37	no

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 .
#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 rubriscoriae (DSM 23986, KCTC 19805, NBRC 107916)

Name and taxonomic classification

Morphology

Cell morphology

Culture and growth conditions

Culture medium

Culture temp

Physiology and metabolism

Oxygen tolerance

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_008087085

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

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