Archive BacDiveID:10.13145/bacdive15569.20230509.8.1

Strain identifier

BacDive ID: 15569

Type strain:

Species: Streptomyces rubiginosus

Strain history: KCC S-0416 <-- IFO 12913 <-- SAJ <-- ISP 5177 <-- INA 11852.

NCBI tax ID(s): 1929 (species)

For citation purpose refer to the digital object identifier (doi) of the current version.

General

@ref: 9370

BacDive-ID: 15569

DSM-Number: 40177

keywords: genome sequence, 16S sequence, Bacteria, spore-forming, mesophilic

description: Streptomyces rubiginosus DSM 40177 is a spore-forming, mesophilic bacterium that builds an aerial mycelium and was isolated from soil.

NCBI tax id

NCBI tax id: 1929
Matching level: species

strain history

@ref	history
9370	<- E.B. Shirling, ISP <- T.P. Preobrazhenskaya, INA
67770	KCC S-0416 <-- IFO 12913 <-- SAJ <-- ISP 5177 <-- INA 11852.

doi: 10.13145/bacdive15569.20230509.8.1

Name and taxonomic classification

LPSN

@ref: 20215
description: domain/bacteria
keyword: phylum/actinomycetota
domain: Bacteria
phylum: Actinomycetota
class: Actinomycetes
order: Kitasatosporales
family: Streptomycetaceae
genus: Streptomyces
species: Streptomyces rubiginosus
full scientific name: Streptomyces rubiginosus (Preobrazhenskaya et al. 1957) Pridham et al. 1958 (Approved Lists 1980)
synonyms
- @ref: 20215
- synonym: Actinomyces rubiginosus

@ref: 9370

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Streptomycetaceae

genus: Streptomyces

species: Streptomyces rubiginosus

full scientific name: Streptomyces rubiginosus (Preobrazhenskaya et al. 1957) Pridham et al. 1958

type strain: yes

Morphology

cell morphology

@ref	motility	confidence	gram stain
69480	no	91.434
69480		100	positive

colony morphology

@ref	incubation period	medium used	colony color
19420	10-14 days	ISP 2
19420	10-14 days	ISP 3	Brown
19420	10-14 days	ISP 4	Brown
19420	10-14 days	ISP 5
19420	10-14 days	ISP 6
19420	10-14 days	ISP 7

multicellular morphology

@ref	forms multicellular complex	complex name	complex color	medium name
19420	yes	Aerial Mycelium	Grey	ISP 2
19420	yes	Aerial Mycelium	White	ISP 3
19420	yes	Aerial Mycelium	Grey	ISP 4
19420	yes	Aerial Mycelium	Grey	ISP 5
19420	no			ISP 6
19420	no			ISP 7

Culture and growth conditions

culture medium

@ref	name	growth	link	composition
9370	GYM STREPTOMYCES MEDIUM (DSMZ Medium 65)	yes	https://mediadive.dsmz.de/medium/65	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
19420	ISP 2	yes		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
19420	ISP 3	yes		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:
19420	ISP 4	yes		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
19420	ISP 5	yes		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
19420	ISP 6	yes		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
19420	ISP 7	yes		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

culture temp

@ref	growth	type	temperature	range
19420	positive	optimum	30	mesophilic
9370	positive	growth	28	mesophilic
67770	positive	growth	28	mesophilic

Physiology and metabolism

spore formation

@ref	spore description	spore formation	confidence
19420	Formation of spore chains: rectiflixibilis	yes
69481		yes	100
69480		yes	100

halophily

@ref: 19420
salt: NaCl
growth: positive
tested relation: maximum
concentration: 7.5 %

metabolite utilization

@ref	Chebi-ID	metabolite	utilization activity	kind of utilization tested
68368	5291	gelatin	+	hydrolysis
68368	27897	tryptophan	-	energy source
68368	16199	urea	-	hydrolysis
68368	16947	citrate	-	assimilation
68368	18257	ornithine	-	degradation
68368	25094	lysine	-	degradation
68368	29016	arginine	-	hydrolysis

metabolite production

@ref	Chebi-ID	metabolite	production
68368	15688	acetoin	yes
68368	35581	indole	no
68368	16136	hydrogen sulfide	no

metabolite tests

@ref	Chebi-ID	metabolite	voges-proskauer-test	indole test
68368	15688	acetoin	+
68368	35581	indole		-

enzymes

@ref	value	activity	ec
68368	gelatinase	+
68368	tryptophan deaminase	-	4.1.99.1
68368	urease	-	3.5.1.5
68368	ornithine decarboxylase	-	4.1.1.17
68368	lysine decarboxylase	-	4.1.1.18
68368	arginine dihydrolase	-	3.5.3.6
68368	beta-galactosidase	-	3.2.1.23

