Streptomyces rubidus (DSM 41947, CGMCC 4.2026, JCM 13277)

Name: Streptomyces rubidus (DSM 41947, CGMCC 4.2026, JCM 13277)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 16431

Type strain

Strain Designation 13c15

Culture col. no. DSM 41947 CGMCC 4.2026 JCM 13277 13c15 NRRL B-24619 2 more

NCBI tax ID(s) 310780

Special Collections DSMZ JCM CIP Literature strains

Links

Streptomyces rubidus 13c15 is an aerobe, spore-forming, mesophilic prokaryote that was isolated from pine forest soil.

spore-forming Gram-positive rod-shaped aerobe mesophilic genome sequence 16S sequence

Name and taxonomic classification

SI-ID 291639

CGMCC 4.2026,JCM 13277,CIP 109249,NBRC 102073,DSM 41947

@ref 20215

Last LPSN update 2025-12-16 09:50:51

Domain Bacillati

Phylum Actinomycetota

Class Actinomycetes

Order Kitasatosporales

Family Streptomycetaceae

Genus Streptomyces

Species Streptomyces rubidus

Full scientific name Streptomyces rubidus Xu et al. 2006

Synonyms (1)

Actinacidiphila rubida

Morphology

Cell morphology

@ref	Gram stain	Cell shape	Confidence
31645	positive	rod-shaped
125438	positive		90.5
125439	positive		99.9
125439			92.7

Pigmentation

31645

Productionyes

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
15750	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
15750	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)	Range
15750	positive	growth	28	mesophilic
31645	positive	growth	20-37
31645	positive	optimum	30-37	mesophilic
67770	positive	growth	28	mesophilic

Culture pH

@ref	Ability	Type	PH
31645	positive	optimum	5.5-7
31645	positive	growth	4.5-7

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
31645	aerobe
125438	aerobe	92.233
125439	obligate aerobe	99.2

Spore formation

@ref	Spore formation	Confidence
31645
125438		90.902
125439		94.3

Observation

@ref	Observation
31645	aggregates in chains
67770	quinones: MK-9(H₆), MK-9(H₈)

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
31645	16449 ChEBI	alanine	+	carbon source
31645	29016 ChEBI	arginine	+	carbon source
31645	17057 ChEBI	cellobiose	+	carbon source
31645	4853 ChEBI	esculin	+	hydrolysis
31645	28260 ChEBI	galactose	+	carbon source
31645	17234 ChEBI	glucose	+	carbon source
31645	17716 ChEBI	lactose	+	carbon source
31645	29864 ChEBI	mannitol	+	carbon source
31645	17814 ChEBI	salicin	+	carbon source

