Streptomyces rubradiris (DSM 40789, CBS 566.70, JCM 4955)

Name: Streptomyces rubradiris (DSM 40789, CBS 566.70, JCM 4955)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 14882

Type strain

Culture col. no. DSM 40789 CBS 566.70 JCM 4955 NRRL 3061 CECT 3075 6 more

NCBI tax ID(s) 285531

Special Collections DSMZ JCM KCTC

History DSMZ <- NRRL JCM <-- KCC S-0955 <-- DSM 40789 <-- NRRL 3061 <-- Upjohn Co., USA; UC 2630.

Links

Streptomyces rubradiris DSM 40789 is a bacterium of the family Streptomycetaceae.

genome sequence 16S sequence Bacteria

Name and taxonomic classification

SI-ID 49801

JCM 4955,NRRL 3061,IFO 14000,NCIMB 9516,CBS 566.70,CECT 3075,NRRL B-3061,KCTC 9742,AS 4.1601,NBRC 14000,CGMCC 4.1601,DSM 40789

@ref 20215

Last LPSN update 2026-05-29 08:28:23

Domain Bacteria

Phylum Actinomycetota

Class Actinomycetes

Order Kitasatosporales

Family Streptomycetaceae

Genus Streptomyces

Species Streptomyces rubradiris

Full scientific name Streptomyces rubradiris (Bhuyan et al. 1965) Komaki and Tamura 2021

Synonyms (1)

Streptomyces achromogenes subsp. rubradiris

Morphology

Cell morphology

@ref	Gram stain	Confidence	Motility
125439	positive	98.614
125439		92.03

Culture and growth conditions

Culture medium

@ref	Name	Medium link	Composition
9797	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
9797	STARCH - MINERAL SALT - AGAR (STMS) (DSMZ Medium 252)	Medium recipe at MediaDive	Name: STARCH - MINERAL SALT - AGAR (STMS) (DSMZ Medium 252) Composition: Agar 20.0 g/l Starch 10.0 g/l (NH4)2SO4 2.0 g/l CaCO3 2.0 g/l K2HPO4 1.0 g/l MgSO4 x 7 H2O 1.0 g/l NaCl 1.0 g/l FeSO4 x 7 H2O 0.001 g/l MnCl2 x 4 H2O 0.001 g/l ZnSO4 x 7 H2O 0.001 g/l Distilled water
9797	ROLLED OATS MINERAL MEDIUM (DSMZ Medium 84)	Medium recipe at MediaDive	Name: ROLLED OATS MINERAL MEDIUM (DSMZ Medium 84) Composition: Agar 20.0 g/l Rolled oats 20.0 g/l ZnSO4 x 7 H2O 0.001 g/l MnCl2 x 4 H2O 0.001 g/l FeSO4 x 7 H2O 0.001 g/l Distilled water

Culture temp

@ref	Growth	Type	Temperature (°C)
9797	positive	growth	28
67770	positive	growth	28

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
125438	aerobe	91.027
125439	obligate aerobe	97.774

Spore formation

@ref	Spore formation	Confidence
125438		92.259

Compound production

9797

Compoundrubradirin

Metabolite production

@ref	Metabolite	Production
67770	rubradirin

Isolation, sampling and environmental information

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
9797	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	Streptomyces achromogenes rubradiris NRRL 3061	complete			2582581335	285531	90.12
66792	ASM1686052v1 assembly for Streptomyces rubradiris NBRC 14000	contig	GCA_016860525	285531.4	8110419219	285531	74.67
66792	ASM1465625v1 assembly for Streptomyces rubradiris JCM 4955	scaffold	GCA_014656255	285531.3	8110883459	285531	63.21

16S sequences

@ref	Description	Accession	Length	NCBI tax ID
20218	Streptomyces achromogenes subsp. rubradiris strain KCTC 9742 16S ribosomal RNA gene, partial sequence	AY999846	1420	285531
20218	Streptomyces achromogenes subsp. rubradiris gene for 16S rRNA, partial sequence, strain: NBRC 14000	AB184561	1459	285531
124043	Streptomyces achromogenes subsp. rubradiris strain JCM 4955 16S ribosomal RNA gene, partial sequence.	MT760636	1399	285531

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: ASM1686052v1 assembly for Streptomyces rubradiris NBRC 14000
NCBI: GCA_016860525

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	97.77	no
125439	motility	BacteriaNetⓘ	no	92.03	no
125439	gram_stain	BacteriaNetⓘ	positive	98.61	no
125439	spore_formation	BacteriaNetⓘ	yes	83.11	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Streptomyces achromogenes subsp. rubradiris strain JCM 4955
PATRIC: 285531.3

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	yes	86.52	no
125438	anaerobic	anaerobicⓘ	no	97.40	no
125438	spore-forming	spore-formingⓘ	yes	92.26	no
125438	aerobic	aerobicⓘ	yes	91.03	no
125438	thermophilic	thermophileⓘ	no	96.49	yes
125438	flagellated	motile2+ⓘ	no	87.60	no

Literature

Title	Authors	Journal	DOI	Year
DNA amplification in Streptomyces achromogenes subsp. rubradiris is accompanied by a deletion, and the amplified sequences are conditionally stable and can be eliminated by two pathways.	Hornemann U, Otto CJ, Zhang XY.	J Bacteriol	10.1128/jb.171.11.5817-5822.1989	1989
Spectinomycin resistance and associated DNA amplification in Streptomyces achromogenes subsp. rubradiris.	Hornemann U, Otto CJ, Hoffman GG, Bertinuson AC.	J Bacteriol	10.1128/jb.169.6.2360-2366.1987	1987
Streptomyces argyrophyllae sp. nov., isolated from the rhizosphere soil of Cathaya argyrophylla.	Mo P, Zhou F, Luo X, Zhang Y, Deng A, Xie P, Wang Y.	Arch Microbiol	10.1007/s00203-023-03668-9	2023

References

#9797	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 40789
#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 )
#20218	Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P.: StrainInfo introduces electronic passports for microorganisms.. Syst Appl Microbiol. 37: 42 - 50 2014 ( DOI 10.1016/j.syapm.2013.11.002 , PubMed 24321274 )
#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;
#124043	Isabel Schober, Julia Koblitz: Data extracted from sequence databases, automatically matched based on designation and taxonomy .
#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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Streptomyces rubradiris (DSM 40789, CBS 566.70, JCM 4955)

Name and taxonomic classification

Morphology

Cell morphology

Culture and growth conditions

Culture medium

Culture temp

Physiology and metabolism

Oxygen tolerance

Spore formation

Compound production

Metabolite production

Isolation, sampling and environmental information

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_016860525

16S sequences

Genome-based predictions

Predictions

Literature

Literature

References

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