Strain identifier

BacDive ID: 16298

Type strain: Yes

Species: Streptomyces ruber

Strain history: KCC A-0131 <-- Y. Okami <-- ATCC 17754 <-- HACC 143.

NCBI tax ID(s): 83378 (species)

« back to strain detail view
For citation purpose refer to the digital object identifier (doi) of the current version.
Archive
version 9.3 (current version):
version 9.2:
version 9.1:
version 9:
version 8.1:
version 8:
version 7.1:
version 7:
version 6:
version 5:
version 4.1:
version 4:
version 3:
version 2.1:
version 2:
version 1:
version 9.3 (current version)

General

@ref: 9446

BacDive-ID: 16298

DSM-Number: 40304

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

description: Streptomyces ruber DSM 40304 is a spore-forming, mesophilic bacterium that builds an aerial mycelium.

NCBI tax id

  • NCBI tax id: 83378
  • Matching level: species

strain history

@refhistory
9446<- E. B. Shirling, ISP (Chainia rubra) <- M. J. Thirumlachar, HACC-143
67770KCC A-0131 <-- Y. Okami <-- ATCC 17754 <-- HACC 143.

doi: 10.13145/bacdive16298.20250331.9.3

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 ruber
  • full scientific name: Streptomyces ruber (Thirumalachar 1955) Goodfellow et al. 1986

  • synonyms

    • @ref: 20215
    • synonym: Chainia rubra

@ref: 9446

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Streptomycetaceae

genus: Streptomyces

species: Streptomyces ruber

full scientific name: Streptomyces ruber (Thirumalachar 1955) Goodfellow et al. 1986

type strain: yes

Morphology

cell morphology

  • @ref: 125439
  • gram stain: positive
  • confidence: 99.7

colony morphology

@refcolony colorincubation periodmedium used
19435Red brown10-14 daysISP 2
19435Red10-14 daysISP 3
19435Orange10-14 daysISP 4
19435Red brown10-14 daysISP 5
19435Orange10-14 daysISP 6
19435Red brown10-14 daysISP 7

multicellular morphology

@refforms multicellular complexcomplex namecomplex colormedium name
19435yesAerial MyceliumRed brownISP 2
19435yesAerial MyceliumRedISP 3
19435yesAerial MyceliumRedISP 4
19435yesAerial MyceliumRedISP 5
19435noISP 6
19435yesAerial MyceliumRedISP 7

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
9446GYM STREPTOMYCES MEDIUM (DSMZ Medium 65)yeshttps://mediadive.dsmz.de/medium/65Name: 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
19435ISP 2yesName: 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
19435ISP 3yesName: 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:
19435ISP 4yesName: 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
19435ISP 5yesName: 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
19435ISP 6yesName: 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
19435ISP 7yesName: 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
9446STARCH - MINERAL SALT - AGAR (STMS) (DSMZ Medium 252)yeshttps://mediadive.dsmz.de/medium/252Name: STARCH - MINERAL SALT - AGAR (STMS) (DSMZ Medium 252) Composition: Agar 14.985 g/l Starch 9.99001 g/l (NH4)2SO4 1.998 g/l CaCO3 1.998 g/l K2HPO4 0.999001 g/l MgSO4 x 7 H2O 0.999001 g/l NaCl 0.999001 g/l FeSO4 x 7 H2O 0.000999001 g/l MnCl2 x 4 H2O 0.000999001 g/l ZnSO4 x 7 H2O 0.000999001 g/l Distilled water

culture temp

@refgrowthtypetemperature
9446positivegrowth28
19435positiveoptimum28
67770positivegrowth28

Physiology and metabolism

oxygen tolerance

  • @ref: 125439
  • oxygen tolerance: obligate aerobe
  • confidence: 99.1

spore formation

@refspore descriptionspore formationconfidence
19435Formation of spore chains: spira, spore surface: smoothyes
125439yes92.7
125438yes94.683

halophily

  • @ref: 19435
  • salt: NaCl
  • growth: positive
  • tested relation: maximum
  • concentration: 2.5 %

observation

  • @ref: 67770
  • observation: quinones: MK-9(H8), MK-9(H6)