Pathway annotation

Computationally determined by

@ref	pathway	enzyme coverage	annotated reactions
66794	acetate fermentation	100	4 of 4
66794	kanosamine biosynthesis II	100	2 of 2
66794	ethanol fermentation	100	2 of 2
66794	pentose phosphate pathway	100	11 of 11
66794	phenylacetate degradation (aerobic)	100	5 of 5
66794	glycolate and glyoxylate degradation	100	6 of 6
66794	adipate degradation	100	2 of 2
66794	enterobactin biosynthesis	100	3 of 3
66794	ribulose monophosphate pathway	100	2 of 2
66794	formaldehyde oxidation	100	3 of 3
66794	glycogen metabolism	100	5 of 5
66794	1,4-dihydroxy-6-naphthoate biosynthesis	100	6 of 6
66794	myo-inositol biosynthesis	100	10 of 10
66794	palmitate biosynthesis	100	22 of 22
66794	threonine metabolism	100	10 of 10
66794	ppGpp biosynthesis	100	4 of 4
66794	methylglyoxal degradation	100	5 of 5
66794	valine metabolism	100	9 of 9
66794	cardiolipin biosynthesis	100	7 of 7
66794	cis-vaccenate biosynthesis	100	2 of 2
66794	metabolism of amino sugars and derivatives	100	5 of 5
66794	starch degradation	100	10 of 10
66794	biotin biosynthesis	100	4 of 4
66794	coenzyme A metabolism	100	4 of 4
66794	aerobactin biosynthesis	100	1 of 1
66794	UDP-GlcNAc biosynthesis	100	3 of 3
66794	folate polyglutamylation	100	1 of 1
66794	anapleurotic synthesis of oxalacetate	100	1 of 1
66794	suberin monomers biosynthesis	100	2 of 2
66794	CDP-diacylglycerol biosynthesis	100	2 of 2
66794	cellulose degradation	100	5 of 5
66794	heme metabolism	92.86	13 of 14
66794	leucine metabolism	92.31	12 of 13
66794	phenylalanine metabolism	92.31	12 of 13
66794	proline metabolism	90.91	10 of 11
66794	Entner Doudoroff pathway	90	9 of 10
66794	chorismate metabolism	88.89	8 of 9
66794	molybdenum cofactor biosynthesis	88.89	8 of 9
66794	serine metabolism	88.89	8 of 9
66794	NAD metabolism	88.89	16 of 18
66794	isoleucine metabolism	87.5	7 of 8
66794	C4 and CAM-carbon fixation	87.5	7 of 8
66794	dTDPLrhamnose biosynthesis	87.5	7 of 8
66794	gluconeogenesis	87.5	7 of 8
66794	photosynthesis	85.71	12 of 14
66794	reductive acetyl coenzyme A pathway	85.71	6 of 7
66794	aclacinomycin biosynthesis	85.71	6 of 7
66794	ubiquinone biosynthesis	85.71	6 of 7
66794	urea cycle	84.62	11 of 13
66794	alanine metabolism	82.76	24 of 29
66794	purine metabolism	81.91	77 of 94
66794	metabolism of disaccharids	81.82	9 of 11
66794	methionine metabolism	80.77	21 of 26
66794	3-chlorocatechol degradation	80	4 of 5
66794	flavin biosynthesis	80	12 of 15
66794	factor 420 biosynthesis	80	4 of 5
66794	peptidoglycan biosynthesis	80	12 of 15
66794	ethylmalonyl-CoA pathway	80	4 of 5
66794	gallate degradation	80	4 of 5
66794	vitamin B12 metabolism	79.41	27 of 34
66794	histidine metabolism	79.31	23 of 29
66794	citric acid cycle	78.57	11 of 14
66794	glutamate and glutamine metabolism	78.57	22 of 28
66794	tetrahydrofolate metabolism	78.57	11 of 14
66794	allantoin degradation	77.78	7 of 9
66794	degradation of hexoses	77.78	14 of 18
66794	d-mannose degradation	77.78	7 of 9
66794	aspartate and asparagine metabolism	77.78	7 of 9
66794	lipid metabolism	77.42	24 of 31
66794	glycolysis	76.47	13 of 17
66794	pyrimidine metabolism	75.56	34 of 45
66794	glycogen biosynthesis	75	3 of 4
66794	degradation of aromatic, nitrogen containing compounds	75	9 of 12
