Strain identifier

BacDive ID: 15172

Type strain: Yes

Species: Streptomyces fradiae

Variant: Isotype of BacDive ID 15204

Strain history: KCC S-0133 <-- K. Tubaki <-- T. Yamaguchi (IAM 0083) <-- M. Kuroya <-- IMRU 3535.

NCBI tax ID(s): 1319510 (strain), 1906 (species)

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General

@ref: 9264

BacDive-ID: 15172

DSM-Number: 40063

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

description: Streptomyces fradiae DSM 40063 is a spore-forming, mesophilic bacterium that produces antibiotic compounds and was isolated from soil.

NCBI tax id

NCBI tax idMatching level
1906species
1319510strain

strain history

@refhistory
9264<- E.B. Shirling, ISP <- S.A. Waksman, IMRU
67770KCC S-0133 <-- K. Tubaki <-- T. Yamaguchi (IAM 0083) <-- M. Kuroya <-- IMRU 3535.

doi: 10.13145/bacdive15172.20230509.8.1

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 fradiae
  • full scientific name: Streptomyces fradiae (Waksman and Curtis 1916) Waksman and Henrici 1948 (Approved Lists 1980)

  • synonyms

    @refsynonym
    20215Actinomyces fradii
    20215Streptomyces roseoflavus

@ref: 9264

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Streptomycetaceae

genus: Streptomyces

species: Streptomyces fradiae

full scientific name: Streptomyces fradiae (Waksman and Curtis 1916) Waksman and Henrici 1948 emend. Lanoot et al. 2004

variant: Isotype of BacDive ID 15204

type strain: yes

Morphology

cell morphology

@refmotilityconfidencegram stain
69480no93.198
69480100positive

multimedia

  • @ref: 9264
  • multimedia content: https://www.dsmz.de/microorganisms/photos/DSM_40063.jpg
  • caption: Medium 65 28°C
  • intellectual property rights: © Leibniz-Institut DSMZ

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
9264GYM 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
9264ROLLED OATS MINERAL MEDIUM (DSMZ Medium 84)yeshttps://www.dsmz.de/microorganisms/medium/pdf/DSMZ_Medium84.pdf

culture temp

@refgrowthtypetemperaturerange
9264positivegrowth28mesophilic
67770positivegrowth28mesophilic

Physiology and metabolism

spore formation

@refspore formationconfidence
69481yes100
69480yes100

compound production

@refcompound
9264fradicin
9264neomycin
20216Fradicidin
20216Neomycin
67770fradicin

observation

  • @ref: 67770
  • observation: quinones: MK-9(H8), MK-9(H6)

metabolite production

  • @ref: 67770
  • Chebi-ID: 7507
  • metabolite: neomycin
  • production: yes

Isolation, sampling and environmental information

isolation

@refsample type
9264soil
67770Soil

isolation source categories

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

taxonmaps

  • @ref: 69479
  • File name: preview.99_1290.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_15;96_91;97_287;98_1019;99_1290&stattab=map
  • Last taxonomy: Streptomyces
  • 16S sequence: AB184776
  • Sequence Identity:
  • Total samples: 775
  • soil counts: 538
  • aquatic counts: 41
  • animal counts: 100
  • plant counts: 96

Safety information

risk assessment

  • @ref: 9264
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Streptomyces fradiae gene for 16S ribosomal RNA, partial sequence, strain: JCM 4579D44246121ena1906
20218Streptomyces fradiae gene for 16S rRNA, partial sequence, strain: NBRC 12174AB1840591470ena1906
20218Streptomyces fradiae gene for 16S rRNA, partial sequence, strain: NBRC 12773AB1841341463ena1906
20218Streptomyces fradiae gene for 16S rRNA, partial sequence, strain: NBRC 3439AB1847761467ena1906
20218Streptomyces fradiae strain NRRL B-1195 16S ribosomal RNA gene, partial sequenceDQ0266301485ena1906

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Streptomyces fradiae ATCC 10745 = DSM 40063GCA_008704425completencbi1319510
66792Streptomyces fradiae ATCC 10745 = DSM 40063GCA_009834665contigncbi1319510
66792Streptomyces fradiae ATCC 10745 = DSM 400631319510.4completepatric1319510
66792Streptomyces fradiae ATCC 10745 = DSM 400631319510.5wgspatric1319510
66792Streptomyces fradiae strain DSM 400631906.13wgspatric1906
66792Streptomyces fradiae DSM 400632916795502draftimg1906
66792Streptomyces fradiae ATCC 107452563366697draftimg1906
66792Streptomyces fradiae ATCC 107452916801548draftimg1906
66792Streptomyces fradiae DSM 40063651716766draftimg1906
67770Streptomyces fradiae ATCC 10745 = DSM 40063GCA_002119225scaffoldncbi1319510
67770Streptomyces fradiae NRRL B-1195GCA_002154445scaffoldncbi1906

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingyes100no
motileno95.139no
flagellatedno98.082no
gram-positiveyes92.284no
anaerobicno99.157no
aerobicyes93.8no
halophileno94.164no
spore-formingyes95.855no
thermophileno98.264no
glucose-utilyes90.458no
glucose-fermentno90.288no