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
1943562968cellulose-
1943516634raffinose-
1943526546rhamnose+/-
1943528757fructose+/-
1943529864mannitol+
1943517268myo-inositol-
1943518222xylose+
1943517992sucrose+
1943522599arabinose-
1943517234glucose+
683685291gelatin+hydrolysis
6836827897tryptophan-energy source
6836816199urea-hydrolysis
6836816947citrate-assimilation
6836818257ornithine-degradation
6836825094lysine-degradation
6836829016arginine-hydrolysis

metabolite production

@refChebi-IDmetaboliteproduction
6836815688acetoinyes
6836835581indoleno
6836816136hydrogen sulfideno

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testindole test
6836815688acetoin+
6836835581indole-

enzymes

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

API 20E

@refONPGADH ArgLDC LysODCCITH2SURETDA TrpINDVPGEL
19435-------+-++

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
94461Risk group (German classification)
194351Risk group (German classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Streptomyces ruber gene for 16S rRNA, partial sequenceAB018203121nuccore83378
20218Streptomyces ruber gene for 16S rRNA, partial sequence, strain: NBRC 14600AB1846041417nuccore83378

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Streptomyces ruber JCM 3131GCA_014648075scaffoldncbi83378
66792Streptomyces ruber strain JCM 313183378.9wgspatric83378

Genome-based predictions

predictions

@refmodeltraitdescriptionpredictionconfidencetraining_data
125438gram-positivegram-positivePositive reaction to Gram-stainingyes86.976no
125438anaerobicanaerobicAbility to grow under anoxygenic conditions (including facultative anaerobes)no97.011no
125438aerobicaerobicAbility to grow under oxygenic conditions (including facultative aerobes)yes86.539no
125438spore-formingspore-formingAbility to form endo- or exosporesyes94.683yes
125438thermophilethermophilicAbility to grow at temperatures above or equal to 45°Cno96.5yes
125438motile2+flagellatedAbility to perform flagellated movementno85.567no
125439BacteriaNetspore_formationAbility to form endo- or exosporesyes92.7
125439BacteriaNetmotilityAbility to perform movementno88.9
125439BacteriaNetgram_stainReaction to gram-stainingpositive99.7
125439BacteriaNetoxygen_toleranceOxygenic conditions needed for growthobligate aerobe99.1

External links

@ref: 9446

culture collection no.: DSM 40304, ATCC 17754, CBS 228.65, IFO 14600, ISP 5304, JCM 3131, KCC A-0131, NBRC 14600, NCIB 10983, BCRC 12358, BCRC 15138, CGMCC 4.1925, CMI 112789, KCTC 19969, NCIMB 10983, NRRL B-5315

straininfo link

  • @ref: 85355
  • straininfo: 36719

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
9446Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 40304)https://www.dsmz.de/collection/catalogue/details/culture/DSM-40304
19435Wink, J.http://www.dsmz.de/microorganisms/wink_pdf/DSM40304.pdfCompendium of Actinobacteria. HZI-Helmholtz-Centre for Infection Research, Braunschweig
20215Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M.10.1099/ijsem.0.004332List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ
20218Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P.10.1016/j.syapm.2013.11.002StrainInfo introduces electronic passports for microorganisms.Syst Appl Microbiol. 37: 42-50 201424321274
66792Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmannhttps://diaspora-project.de/progress.html#genomesAutomatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
68368Automatically annotated from API 20E
85355Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID36719.1StrainInfo: A central database for resolving microbial strain identifiers
125438Julia Koblitz, Lorenz Christian Reimer, Rüdiger Pukall, Jörg Overmann10.1101/2024.08.12.607695Predicting bacterial phenotypic traits through improved machine learning using high-quality, curated datasets
125439Philipp Münch, René Mreches, Martin Binder, Hüseyin Anil Gündüz, Xiao-Yin To, Alice McHardyhttps://github.com/GenomeNet/deepGdeepG: Deep Learning for Genome Sequence Data. R package version 0.3.1