66794	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	75	6 of 8
66794	sulfopterin metabolism	75	3 of 4
66794	ketogluconate metabolism	75	6 of 8
66794	butanoate fermentation	75	3 of 4
66794	tryptophan metabolism	73.68	28 of 38
66794	degradation of sugar acids	72	18 of 25
66794	degradation of pentoses	71.43	20 of 28
66794	oxidative phosphorylation	71.43	65 of 91
66794	glutathione metabolism	71.43	10 of 14
66794	non-pathway related	71.05	27 of 38
66794	propionate fermentation	70	7 of 10
66794	vitamin B1 metabolism	69.23	9 of 13
66794	degradation of sugar alcohols	68.75	11 of 16
66794	cyanate degradation	66.67	2 of 3
66794	4-hydroxymandelate degradation	66.67	6 of 9
66794	acetyl CoA biosynthesis	66.67	2 of 3
66794	octane oxidation	66.67	2 of 3
66794	cysteine metabolism	66.67	12 of 18
66794	arginine metabolism	66.67	16 of 24
66794	L-lactaldehyde degradation	66.67	2 of 3
66794	IAA biosynthesis	66.67	2 of 3
66794	acetoin degradation	66.67	2 of 3
66794	CO2 fixation in Crenarchaeota	66.67	6 of 9
66794	isoprenoid biosynthesis	65.38	17 of 26
66794	phenol degradation	65	13 of 20
66794	d-xylose degradation	63.64	7 of 11
66794	arachidonate biosynthesis	60	3 of 5
66794	lipoate biosynthesis	60	3 of 5
66794	glycine betaine biosynthesis	60	3 of 5
66794	vitamin K metabolism	60	3 of 5
66794	propanol degradation	57.14	4 of 7
66794	tyrosine metabolism	57.14	8 of 14
66794	lysine metabolism	57.14	24 of 42
66794	nitrate assimilation	55.56	5 of 9
66794	daunorubicin biosynthesis	55.56	5 of 9
66794	sulfate reduction	53.85	7 of 13
66794	glycine metabolism	50	5 of 10
66794	aminopropanol phosphate biosynthesis	50	1 of 2
66794	4-hydroxyphenylacetate degradation	50	5 of 10
66794	pantothenate biosynthesis	50	3 of 6
66794	quinate degradation	50	1 of 2
66794	ascorbate metabolism	50	11 of 22
66794	lactate fermentation	50	2 of 4
66794	CMP-KDO biosynthesis	50	2 of 4
66794	toluene degradation	50	2 of 4
66794	grixazone biosynthesis	50	1 of 2
66794	cyclohexanol degradation	50	2 of 4
66794	mannosylglycerate biosynthesis	50	1 of 2
66794	androgen and estrogen metabolism	50	8 of 16
66794	phenylmercury acetate degradation	50	1 of 2
66794	carnitine metabolism	50	4 of 8
66794	bile acid biosynthesis, neutral pathway	47.06	8 of 17
66794	phenylpropanoid biosynthesis	46.15	6 of 13
66794	phosphatidylethanolamine bioynthesis	46.15	6 of 13
66794	lipid A biosynthesis	44.44	4 of 9
66794	mevalonate metabolism	42.86	3 of 7
66794	benzoyl-CoA degradation	42.86	3 of 7
66794	3-phenylpropionate degradation	40	6 of 15
66794	creatinine degradation	40	2 of 5
66794	bacilysin biosynthesis	40	2 of 5
66794	coenzyme M biosynthesis	40	4 of 10
66794	hydrogen production	40	2 of 5
66794	polyamine pathway	39.13	9 of 23
66794	arachidonic acid metabolism	38.89	7 of 18
66794	cholesterol biosynthesis	36.36	4 of 11
66794	vitamin B6 metabolism	36.36	4 of 11
66794	carotenoid biosynthesis	36.36	8 of 22
66794	(5R)-carbapenem carboxylate biosynthesis	33.33	1 of 3
66794	selenocysteine biosynthesis	33.33	2 of 6
66794	chlorophyll metabolism	33.33	6 of 18
66794	sphingosine metabolism	33.33	2 of 6
66794	sulfoquinovose degradation	33.33	1 of 3
66794	methane metabolism	33.33	1 of 3
66794	dolichyl-diphosphooligosaccharide biosynthesis	27.27	3 of 11
66794	vitamin E metabolism	25	1 of 4
66794	methanogenesis from CO2	25	3 of 12

