Strain identifier

BacDive ID: 15254

Type strain: Yes

Species: Streptomyces goshikiensis

Strain history: KCC S-0294 <-- S. T. Williams A-105 <-- ISP 5190 <-- Meiji Seika Kaisha, Ltd..

NCBI tax ID(s): 1942 (species)

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General

@ref: 9252

BacDive-ID: 15254

DSM-Number: 40190

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

description: Streptomyces goshikiensis DSM 40190 is a spore-forming, mesophilic bacterium that produces antibiotic compounds and was isolated from soil.

NCBI tax id

  • NCBI tax id: 1942
  • Matching level: species

strain history

@refhistory
9252<- E.B. Shirling, ISP <- M. Oda, Meiji Seiko Co
67770KCC S-0294 <-- S. T. Williams A-105 <-- ISP 5190 <-- Meiji Seika Kaisha, Ltd..

doi: 10.13145/bacdive15254.20230509.8.1

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 goshikiensis
  • full scientific name: Streptomyces goshikiensis Niida 1966 (Approved Lists 1980)

@ref: 9252

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Streptomycetaceae

genus: Streptomyces

species: Streptomyces goshikiensis

full scientific name: Streptomyces goshikiensis Niida 1966

type strain: yes

Morphology

cell morphology

@refmotilityconfidencegram stain
69480no92.141
69480100positive

Culture and growth conditions

culture medium

  • @ref: 9252
  • name: GYM STREPTOMYCES MEDIUM (DSMZ Medium 65)
  • growth: yes
  • link: https://mediadive.dsmz.de/medium/65
  • composition: 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

culture temp

@refgrowthtypetemperaturerange
18554positiveoptimum28mesophilic
9252positivegrowth28mesophilic
67770positivegrowth28mesophilic

Physiology and metabolism

spore formation

@refspore formationconfidence
69481yes100
69480yes100

compound production

@refcompound
9252bandamycin A
9252bandamycin B
9252pentaene antibiotic
9252bandamycin A, B
9252restriction endonuclease
20216Bandamycin A
20216Bandamycin B
20216Pentaenic antibiotic
20216Endonuclease SgoI

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
1855417234glucose+
1855422599arabinose-
1855417992sucrose+
1855418222xylose+
1855417268myo-inositol+
1855429864mannitol-
1855428757fructose+
1855426546rhamnose+
1855416634raffinose+
1855462968cellulose+
683685291gelatin+hydrolysis
6836827897tryptophan-energy source
6836816199urea+hydrolysis
6836816947citrate+assimilation
6836818257ornithine+degradation
6836825094lysine+degradation
6836829016arginine+hydrolysis

metabolite production

@refmetaboliteproductionChebi-ID
67770bandamycinyes
68368acetoinno15688
68368indoleno35581
68368hydrogen sulfideno16136

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
68382alkaline phosphatase+3.1.3.1
68382esterase (C 4)+
68382esterase lipase (C 8)-
68382lipase (C 14)-
68382leucine arylamidase+3.4.11.1
68382valine arylamidase+
68382cystine arylamidase+3.4.11.3
68382trypsin+3.4.21.4
68382alpha-chymotrypsin+3.4.21.1
68382acid phosphatase+3.1.3.2
68382naphthol-AS-BI-phosphohydrolase+
68382alpha-galactosidase-3.2.1.22
68382beta-galactosidase-3.2.1.23
68382beta-glucuronidase-3.2.1.31
68382alpha-glucosidase+3.2.1.20
68382beta-glucosidase+3.2.1.21
68382N-acetyl-beta-glucosaminidase+3.2.1.52
68382alpha-mannosidase-3.2.1.24
68382alpha-fucosidase-3.2.1.51

API zym

@refAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
18554++--+++++++---+++--

API 20E

@refADH ArgLDC LysODCCITH2SURETDA TrpINDVPGEL
18554++++-+---+

Isolation, sampling and environmental information

isolation

@refsample typecountryorigin.countrycontinentgeographic location
9252soilJapanJPNAsia
67770SoilJapanJPNAsiaFukushima Pref.

isolation source categories

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

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: EF178693
  • 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
185541German classification
92521Risk group (German classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Streptomyces goshikiensis gene for 16S ribosomal RNA, partial sequence, strain: JCM 4294D44044120ena1942
20218Streptomyces goshikiensis gene for 16S rRNA, partial sequence, strain: NBRC 12868AB1842041452ena1942
20218Streptomyces goshikiensis strain NRRL B-5428 16S ribosomal RNA gene, partial sequenceEF1786931481ena1942

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Streptomyces goshikiensis JCM 4640GCA_014650555scaffoldncbi1942
66792Streptomyces goshikiensis strain JCM 46401942.3wgspatric1942

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingyes100no
flagellatedno97.4no
gram-positiveyes87.025no
anaerobicno98.868no
aerobicyes86.835no
halophileno95.782no
spore-formingyes94.26no
glucose-utilyes90.307yes
thermophileno99.202yes
motileno93.362no
glucose-fermentno89.06no

External links

@ref: 9252

culture collection no.: DSM 40190, ATCC 23914, CBS 835.68, IFO 12868, ISP 5190, NBRC 12868, RIA 1144, JCM 4294, BCRC 12330, CCUG 11121, CGMCC 4.1961, IMET 42067, JCM 4640, NCIMB 9828, NRRL B-5428, VKM Ac-1212

straininfo link

  • @ref: 84350
  • straininfo: 92906

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
9252Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 40190)https://www.dsmz.de/collection/catalogue/details/culture/DSM-40190
18554Wink, J.http://www.dsmz.de/microorganisms/wink_pdf/DSM40190.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
68382Automatically annotated from API zym
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
84350Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID92906.1StrainInfo: A central database for resolving microbial strain identifiers