Strain identifier

BacDive ID: 15098

Type strain: Yes

Species: Streptomyces virginiae

Strain Designation: Ah-304

Strain history: KCC S-0019 <-- T. Yamaguchi (IAM 0020) <-- Y. Okami 154-T4 (NIHJ 35).

NCBI tax ID(s): 1961 (species)

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General

@ref: 9809

BacDive-ID: 15098

DSM-Number: 40803

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

description: Streptomyces virginiae Ah-304 is a spore-forming, mesophilic bacterium that builds an aerial mycelium and was isolated from Soil.

NCBI tax id

  • NCBI tax id: 1961
  • Matching level: species

strain history

@refhistory
9809<- H.D. Tresner, AH-304
67770KCC S-0019 <-- T. Yamaguchi (IAM 0020) <-- Y. Okami 154-T4 (NIHJ 35).

doi: 10.13145/bacdive15098.20230509.8.1

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 virginiae
  • full scientific name: Streptomyces virginiae Grundy et al. 1952 (Approved Lists 1980)

  • synonyms

    • @ref: 20215
    • synonym: Streptomyces cinnamonensis

@ref: 9809

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Streptomycetaceae

genus: Streptomyces

species: Streptomyces cinnamonensis

full scientific name: Streptomyces cinnamonensis Okami 1952

strain designation: Ah-304

type strain: yes

Morphology

cell morphology

@refmotilityconfidencegram stain
69480no92.591
69480100positive

colony morphology

@refcolony colorincubation periodmedium used
19489Beige10-14 daysISP 2
19489Beige10-14 daysISP 3
19489Beige10-14 daysISP 4
19489Yellow10-14 daysISP 5
1948910-14 daysISP 6
19489Yellow10-14 daysISP 7

multicellular morphology

@refforms multicellular complexcomplex namecomplex colormedium name
19489yesAerial MyceliumWhiteISP 2
19489yesAerial MyceliumWhiteISP 3
19489yesAerial MyceliumGrayISP 4
19489yesAerial MyceliumGrayISP 5
19489noISP 6
19489yesAerial MyceliumRedISP 7

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
9809GYM 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
19489ISP 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
19489ISP 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:
19489ISP 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
19489ISP 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
19489ISP 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
19489ISP 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
9809STARCH - MINERAL SALT - AGAR (STMS) (DSMZ Medium 252)yeshttps://www.dsmz.de/microorganisms/medium/pdf/DSMZ_Medium252.pdf

culture temp

@refgrowthtypetemperaturerange
19489positiveoptimum28mesophilic
9809positivegrowth28mesophilic
67770positivegrowth28mesophilic

Physiology and metabolism

spore formation

@refspore descriptiontype of sporespore formationconfidence
19489Formation of spore chains (rectiflixibilis), spore surface smoothsporeyes
69481yes100
69480yes100

compound production

@refcompound
9809actithiazic acid
9809anti-mycobacterial antibiotic
9809biotin antagonist
19489Cephamycin B
19489Phenazine antibiotic
19489Kirrothricin
19489Monensin

halophily

  • @ref: 19489
  • salt: NaCl
  • growth: positive
  • tested relation: maximum
  • concentration: 2.5 %

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
1948962968cellulose-
1948916634raffinose-
1948926546rhamnose-
1948928757fructose-
1948929864mannitol-
1948917268myo-inositol-
1948918222xylose-
1948917992sucrose-
1948922599arabinose-
1948917234glucose+
683685291gelatin-hydrolysis
6836827897tryptophan-energy source
6836816199urea-hydrolysis
6836816947citrate-assimilation
6836818257ornithine-degradation
6836825094lysine-degradation
6836829016arginine+hydrolysis

metabolite production

@refChebi-IDmetaboliteproduction
6836815688acetoinno
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
19489-+---+-+---

