Strain identifier

BacDive ID: 15420

Type strain: Yes

Species: Streptomyces narbonensis

Strain history: KCC S-0147 <-- Y. Okami (NIHJ 181) <-- ETH 7346.

NCBI tax ID(s): 67333 (species)

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General

@ref: 9217

BacDive-ID: 15420

DSM-Number: 40016

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

description: Streptomyces narbonensis DSM 40016 is a spore-forming, mesophilic bacterium that produces antibiotic compounds and was isolated from soil.

NCBI tax id

  • NCBI tax id: 67333
  • Matching level: species

strain history

@refhistory
9217<- E.B. Shirling, ISP <- R. Hütter, ETH, 7346
67770KCC S-0147 <-- Y. Okami (NIHJ 181) <-- ETH 7346.

doi: 10.13145/bacdive15420.20230509.8.1

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 narbonensis
  • full scientific name: Streptomyces narbonensis Corbaz et al. 1955 (Approved Lists 1980)

@ref: 9217

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Streptomycetaceae

genus: Streptomyces

species: Streptomyces narbonensis

full scientific name: Streptomyces narbonensis Corbaz et al. 1955

type strain: yes

Morphology

cell morphology

@refmotilityconfidencegram stain
69480no93.313
69480100positive

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
9217GYM 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
9217ROLLED OATS MINERAL MEDIUM (DSMZ Medium 84)yeshttps://mediadive.dsmz.de/medium/84Name: ROLLED OATS MINERAL MEDIUM (DSMZ Medium 84) Composition: Agar 20.0 g/l Rolled oats 20.0 g/l ZnSO4 x 7 H2O 0.001 g/l MnCl2 x 4 H2O 0.001 g/l FeSO4 x 7 H2O 0.001 g/l Distilled water

culture temp

@refgrowthtypetemperaturerange
18464positiveoptimum30mesophilic
9217positivegrowth28mesophilic
67770positivegrowth28mesophilic

Physiology and metabolism

spore formation

@refspore formationconfidence
69481yes100
69480yes100

compound production

  • @ref: 9217
  • compound: narbomycin

halophily

  • @ref: 18464
  • salt: NaCl
  • growth: positive
  • tested relation: maximum
  • concentration: 2.5 %

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
1846417234glucose+
1846422599arabinose+
1846417992sucrose+
1846418222xylose+
1846417268myo-inositol-
1846429864mannitol-
1846428757fructose+
1846426546rhamnose-
1846416634raffinose+
1846462968cellulose-
683685291gelatin+hydrolysis
6836827897tryptophan-energy source
6836816199urea+hydrolysis
6836816947citrate+assimilation
6836818257ornithine-degradation
6836825094lysine+degradation
6836829016arginine-hydrolysis

metabolite production

@refChebi-IDmetaboliteproduction
6777029649narbomycinyes
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
18464+-+-+-++--+

Isolation, sampling and environmental information

isolation

@refsample typecountryorigin.countrycontinentgeographic location
9217soilFranceFRAEurope
67770SoilFranceFRAEuropeCannes, Côte d'Azur

isolation source categories

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

taxonmaps

  • @ref: 69479
  • File name: preview.99_490.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_15;96_102;97_109;98_403;99_490&stattab=map
  • Last taxonomy: Streptomyces
  • 16S sequence: AB184157
  • Sequence Identity:
  • Total samples: 9252
  • soil counts: 6254
  • aquatic counts: 336
  • animal counts: 471
  • plant counts: 2191

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
184641German classification
92171Risk group (German classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Streptomyces narbonensis gene for 16S ribosomal RNA, partial sequence, strain: JCM 4596D44255120ena67333
20218Streptomyces narbonensis gene for 16S rRNA, partial sequence, strain: NBRC 12801AB1841571473ena67333
20218Streptomyces narbonensis strain NRRL B-1680 16S ribosomal RNA gene, partial sequenceDQ4457941510ena67333

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Streptomyces narbonensis JCM 4147GCA_014649015scaffoldncbi67333
66792Streptomyces narbonensis strain JCM 414767333.3wgspatric67333

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingyes100no
flagellatedno97.513no
gram-positiveyes89.172no
anaerobicno99.35no
aerobicyes94.031no
halophileno93.439no
spore-formingyes94.155no
glucose-utilyes89.422yes
thermophileno99.027no
motileno94.525no
glucose-fermentno87.944no

External links

@ref: 9217

culture collection no.: DSM 40016, ATCC 19790, CBS 542.68, IFO 12801, ISP 5016, JCM 4147, NBRC 12801, RIA 1069, ETH 7346, BCRC 13651, CBS 310.55, CCM 4151, CGMCC 4.1737, JCM 4596, NRRL B-1680, RIA 529, VKM Ac-1891

straininfo link

  • @ref: 84508
  • straininfo: 389353

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
9217Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 40016)https://www.dsmz.de/collection/catalogue/details/culture/DSM-40016
18464Wink, J.http://www.dsmz.de/microorganisms/wink_pdf/DSM40016.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
84508Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID389353.1StrainInfo: A central database for resolving microbial strain identifiers