Strain identifier

BacDive ID: 15552

Type strain: Yes

Species: Streptomyces rishiriensis

Strain Designation: 404Y3

Strain history: KCC S-0821 <-- IFO 13407 <-- SAJ <-- ISP 5489 <-- ATCC 14812 <-- Banyu Res. Labs.; 404Y3.

NCBI tax ID(s): 68264 (species)

« back to strain detail view
For citation purpose refer to the digital object identifier (doi) of the current version.
Archive
version 9.1 (current version):
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 9.1 (current version)

General

@ref: 9594

BacDive-ID: 15552

DSM-Number: 40489

keywords: genome sequence, 16S sequence, Bacteria, spore-forming, antibiotic compound production

description: Streptomyces rishiriensis 404Y3 is a spore-forming bacterium that builds an aerial mycelium and produces antibiotic compounds.

NCBI tax id

  • NCBI tax id: 68264
  • Matching level: species

strain history

@refhistory
9594<- E.B. Shirling, ISP <- ATCC <- Bristol-Banyu Res. Inst., 404Y3
67770KCC S-0821 <-- IFO 13407 <-- SAJ <-- ISP 5489 <-- ATCC 14812 <-- Banyu Res. Labs.; 404Y3.

doi: 10.13145/bacdive15552.20240916.9.1

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 rishiriensis
  • full scientific name: Streptomyces rishiriensis Kawaguchi et al. 1965 (Approved Lists 1980)

@ref: 9594

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Streptomycetaceae

genus: Streptomyces

species: Streptomyces rishiriensis

full scientific name: Streptomyces rishiriensis Kawaguchi et al. 1965

strain designation: 404Y3

type strain: yes

Morphology

cell morphology

  • @ref: 69480
  • gram stain: positive
  • confidence: 90.939

colony morphology

@refcolony colorincubation periodmedium used
19464Brown10-14 daysISP 2
19464Yellow10-14 daysISP 3
19464Beige10-14 daysISP 4
19464Yellow10-14 daysISP 5

multicellular morphology

@refforms multicellular complexcomplex namecomplex colormedium name
19464yesAerial MyceliumGreyISP 2
19464yesAerial MyceliumYellow/ greyISP 3
19464yesAerial MyceliumGreyISP 4
19464yesAerial MyceliumWhiteISP 5
19464noISP 6
19464noISP 7

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
9594GYM 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
19464ISP 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
19464ISP 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:
19464ISP 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
19464ISP 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
9594SPORULATION-AGAR (SA) (DSMZ Medium 555)yeshttps://www.dsmz.de/microorganisms/medium/pdf/DSMZ_Medium555.pdf

culture temp

@refgrowthtypetemperature
19464positiveoptimum28
9594positivegrowth28
67770positivegrowth28

Physiology and metabolism

tolerance

  • @ref: 19464
  • compound: Lysozyme
  • percentage: 0.1

oxygen tolerance

  • @ref: 69480
  • oxygen tolerance: aerobe
  • confidence: 92.469

spore formation

@refspore descriptiontype of sporespore formationconfidence
19464Formation of spore chains (rectiflixibilis), spore surface smoothsporeyes
69480yes90.85
69481yes100

compound production

@refcompound
9594coumermycin complex
9594notomycin
20216Coumermycin complex
20216Notomycin
19464Ansatrienin
19464Chloradenosin
19464Phosphophenylalanylarginine
19464Coumermycin (Notomycin)
19464Rishirilide
67770Coumermycins

halophily

  • @ref: 19464
  • salt: NaCl
  • growth: positive
  • tested relation: maximum
  • concentration: 2.5 %

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
1946416634raffinose-
1946426546rhamnose+
1946428757fructose+
1946429864mannitol+
1946417268myo-inositol+
1946418222xylose+
1946417992sucrose+
1946422599arabinose+
1946417234glucose+
683685291gelatin-hydrolysis
6836827897tryptophan-energy source
6836816199urea-hydrolysis
6836816947citrate-assimilation
6836818257ornithine-degradation
6836825094lysine-degradation
6836829016arginine-hydrolysis

metabolite production

@refChebi-IDmetaboliteproduction
6836815688acetoinno
6836835581indoleno
6836816136hydrogen sulfideno

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
19464+------+---

Isolation, sampling and environmental information

isolation

@refsample typecountryorigin.countrycontinentgeographic location
9594soilJapanJPNAsia
67770SoilJapanJPNAsiaRishiri Island, Hokkaido

isolation source categories

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

taxonmaps

  • @ref: 69479
  • File name: preview.99_174.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_15;96_102;97_135;98_152;99_174&stattab=map
  • Last taxonomy: Streptomyces
  • 16S sequence: AB184383
  • Sequence Identity:
  • Total samples: 9844
  • soil counts: 6184
  • aquatic counts: 336
  • animal counts: 393
  • plant counts: 2931

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
95941Risk group (German classification)
194641Risk group (German classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Streptomyces rishiriensis gene for 16S ribosomal RNA, partial sequence, strain: JCM 4821D44388120nuccore68264
20218Streptomyces rishiriensis gene for 16S rRNA, partial sequence, strain: NBRC 13407AB1843831473nuccore68264
20218Streptomyces rishiriensis strain NRRL B-3239 16S ribosomal RNA gene, partial sequenceEF1786821474nuccore68264