External links

@ref: 9264

culture collection no.: DSM 40063, ATCC 10745, ATCC 19760, CBS 498.68, ETH 13363, ETH 13472, ETH 28510, IFO 12773, IMRU 3535, ISP 5063, JCM 4133, JCM 4579, NBRC 12773, NCIB 8233, NRRL B-1195, RIA 1040, BCRC 12196, CCM 3174, CECT 3197, CGMCC 4.0576, HAMBI 965, HUT 6095, IFM 1030, IFO 3439, IFO 3718, IMET 42051, IMI 61202, KCTC 9760, MTCC 321, NBIMCC 2443, NBRC 3439, NBRC 3718, NCIMB 11005, NCIMB 8233, PCM 2330, RIA 97, VKM Ac-150, VKM Ac-151, VKM Ac-152, VKM Ac-764

straininfo link

  • @ref: 84275
  • straininfo: 63952

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Metabolism236085Degradation of feather keratin by culture filtrates of Streptomyces fradiae.Young RA, Smith RECan J Microbiol10.1139/m75-0841975Animals, Chickens, Feathers, Hydrogen-Ion Concentration, Hydrolases/*metabolism, Keratins/*metabolism, Kinetics, Streptomyces/*enzymology, TemperatureEnzymology
Metabolism1125855Production of methionine-excreting mutants of Streptomyces fradiae.Young RA, Smith RECan J Microbiol10.1139/m75-0851975Amino Acids/metabolism, Diaminopimelic Acid/biosynthesis, Methionine/*metabolism, Methylnitronitrosoguanidine/*pharmacology, Mutagens, *Mutation, Nitrosoguanidines/*pharmacology, Streptomyces/drug effects/*metabolismBiotechnology
Enzymology6310563Nucleotide sequence of a streptomycete aminoglycoside phosphotransferase gene and its relationship to phosphotransferases encoded by resistance plasmids.Thompson CJ, Gray GSProc Natl Acad Sci U S A10.1073/pnas.80.17.51901983Amino Acid Sequence, Base Sequence, Cloning, Molecular, Codon, DNA Restriction Enzymes, Drug Resistance, Microbial, *Genes, *Genes, Bacterial, Kanamycin Kinase, Neomycin/*pharmacology, Phosphotransferases/*genetics, *Plasmids, Streptomyces/drug effects/*enzymology/geneticsPathogenicity
Metabolism8166572[Use of the protoplast fusion and regeneration method for screening antibiotic producers among inactive strains of Streptomyces].Malanicheva IA, Koz'mian LI, Belova AIu, Dudnik IuVAntibiot Khimioter1993Anti-Bacterial Agents/*biosynthesis, Genetic Testing, Neomycin/biosynthesis, Protoplasts/*physiology, Regeneration/*physiology, Streptomyces/genetics/*metabolism/ultrastructure
Enzymology15827636The neomycin biosynthetic gene cluster of Streptomyces fradiae NCIMB 8233: characterisation of an aminotransferase involved in the formation of 2-deoxystreptamine.Huang F, Haydock SF, Mironenko T, Spiteller D, Li Y, Spencer JBOrg Biomol Chem10.1039/b501199j2005Amination, Carbohydrate Conformation, Chromatography, Liquid, Cloning, Molecular, Hexosamines/biosynthesis, Multigene Family/*genetics, Neomycin/*biosynthesis, Open Reading Frames/genetics, Ribose/chemistry, Spectrum Analysis, Streptomyces/classification/*enzymology/*genetics, Transaminases/*chemistryPhylogeny
Enzymology16506694Biosynthesis of 2-deoxystreptamine by three crucial enzymes in Streptomyces fradiae NBRC 12773.Kudo F, Yamamoto Y, Yokoyama K, Eguchi T, Kakinuma KJ Antibiot (Tokyo)10.1038/ja.2005.1042005Amino Acid Sequence, Anti-Bacterial Agents/*biosynthesis, Carbohydrate Sequence, Chromatography, High Pressure Liquid, Chromatography, Liquid, Hexosamines/biosynthesis, Mass Spectrometry, Molecular Sequence Data, Multigene Family, Streptomyces/*enzymology/geneticsGenetics
Enzymology17206729Elaboration of neosamine rings in the biosynthesis of neomycin and butirosin.Huang F, Spiteller D, Koorbanally NA, Li Y, Llewellyn NM, Spencer JBChembiochem10.1002/cbic.2006003712007Anti-Bacterial Agents/*biosynthesis, Bacillus/enzymology/genetics, Butirosin Sulfate/*biosynthesis, Carbohydrate Sequence, Cyclization, Glucosamine/*analogs & derivatives/chemistry/classification, Molecular Sequence Data, Multigene Family, Neomycin/*biosynthesis, Oxidoreductases/*chemistry/genetics/metabolism, Streptomyces/enzymology/genetics, Transaminases/*chemistry/genetics/metabolismGenetics
Metabolism18802637The neomycin biosynthetic gene cluster of Streptomyces fradiae NCIMB 8233: genetic and biochemical evidence for the roles of two glycosyltransferases and a deacetylase.Fan Q, Huang F, Leadlay PF, Spencer JBOrg Biomol Chem10.1039/b808734b2008Acetylglucosamine/chemistry/metabolism, Amidohydrolases/classification/genetics/*metabolism, Amino Acid Sequence, Conserved Sequence, Glycosyltransferases/chemistry/classification/genetics/*metabolism, Hexosamines/chemistry/metabolism, Mass Spectrometry, Molecular Sequence Data, Molecular Structure, Multigene Family/*genetics, Neomycin/*biosynthesis/chemistry, Sequence Alignment, Streptomyces/*enzymology/*geneticsPhylogeny
Genetics28705965Draft Genome Sequences of Three Actinobacteria Strains Presenting New Candidate Organisms with High Potentials for Specific P450 Cytochromes.Grumaz C, Vainshtein Y, Kirstahler P, Luetz S, Kittelmann M, Schroer K, Eggimann FK, Czaja R, Vogel A, Hilberath T, Worsch A, Girhard M, Urlacher VB, Sandberg M, Sohn KGenome Announc10.1128/genomeA.00532-172017

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
9264Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 40063)https://www.dsmz.de/collection/catalogue/details/culture/DSM-40063
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/
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
84275Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID63952.1StrainInfo: A central database for resolving microbial strain identifiers