Isolation, sampling and environmental information

isolation

  • @ref: 67770
  • sample type: Soil
  • geographic location: Kanegasaki, Iwate Pref.
  • country: Japan
  • origin.country: JPN
  • continent: Asia

taxonmaps

  • @ref: 69479
  • File name: preview.99_163.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_15;96_102;97_109;98_144;99_163&stattab=map
  • Last taxonomy: Streptomyces
  • 16S sequence: DQ227422
  • Sequence Identity:
  • Total samples: 26399
  • soil counts: 19336
  • aquatic counts: 1680
  • animal counts: 1702
  • plant counts: 3681

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
98091Risk group (German classification)
194891Risk group (German classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Streptomyces cinnamonensis strain CBS 411.63 16S ribosomal RNA geneDQ2274221353ena1900
20218Streptomyces cinnamonensis strain JCM 4019 16S ribosomal RNA gene, partial sequenceAY9997461434ena1900
20218Streptomyces cinnamonensis gene for 16S ribosomal RNA, partial sequence, strain: JCM 4019D43988120ena1900
20218Streptomyces cinnamonensis gene for 16S rRNA, partial sequence, strain: NBRC 15873AB1847071470ena1900

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Streptomyces virginiae DSM 40803GCA_017876235contigncbi1961
66792Streptomyces virginiae JCM 4019GCA_014648795scaffoldncbi1961
66792Streptomyces cinnamonensis strain DSM 408031900.14wgspatric1900
66792Streptomyces cinnamonensis strain JCM 40191900.12wgspatric1900
66792Streptomyces cinnamonensis strain NBRC 158731900.13wgspatric1900
66792Streptomyces cinnamonensis DSM 408032918290305draftimg1900
67770Streptomyces virginiae NBRC 15873GCA_016755835contigncbi1961

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingyes100no
flagellatedno97.526no
gram-positiveyes86.455no
anaerobicno99.098no
aerobicyes88.167no
halophileno95.64no
spore-formingyes94.61yes
thermophileno99.21yes
glucose-utilyes89.864yes
motileno94.03no
glucose-fermentno89.013no

External links

@ref: 9809

culture collection no.: DSM 40803, ATCC 12308, CBS 411.63, IFO 3414, NBRC 3414, NRRL B-1588, JCM 4019, CECT 3198, CGMCC 4.1619, HUT 6050, IFO 15873, KCTC 9708, NBIMCC 67, NBRC 15873, NCIMB 12604, RIA 518, VKM Ac-1912

straininfo link

  • @ref: 84205
  • straininfo: 35533

literature

  • topic: Phylogeny
  • Pubmed-ID: 22421918
  • title: Streptomyces manipurensis sp. nov., a novel actinomycete isolated from a limestone deposit site in Manipur, India.
  • authors: Nimaichand S, Zhu WY, Yang LL, Ming H, Nie GX, Tang SK, Ningthoujam DS, Li WJ
  • journal: Antonie Van Leeuwenhoek
  • DOI: 10.1007/s10482-012-9720-4
  • year: 2012
  • mesh: Base Composition, *Calcium Carbonate, Carbohydrates/analysis, Cell Wall/chemistry, Cluster Analysis, Cytosol/chemistry, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Diaminopimelic Acid/analysis, Fatty Acids/analysis, Geologic Sediments/*microbiology, India, Molecular Sequence Data, Phospholipids/analysis, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Streptomyces/*classification/genetics/*isolation & purification, Vitamin K 2/analysis
  • topic2: Genetics

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
9809Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 40803)https://www.dsmz.de/collection/catalogue/details/culture/DSM-40803
19489Wink, J.http://www.dsmz.de/microorganisms/wink_pdf/DSM40803.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
69480Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmannhttps://diaspora-project.de/progress.html#genomesPredictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)
69481Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch10.21203/rs.3.rs-2527258/v1Predictions based on the model GenomeNet Sporulation v. 1
84205Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID35533.1StrainInfo: A central database for resolving microbial strain identifiers