Strain identifier

BacDive ID: 14903

Type strain: No

Species: Streptomyces albidoflavus

Strain history: KCC S-0515 <-- IFO 13083 <-- SAJ <-- ISP 5394 <-- IMRU 3371 <-- W. A. Millard 8.

NCBI tax ID(s): 42239 (species), 1886 (species)

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General

@ref: 9518

BacDive-ID: 14903

DSM-Number: 40394

keywords: genome sequence, 16S sequence, Bacteria, spore-forming, Gram-positive

description: Streptomyces albidoflavus DSM 40394 is a spore-forming, Gram-positive bacterium that was isolated from potato scab.

NCBI tax id

NCBI tax idMatching level
42239species
1886species

strain history

@refhistory
9518<- E.B. Shirling, ISP <- S.A. Waksman, IMRU <- W. A. Millard, 8
67770KCC S-0515 <-- IFO 13083 <-- SAJ <-- ISP 5394 <-- IMRU 3371 <-- W. A. Millard 8.

doi: 10.13145/bacdive14903.20240916.9.1

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 albidoflavus
  • full scientific name: Streptomyces albidoflavus (Rossi Doria 1891) Waksman and Henrici 1948 (Approved Lists 1980)

  • synonyms

    @refsynonym
    20215Streptomyces griseus subsp. solvifaciens
    20215Streptomyces limosus
    20215Actinomyces sampsonii
    20215Actinomyces globisporus subsp. caucasicus
    20215Cladothrix odorifera
    20215Streptomyces felleus
    20215Streptomyces sampsonii
    20215Streptomyces odorifer
    20215Streptomyces coelicolor
    20215Streptothrix coelicolor
    20215Streptotrix albidoflava
    20215Streptomyces globisporus subsp. caucasicus
    20215Streptomyces canescens
    20215Streptomyces champavatii

@ref: 9518

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Streptomycetaceae

genus: Streptomyces

species: Streptomyces albidoflavus

full scientific name: Streptomyces albidoflavus (Rossi Doria 1891) Waksman and Henrici 1948 emend. Nouioui et al. 2018

type strain: no

Morphology

cell morphology

@refmotilityconfidencegram stain
69480no91.5
6948091.329positive

Culture and growth conditions

culture medium

  • @ref: 9518
  • 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

@refgrowthtypetemperature
18588positiveoptimum30
9518positivegrowth28
67770positivegrowth28

Physiology and metabolism

spore formation

  • @ref: 69480
  • spore formation: yes
  • confidence: 94.516

halophily

  • @ref: 18588
  • salt: NaCl
  • growth: positive
  • tested relation: maximum
  • concentration: 7.5 %

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
1858817234glucose+
1858822599arabinose+
1858817992sucrose-
1858818222xylose-
1858817268myo-inositol-
1858829864mannitol+
1858828757fructose+
1858826546rhamnose-
1858816634raffinose-
1858862968cellulose-
683685291gelatin-hydrolysis
6836827897tryptophan-energy source
6836816199urea-hydrolysis
6836816947citrate-assimilation
6836818257ornithine-degradation
6836825094lysine-degradation
6836829016arginine-hydrolysis

metabolite production

@refChebi-IDmetaboliteproduction
6836815688acetoinyes
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
18588---------+-

Isolation, sampling and environmental information

isolation

  • @ref: 9518
  • sample type: potato scab

isolation source categories

Cat1Cat2Cat3
#Host#Plants#Herbaceous plants (Grass,Crops)
#Host Body-Site#Other#Wound
#Host Body-Site#Plant#Root (Rhizome)

taxonmaps

  • @ref: 69479
  • File name: preview.99_720.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_15;96_91;97_287;98_384;99_720&stattab=map
  • Last taxonomy: Streptomyces
  • 16S sequence: Z76680
  • Sequence Identity:
  • Total samples: 129
  • soil counts: 39
  • aquatic counts: 5
  • animal counts: 85

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
185881German classification
95181Risk group (German classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Streptomyces sampsonii gene for 16S rRNA, partial sequence, strain: NBRC 13083AB1842991465nuccore42239
20218Streptomyces sampsonii strain DSM40394 16S-23S intergenic spacer region, partial sequenceAF363494308nuccore42239
20218Streptomyces sampsonii strain DSM 40394 clone ITS17 16S-23S ribosomal RNA intergenic spacer, partial sequenceAY296953283nuccore42239
20218Streptomyces sampsonii strain DSM 40394 clone ITS1 16S-23S ribosomal RNA intergenic spacer, partial sequenceAY296956287nuccore42239
20218Streptomyces sampsonii strain DSM 40394 clone ITS11 16S-23S ribosomal RNA intergenic spacer, partial sequenceAY296957284nuccore42239
20218Streptomyces sampsonii strain DSM 40394 clone ITS17 16S-23S ribosomal RNA intergenic spacer, partial sequenceAY296958283nuccore42239
20218Streptomyces sampsonii strain DSM 40394 clone ITS19 16S-23S ribosomal RNA intergenic spacer, partial sequenceAY296959285nuccore42239
20218Streptomyces sampsonii strain DSM 40394 clone ITS4 16S-23S ribosomal RNA intergenic spacer, partial sequenceAY296960284nuccore42239
20218Streptomyces sampsonii strain DSM 40394 clone ITS8 16S-23S ribosomal RNA intergenic spacer, partial sequenceAY296961284nuccore42239
20218Streptomyces sampsonii gene for 16S ribosomal RNA, partial sequence, strain: JCM 4516D44203120nuccore42239
20218Streptomyces sampsonii 16S ribosomal RNA gene, partial sequenceEU9289701385nuccore42239
20218S.sampsonii (DSM 40394T) 16S rRNA geneZ766801476nuccore42239
9518Streptomyces sampsonii 16S ribosomal RNA, complete sequenceD638711531nuccore42239

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Streptomyces albidoflavus strain NBRC 130831886.39wgspatric1886
67770Streptomyces albidoflavus NBRC 13083GCA_004195755contigncbi1886

Genome-based predictions

predictions

@reftraitmodeldescriptionpredictionconfidencetraining_data
69480gram-positivegram-positivePositive reaction to Gram-stainingyes91.329no
69480anaerobicanaerobicAbility to grow under anoxygenic conditions (including facultative anaerobes)no97.894no
69480spore-formingspore-formingAbility to form endo- or exosporesyes94.516no
69480aerobicaerobicAbility to grow under oxygenic conditions (including facultative aerobes)yes87.746no
69480thermophilicthermophileAbility to grow at temperatures above or equal to 45°Cno95.5yes
69480flagellatedmotile2+Ability to perform flagellated movementno91.5no

External links

@ref: 9518

culture collection no.: DSM 40394, ATCC 25495, CBS 955.69, ETH 23691, IFO 13083, IMRU 3371, ISP 5394, JCM 4515, KCC S-0515, NBRC 13083, RIA 1275, BCRC 13705, KACC 20132, LMG 8574, NRRL B-12325, VKM Ac-851, VTT E-073026

straininfo link

  • @ref: 84012
  • straininfo: 14079

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
9518Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 40394)https://www.dsmz.de/collection/catalogue/details/culture/DSM-40394
18588Wink, J.http://www.dsmz.de/microorganisms/wink_pdf/DSM40394.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)
84012Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID14079.1StrainInfo: A central database for resolving microbial strain identifiers