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Streptomyces rishiriensis strain NBRC 1340768264.3wgspatric68264
66792Streptomyces rishiriensis DSM 404892563366710draftimg68264
66792Streptomyces rishiriensis NBRC 134072862413135draftimg68264
67770Streptomyces rishiriensis NBRC 13407GCA_003112535scaffoldncbi68264

Genome-based predictions

predictions

@reftraitmodeldescriptionpredictionconfidencetraining_data
69481spore-formingspore-formingAbility to form endo- or exosporesyes100no
69480gram-positivegram-positivePositive reaction to Gram-stainingyes90.939no
69480anaerobicanaerobicAbility to grow under anoxygenic conditions (including facultative anaerobes)no97.407no
69480spore-formingspore-formingAbility to form endo- or exosporesyes90.85no
69480aerobicaerobicAbility to grow under oxygenic conditions (including facultative aerobes)yes92.469no
69480thermophilicthermophileAbility to grow at temperatures above or equal to 45°Cno95.994yes
69480flagellatedmotile2+Ability to perform flagellated movementno87.5no

External links

@ref: 9594

culture collection no.: DSM 40489, ATCC 14812, CBS 708.72, IFO 13407, ISP 5489, JCM 4821, NBRC 13407, RIA 1368, BCRC 12333, CGMCC 4.1793, NCIMB 11890, NRRL B-3239, VKM Ac-1188

straininfo link

  • @ref: 84638
  • straininfo: 389317

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Enzymology11036020Identification of the coumermycin A(1) biosynthetic gene cluster of Streptomyces rishiriensis DSM 40489.Wang ZX, Li SM, Heide LAntimicrob Agents Chemother10.1128/AAC.44.11.3040-3048.20002000Aminocoumarins, Cloning, Molecular, Coumarins/chemistry/*metabolism, *Genes, Bacterial, Molecular Sequence Data, Multigene Family, Mutagenesis, Insertional, Open Reading Frames, Restriction Mapping, Streptomyces/*genetics/metabolism, Transformation, BacterialMetabolism
Enzymology14622269An unusual amide synthetase (CouL) from the coumermycin A1 biosynthetic gene cluster from Streptomyces rishiriensis DSM 40489.Schmutz E, Steffensky M, Schmidt J, Porzel A, Li SM, Heide LEur J Biochem10.1046/j.1432-1033.2003.03830.x2003Amino Acid Sequence, Aminocoumarins, Cloning, Molecular, Coumarins/*metabolism, Kinetics, Mixed Function Oxygenases/*chemistry/genetics/*metabolism, Molecular Sequence Data, Multienzyme Complexes/*chemistry/genetics/*metabolism, Novobiocin/*analogs & derivatives/biosynthesis, Sequence Homology, Amino Acid, Streptomyces/*enzymology/*genetics, Substrate SpecificityMetabolism
Enzymology14993313Identification of a topoisomerase IV in actinobacteria: purification and characterization of ParYR and GyrBR from the coumermycin A1 producer Streptomyces rishiriensis DSM 40489.Schmutz E, Hennig S, Li SM, Heide LMicrobiology (Reading)10.1099/mic.0.26867-02004Actinobacteria/*enzymology/genetics, Aminocoumarins, Anti-Bacterial Agents/biosynthesis, Base Sequence, Coumarins/*metabolism/pharmacology, DNA Gyrase/genetics/*isolation & purification/metabolism, DNA Topoisomerase IV/genetics/*isolation & purification/metabolism, DNA, Bacterial/chemistry/genetics/metabolism, Genes, Bacterial, Genetic Complementation Test, Multigene Family, Mutation, Nucleic Acid Conformation, Protein Subunits, Streptomyces/*enzymology/genetics, TemperatureMetabolism
Phylogeny33174827Streptomyces phaeolivaceus sp. nov. and Streptomyces broussonetiae sp. nov., isolated from the leaves and rhizosphere soil of Broussonetia papyrifera.Mo P, Liu J, Zhao Y, Xu ZInt J Syst Evol Microbiol10.1099/ijsem.0.0045562020Bacterial Typing Techniques, Base Composition, Broussonetia/*microbiology, China, DNA, Bacterial/genetics, Fatty Acids/chemistry, Nucleic Acid Hybridization, *Phylogeny, Plant Leaves, RNA, Ribosomal, 16S/genetics, Rhizosphere, Sequence Analysis, DNA, *Soil Microbiology, Streptomyces/*classification/isolation & purificationTranscriptome

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
9594Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 40489)https://www.dsmz.de/collection/catalogue/details/culture/DSM-40489
19464Wink, J.http://www.dsmz.de/microorganisms/wink_pdf/DSM40489.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
20216Curators of the HKIhttp://www.leibniz-hki.de/de/Collection Description Leibniz-Institut für Naturstoff-Forschung und Infektionsbiologie e. V. Hans-Knöll-Institut (HKI)
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
84638Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID389317.1StrainInfo: A central database for resolving microbial strain identifiers