API 20E

@ref	ONPG	ADH Arg	LDC Lys	ODC	CIT	H2S	URE	TDA Trp	IND	VP	GEL
19420	-	-	-	-	-	-	-	-	-	+	+

Isolation, sampling and environmental information

isolation

@ref: 9370
sample type: soil

isolation source categories

Cat1: #Environmental
Cat2: #Terrestrial
Cat3: #Soil

taxonmaps

@ref: 69479
File name: preview.99_6264.png
url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_15;96_91;97_97;98_1662;99_6264&stattab=map
Last taxonomy: Streptomyces
16S sequence: LC034307
Sequence Identity:
Total samples: 166
soil counts: 112
aquatic counts: 2
animal counts: 49
plant counts: 3

Safety information

risk assessment

@ref	biosafety level	biosafety level comment
9370	1	Risk group (German classification)
19420	1	Risk group (German classification)

Sequence information

16S sequences

@ref	description	accession	length	database	NCBI tax ID
20218	Streptomyces rubiginosus gene for 16S rRNA, partial sequence	AB122724	565	ena	1929
20218	Streptomyces rubiginosus gene for 16S ribosomal RNA, partial sequence, strain: JCM 4416	D44130	121	ena	1929
20218	Streptomyces rubiginosus strain KCTC 9042 16S ribosomal RNA gene, partial sequence	AY999810	1416	ena	1929
20218	Streptomyces rubiginosus gene for 16S rRNA, partial sequence, strain: NBRC 12913	AB184241	1432	ena	1929
67770	Streptomyces rubiginosus gene for 16S ribosomal RNA, partial sequence, strain: JCM 4416	LC034307	1484	ena	1929

Genome sequences

@ref	description	accession	assembly level	database	NCBI tax ID
66792	Streptomyces rubiginosus JCM 4416	GCA_014649895	scaffold	ncbi	1929
66792	Streptomyces rubiginosus strain JCM 4416	1929.3	wgs	patric	1929

Genome-based predictions

predictions

trait	prediction	confidence	training_data
spore-forming	yes	100	no
flagellated	no	97.316	no
gram-positive	yes	89.816	no
anaerobic	no	99.125	no
aerobic	yes	92.646	no
halophile	no	91.648	no
spore-forming	yes	96.675	yes
glucose-util	yes	89.175	no
thermophile	no	98.445	no
motile	no	93.95	no
glucose-ferment	no	89.817	no

External links

@ref: 9370

culture collection no.: DSM 40177, ATCC 19927, ATCC 23961, CBS 944.68, ETH 28445, IFO 12913, INA 11852, ISP 5177, JCM 4416, KCC S-0416, NBRC 12913, RIA 1137, BCRC 13781, CGMCC 4.1773, KCTC 9042, NRRL B-3983, VKM Ac-1089

straininfo link

@ref: 84656
straininfo: 389330

Reference

@id	authors	catalogue	doi/url	title	journal	pubmed
9370	Curators of the DSMZ	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 40177)	https://www.dsmz.de/collection/catalogue/details/culture/DSM-40177
19420	Wink, J.		http://www.dsmz.de/microorganisms/wink_pdf/DSM40177.pdf	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.		10.1099/ijsem.0.004332	List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ
20218	Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P.		10.1016/j.syapm.2013.11.002	StrainInfo introduces electronic passports for microorganisms.	Syst Appl Microbiol. 37: 42-50 2014	24321274
66792	Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann		https://diaspora-project.de/progress.html#genomes	Automatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)
67770	Curators of the JCM		https://jcm.brc.riken.jp/en/
68368				Automatically annotated from API 20E
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.		https://microbeatlas.org/	MicrobeAtlas 1.0 beta
69480	Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann		https://diaspora-project.de/progress.html#genomes	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		10.21203/rs.3.rs-2527258/v1	Predictions based on the model GenomeNet Sporulation v. 1
84656	Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.		10.60712/SI-ID389330.1	StrainInfo: A central database for resolving microbial strain identifiers

General

NCBI tax id

strain history

Name and taxonomic classification

LPSN

synonyms

Morphology

cell morphology

colony morphology

multicellular morphology

Culture and growth conditions

culture medium

culture temp

Physiology and metabolism

spore formation

halophily

metabolite utilization

metabolite production

metabolite tests

enzymes

API 20E

Isolation, sampling and environmental information

isolation

isolation source categories

taxonmaps

Safety information

risk assessment

Sequence information

16S sequences

Genome sequences

Genome-based predictions

predictions

External links

straininfo link

Reference