Strain identifier

BacDive ID: 16328

Type strain: No

Species: Streptomyces rameus

Strain history: KCC S-1064 <-- ATCC 21273 <-- Kyowa Hakko Kogyo Co., Ltd.; 154.

NCBI tax ID(s): 68261 (species)

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General

@ref: 10468

BacDive-ID: 16328

DSM-Number: 41685

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

description: Streptomyces rameus DSM 41685 is a spore-forming, mesophilic bacterium that builds an aerial mycelium and was isolated from soil.

NCBI tax id

  • NCBI tax id: 68261
  • Matching level: species

strain history

@refhistory
10468<- ATCC <- Kyowa Ferm. Inc. Co., Ltd., 154
67770KCC S-1064 <-- ATCC 21273 <-- Kyowa Hakko Kogyo Co., Ltd.; 154.

doi: 10.13145/bacdive16328.20230509.8.1

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 rameus
  • full scientific name: Streptomyces rameus Shibata 1959 (Approved Lists 1980)

@ref: 10468

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Streptomycetaceae

genus: Streptomyces

species: Streptomyces rameus

full scientific name: Streptomyces rameus Shibata 1959

type strain: no

Morphology

colony morphology

@refcolony colorincubation periodmedium used
19524Brown10-14 daysISP 2
19524Green10-14 daysISP 3
19524Green10-14 daysISP 4
19524Green10-14 daysISP 5
19524Brown10-14 daysISP 6
19524Brown10-14 daysISP 7

multicellular morphology

@refforms multicellular complexcomplex namecomplex colormedium name
19524yesAerial MyceliumGreyISP 2
19524yesAerial MyceliumGreyISP 3
19524yesAerial MyceliumGreyISP 4
19524yesAerial MyceliumGreyISP 5
19524noISP 6
19524yesAerial MyceliumGreyISP 7

Culture and growth conditions

culture medium

@refnamegrowthcomposition
19524ISP 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
19524ISP 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:
19524ISP 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
19524ISP 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
19524ISP 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
19524ISP 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

culture temp

@refgrowthtypetemperaturerange
19524positiveoptimum28mesophilic
67770positivegrowth28mesophilic

Physiology and metabolism

spore formation

  • @ref: 19524
  • spore description: Formation of spore chains: spirales, spore surface: smooth
  • type of spore: spore
  • spore formation: yes

compound production

@refcompound
10468plant antiviral agent 84-B-3
67770Anti-virus substance 84-B-3

halophily

  • @ref: 19524
  • salt: NaCl
  • growth: positive
  • tested relation: maximum
  • concentration: 5 %

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
1952462968cellulose-
1952416634raffinose-
1952426546rhamnose-
1952428757fructose-
1952429864mannitol-
1952417268myo-inositol+
1952418222xylose-
1952417992sucrose+
1952422599arabinose+
1952417234glucose+
683685291gelatin+hydrolysis
6836827897tryptophan-energy source
6836816199urea+hydrolysis
6836816947citrate-assimilation
6836818257ornithine-degradation
6836825094lysine-degradation
6836829016arginine-hydrolysis

metabolite production

@refChebi-IDmetaboliteproduction
6836815688acetoinyes
6836835581indoleno
6836816136hydrogen sulfideyes

metabolite tests

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

enzymes

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

API 20E

@refONPGADH ArgLDC LysODCCITH2SURETDA TrpINDVPGEL
19524+----+++-++

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
10468soilTokyo, Setagaya-kuJapanJPNAsia
67770SoilSetagaya-ku, TokyoJapanJPNAsia

isolation source categories

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

taxonmaps

  • @ref: 69479
  • File name: preview.99_3790.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_15;96_91;97_287;98_1422;99_3790&stattab=map
  • Last taxonomy: Streptomyces
  • 16S sequence: AB184679
  • Sequence Identity:
  • Total samples: 78
  • soil counts: 67
  • animal counts: 9
  • plant counts: 2

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
104681Risk group (German classification)
195241Risk group (German classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Streptomyces rameus gene for 16S ribosomal RNA, partial sequence, strain: JCM 5064D44433120ena68261
20218Streptomyces rameus strain KCTC 9767 16S ribosomal RNA gene, partial sequenceAY9998211422ena68261
20218Streptomyces rameus 16S rRNA gene, type strain LMG 20326AJ7813791479ena68261
20218Streptomyces rameus gene for 16S rRNA, partial sequence, strain: NBRC 15453AB1846791474ena68261

Genome sequences

  • @ref: 66792
  • description: Streptomyces tricolor DSM 41685
  • accession: GCA_021892415
  • assembly level: contig
  • database: ncbi
  • NCBI tax ID: 68277

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
flagellatedno97.807no
gram-positiveyes88.793no
anaerobicno99.321no
aerobicyes94.398no
halophileno93.856no
spore-formingyes95.53yes
motileno93.109no
glucose-fermentno91.56no
thermophileno98.098yes
glucose-utilyes89.619no

External links

@ref: 10468

culture collection no.: DSM 41685, ATCC 21273, HUT 6618, IFO 16196, JCM 5064, KCC S-1064, KCTC 9767, NBRC 16196, NRRL B-16924, BCRC 12045, CGMCC 4.1763, IFO 15453, NBRC 15453

straininfo link

  • @ref: 85384
  • straininfo: 92882

literature

  • topic: Phylogeny
  • Pubmed-ID: 15653925
  • title: Strain NBRC (formerly IFO) 3782 is the type strain of Streptomyces rameus Shibata 1959. Opinion 76.
  • authors: Judicial Commission Of The International Committee On Systematics Of Prokaryotes
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijs.0.63545-0
  • year: 2005
  • mesh: Streptomyces/*classification, *Terminology as Topic

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
10468Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 41685)https://www.dsmz.de/collection/catalogue/details/culture/DSM-41685
19524Wink, J.http://www.dsmz.de/microorganisms/wink_pdf/DSM41685.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
69479João 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
85384Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID92882.1StrainInfo: A central database for resolving microbial strain identifiers