Strain identifier

BacDive ID: 16356

Type strain: Yes

Species: Streptomyces yatensis

Strain history: DSM 41771 <-- M. Goodfellow SFOCin 76.

NCBI tax ID(s): 155177 (species)

For citation purpose refer to the digital object identifier (doi) of the current version.
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General

@ref: 10557

BacDive-ID: 16356

DSM-Number: 41771

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

description: Streptomyces yatensis DSM 41771 is a spore-forming, mesophilic bacterium that builds an aerial mycelium and was isolated from soil.

NCBI tax id

  • NCBI tax id: 155177
  • Matching level: species

strain history

@refhistory
10557<- M. Goodfellow; SFOcin 76
67770DSM 41771 <-- M. Goodfellow SFOCin 76.

doi: 10.13145/bacdive16356.20230509.8.1

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 yatensis
  • full scientific name: Streptomyces yatensis Saintpierre et al. 2003

@ref: 10557

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Streptomycetaceae

genus: Streptomyces

species: Streptomyces yatensis

full scientific name: Streptomyces yatensis Saintpierre et al. 2003

type strain: yes

Morphology

cell morphology

@refmotilityconfidencegram stain
69480no91.648
69480100positive

colony morphology

@refcolony colormedium used
69301Beige (1001)ISP 7
69301Ivory (1014)ISP 2
69301Ivory (1014)ISP 3
69301Ivory (1014)ISP 5
69301Ivory (1014)ISP 6
69301Light ivory (1015)ISP 4
69301Light ivory (1015)suter without tyrosine
69301Ochre yellow (1024)suter with tyrosine

multicellular morphology

@refforms multicellular complexcomplex namecomplex colormedium name
69301yesAerial myceliumLight ivory (1015), signal black (9004)ISP 2
69301yesAerial myceliumDusty grey (7037), signal black (9004)ISP 3
69301yesAerial myceliumTraffic white (9016)ISP 4
69301yesAerial myceliumQuarz grey (7039), signal white (9003)ISP 5
69301noAerial myceliumISP 6
69301yesAerial myceliumDusty grey (7037), signal white (9003)ISP 7
69301yesAerial myceliumsuter with tyrosine
69301yesAerial myceliumsuter without tyrosine

pigmentation

@refproductionnamecolor
69301yesMelanin
69301yessoluble pigmentIvory (1014), ochre yellow (1024), light ivory (1015)

multimedia

@refmultimedia contentcaptionintellectual property rights
69301DSM_41771_image3.jpegPlates (65, ISP2, ISP3, ISP4, ISP5, ISP7)Helmholtz-Zentrum für Infektionsforschung GmbH
69301DSM_41771_image4.jpegPlates (65, ISP2, ISP3, ISP4, ISP5, ISP7)Helmholtz-Zentrum für Infektionsforschung GmbH
69301DSM_41771_image5.jpeg(ISP6, SSM+T, SSM-T)Helmholtz-Zentrum für Infektionsforschung GmbH
69301DSM_41771_image6.jpeg(ISP6, SSM+T, SSM-T)Helmholtz-Zentrum für Infektionsforschung GmbH

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
10557GYM 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
10557ROLLED 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
10557STARCH - MINERAL SALT - AGAR (STMS) (DSMZ Medium 252)yeshttps://mediadive.dsmz.de/medium/252Name: STARCH - MINERAL SALT - AGAR (STMS) (DSMZ Medium 252) Composition: Agar 14.985 g/l Starch 9.99001 g/l (NH4)2SO4 1.998 g/l CaCO3 1.998 g/l K2HPO4 0.999001 g/l MgSO4 x 7 H2O 0.999001 g/l NaCl 0.999001 g/l FeSO4 x 7 H2O 0.000999001 g/l MnCl2 x 4 H2O 0.000999001 g/l ZnSO4 x 7 H2O 0.000999001 g/l Distilled water

culture temp

@refgrowthtypetemperaturerange
10557positivegrowth28mesophilic
67770positivegrowth28mesophilic