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Environmental	#Terrestrial	#Forest
#Environmental	#Terrestrial	#Soil
#Host	#Plants	#Tree

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent
15750	pine forest soil	Yanglin, Yunnan province	China	CHN	Asia
67770	Pine-forest soil	Yanglin, Yunnan Province	China	CHN	Asia

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
15750	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
67770	IMG-taxon 2671180039 annotated assembly for Actinacidiphila rubida CGMCC 4.2026	scaffold	GCA_900110255	310780.5	2671180039	310780	55.51
67770	ASM172306v1 assembly for Actinacidiphila rubida NRRL B-24619	scaffold	GCA_001723065		2802429643	310780

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
15750	Streptomyces rubidus strain 13C15 16S ribosomal RNA gene, partial sequence	AY876941	1414		310780

GC content

@ref	GC-content (mol%)	Method
15750	70.6
67770	72.9	genome sequence analysis
67770	70.6	thermal denaturation, midpoint method (Tm)

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Actinacidiphila rubida CGMCC 4.2026
NCBI: GCA_900110255

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	yes	94.30	no
125439	motility	BacteriaNetⓘ	no	92.70	no
125439	gram_stain	BacteriaNetⓘ	positive	99.90	no
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	99.20	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Streptomyces rubidus strain CGMCC 4.2026
PATRIC: 310780.5

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	yes	90.50	yes
125438	anaerobic	anaerobicⓘ	no	96.40	no
125438	spore-forming	spore-formingⓘ	yes	90.90	yes
125438	aerobic	aerobicⓘ	yes	92.23	no
125438	thermophilic	thermophileⓘ	no	96.90	yes
125438	flagellated	motile2+ⓘ	no	88.00	yes

Literature

Topic	Title	Authors	Journal	DOI	Year
	Comparative Genomic Analysis of Soil Dwelling Bacteria Utilizing a Combinational Codon Usage and Molecular Phylogenetic Approach Accentuating on Key Housekeeping Genes.	Saha J, Saha BK, Pal Sarkar M, Roy V, Mandal P, Pal A.	Front Microbiol	10.3389/fmicb.2019.02896	2019
Metabolism	Prokaryotic viperins produce diverse antiviral molecules.	Bernheim A, Millman A, Ofir G, Meitav G, Avraham C, Avraham C, Shomar H, Rosenberg MM, Tal N, Melamed S, Amitai G, Sorek R.	Nature	10.1038/s41586-020-2762-2	2021
Phylogeny	Streptomyces acidipaludis sp. nov., an actinobacterium isolated from peat swamp forest soil.	Nammali A, Duangupama T, Pittayakhajonwut P, Intaraudom C, Suriyachadkun C, He YW, Tanasupawat S, Thawai C.	Int J Syst Evol Microbiol	10.1099/ijsem.0.005626	2022
Phylogeny	Streptomyces buecherae sp. nov., an actinomycete isolated from multiple bat species.	Hamm PS, Dunlap CA, Mullowney MW, Caimi NA, Kelleher NL, Thomson RJ, Porras-Alfaro A, Northup DE	Antonie Van Leeuwenhoek	10.1007/s10482-020-01493-4	2020
Phylogeny	Neutrotolerant acidophilic Streptomyces species isolated from acidic soils in China: Streptomyces guanduensis sp. nov., Streptomyces paucisporeus sp. nov., Streptomyces rubidus sp. nov. and Streptomyces yanglinensis sp. nov.	Xu C, Wang L, Cui Q, Huang Y, Liu Z, Zheng G, Goodfellow M	Int J Syst Evol Microbiol	10.1099/ijs.0.63959-0	2006

References

#15750	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 41947
#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 )
#31645	Barberan A, Caceres Velazquez H, Jones S, Fierer N.: Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information. mSphere 2: 2017 ( DOI 10.1128/mSphere.00237-17 , PubMed 28776041 ) - originally annotated from #27928 (see below)
#66794	Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg: BRENDA, the ELIXIR core data resource in 2021: new developments and updates. Nucleic Acids Res. 49: D498 - D508 2020 ( DOI 10.1093/nar/gkaa1025 , PubMed 33211880 )
#67770	Japan Collection of Microorganism (JCM) ; Curators of the JCM;
#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 )

Rate our new design

Content

About us

Streptomyces rubidus (DSM 41947, CGMCC 4.2026, JCM 13277)

Name and taxonomic classification

Morphology

Cell morphology

Pigmentation

Culture and growth conditions

Culture medium

Culture temp

Culture pH

Physiology and metabolism

Oxygen tolerance

Spore formation

Observation

Metabolite utilization

Pathway annotation

Isolation, sampling and environmental information

Isolation source categories

Isolation

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_900110255

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

Help

Social Media