Physiology and metabolism

spore formation

@refspore formationconfidence
69481yes100
69480yes100

halophily

  • @ref: 69301
  • salt: NaCl
  • growth: positive
  • tested relation: growth
  • concentration: 0 %

observation

  • @ref: 67770
  • observation: quinones: MK-9(H8)

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
6930122599arabinose+/-growth
6930162968cellulose-growth
6930128757fructose-growth
6930117234glucose+growth
6930117268inositol+growth
6930137684mannose+growth
6930116634raffinose+growth
6930126546rhamnose+growth
6930117992sucrose-growth
6930118222xylose+growth
6837917632nitrate-reduction
6837916199urea-hydrolysis
683795291gelatin+hydrolysis
6837917634D-glucose-fermentation
6837916988D-ribose-fermentation
6837965327D-xylose-fermentation
6837916899D-mannitol-fermentation
6837917306maltose-fermentation
6837917716lactose-fermentation
6837917992sucrose-fermentation
6837928087glycogen-fermentation

enzymes

@refvalueactivityec
68379gelatinase+
68379urease-3.5.1.5
68379N-acetyl-beta-glucosaminidase+3.2.1.52
68379alpha-glucosidase-3.2.1.20
68379beta-glucuronidase-3.2.1.31
68379alkaline phosphatase+3.1.3.1
68379pyrrolidonyl arylamidase-3.4.19.3
68379pyrazinamidase-3.5.1.B15
68382alkaline phosphatase+3.1.3.1
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
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 coryne

@refNITPYZPYRAPALbeta GURbeta GALalpha GLUbeta NAGESCUREGELGLURIBXYLMANMALLACSACGLYG
69301---+-+/--++/--+--------

API zym

@refAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
69301++/-+/-+/-++++-++++-+/-+++-

Isolation, sampling and environmental information

isolation

@refsample typecountryorigin.countrycontinentgeographic location
10557soilNew CaledoniaNCLAustralia and Oceania
67770Ultramafic soilFranceFRAEuropeNarbonne

isolation source categories

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

Safety information

risk assessment

  • @ref: 10557
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Streptomyces yatensis 16S ribosomal RNA gene, partial sequenceAF3368001493ena155177
20218Streptomyces yatensis gene for 16S rRNA, partial sequence, strain: NBRC 101000AB2499621460ena155177

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Streptomyces yatensis DSM 41771GCA_018069625completencbi155177
66792Streptomyces yatensis strain DSM 41771155177.3completepatric155177

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingyes100no
flagellatedno98.178no
gram-positiveyes87.475no
anaerobicno99.321no
aerobicyes93.074no
halophileno89.273no
spore-formingyes94.995no
thermophileno98.154yes
glucose-utilyes90.849no
motileno92.801no
glucose-fermentno90.368yes

External links

@ref: 10557

culture collection no.: DSM 41771, CIP 109043, NBRC 101000, NRRL B-24116, SFOcin 76, JCM 13244, NCIMB 14454

straininfo link

  • @ref: 85411
  • straininfo: 87964

literature

  • topic: Phylogeny
  • Pubmed-ID: 28829023
  • title: Streptomyces solisilvae sp. nov., isolated from tropical forest soil.
  • authors: Zhou S, Yang X, Huang D, Huang X
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijsem.0.002166
  • year: 2017
  • mesh: Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, *Forests, Nucleic Acid Hybridization, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Streptomyces/*classification/genetics/isolation & purification, Tropical Climate
  • topic2: Transcriptome

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
10557Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 41771)https://www.dsmz.de/collection/catalogue/details/culture/DSM-41771
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/
68379Automatically annotated from API Coryne
68382Automatically annotated from API zym
69301Wink, J.https://cdn.dsmz.de/wink/DSM%2041771.pdfCompendium of Actinobacteria. HZI-Helmholtz-Centre for Infection Research, Braunschweig
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
85411Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID87964.1StrainInfo: A central database for resolving microbial strain identifiers