Strain identifier

BacDive ID: 16026

Type strain: Yes

Species: Streptomyces sparsogenes

Strain history: KCC S-1517 <-- IFO 13086 <-- SAJ <-- ISP 5356 <-- NRRL 2940 <-- Upjohn Co., USA; UC 2474.

NCBI tax ID(s): 1331668 (strain), 67365 (species)

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General

@ref: 9479

BacDive-ID: 16026

DSM-Number: 40356

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

description: Streptomyces sparsogenes DSM 40356 is a spore-forming, mesophilic bacterium that produces antibiotic compounds and was isolated from soil.

NCBI tax id

NCBI tax idMatching level
67365species
1331668strain

strain history

@refhistory
9479<- E.B. Shirling, ISP <- NRRL <- Upjohn Comp., UC 2474
67770KCC S-1517 <-- IFO 13086 <-- SAJ <-- ISP 5356 <-- NRRL 2940 <-- Upjohn Co., USA; UC 2474.

doi: 10.13145/bacdive16026.20230509.8.1

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 sparsogenes
  • full scientific name: Streptomyces sparsogenes Owen et al. 1963 (Approved Lists 1980)

@ref: 9479

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Streptomycetaceae

genus: Streptomyces

species: Streptomyces sparsogenes

full scientific name: Streptomyces sparsogenes Owen et al. 1963 emend. Goodfellow et al. 2007

type strain: yes

Morphology

cell morphology

@refmotilityconfidencegram stain
69480no92.841
69480100positive

multimedia

  • @ref: 9479
  • multimedia content: https://www.dsmz.de/microorganisms/photos/DSM_40356.jpg
  • caption: Medium 65 28°C
  • intellectual property rights: Leibniz-Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
9479GYM 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
9479ROLLED OATS MINERAL MEDIUM (DSMZ Medium 84)yeshttps://www.dsmz.de/microorganisms/medium/pdf/DSMZ_Medium84.pdf

culture temp

@refgrowthtypetemperaturerange
9479positivegrowth28mesophilic
67770positivegrowth28mesophilic

Physiology and metabolism

spore formation

@refspore formationconfidence
69481yes100
69480yes100

compound production

@refcompound
9479sparsomycine
9479tubercidin

metabolite production

  • @ref: 67770
  • Chebi-ID: 48267
  • metabolite: tubercidin
  • production: yes

Isolation, sampling and environmental information

isolation

@refsample type
9479soil
67770Soil

isolation source categories

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

Safety information

risk assessment

  • @ref: 9479
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Streptomyces sparsogenes gene for 16S ribosomal RNA, partial sequence, strain: JCM 4517D44205120ena67365
20218Streptomyces sparsogenes gene for 16S rRNA, partial sequence, strain: NBRC 13086AB1843011460ena67365
20218Streptomyces sparsogenes partial 16S rRNA gene, type strain NRRL 2940TAJ3918171493ena67365

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Streptomyces sparsogenes DSM 40356 strain DSM 403561331668.3wgspatric1331668
66792Streptomyces sparsogenes strain ATCC 2549867365.3wgspatric67365
66792Streptomyces sparsogenes DSM 403562868405050draftimg1331668
66792Streptomyces sparsogenes ATCC 254982865833183draftimg67365
67770Streptomyces sparsogenes DSM 40356GCA_001969965contigncbi1331668
67770Streptomyces sparsogenes ATCC 25498GCA_001704635contigncbi67365

GC content

  • @ref: 67770
  • GC-content: 71.9
  • method: thermal denaturation, midpoint method (Tm)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingyes100no
motileno93.392no
gram-positiveyes88.963no
anaerobicno99.173no
halophileno89.642no
spore-formingyes96.254no
glucose-utilyes88.174no
aerobicyes93.051no
flagellatedno97.736no
thermophileno98.328yes
glucose-fermentno89.938no

External links

@ref: 9479

culture collection no.: DSM 40356, ATCC 25498, CBS 672.69, CBS 958.69, CGMCC AS 4.1446, IFO 13086, ISP 5356, JCM 4517, NBRC 13086, NCIB 9449, NRRL 2940, RIA 1278, UC 2474, BCRC 12085, LMG 19378, LMG 5985, NCIMB 9449, RIA 905, VKM Ac-1744

straininfo link

  • @ref: 85099
  • straininfo: 5018

literature

topicPubmed-IDtitleauthorsjournalyearmeshtopic2DOI
Genetics9795282Structure of teichoic acid of the cell wall of Streptomyces sparsogenes VKM Ac-1744T.Shashkov AS, Tul'skaya EM, Grachev AA, Evtushenko LI, Bueva OV, Naumova IBBiochemistry (Mosc)1998Carbohydrate Sequence, Cell Wall/chemistry, DNA/genetics, Magnetic Resonance Spectroscopy, Molecular Sequence Data, Molecular Structure, Species Specificity, Streptomyces/*chemistry/genetics, Teichoic Acids/*chemistryPhylogeny
Phylogeny17407000The Streptomyces violaceusniger clade: a home for Streptomycetes with rugose ornamented spores.Goodfellow M, Kumar Y, Labeda DP, Sembiring LAntonie Van Leeuwenhoek2007Molecular Sequence Data, Phylogeny, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Species Specificity, Spores, Bacterial/*cytology, Streptomyces/*classification/*cytology/geneticsGenetics10.1007/s10482-007-9146-6
Genetics29111481Draft genome sequence of broad-spectrum antibiotic sparsomycin-producing Streptomyces sparsogenes ATCC 25498 from the American Type Culture Collection.Zhang H, Zhou Q, Lou T, Wang S, Ruan HJ Glob Antimicrob Resist2017Genome Size, *Genome, Bacterial, High-Throughput Nucleotide Sequencing, Humans, Multigene Family, Secondary Metabolism, Sequence Analysis, DNA/*methods, Sparsomycin/*biosynthesis, Streptomyces/genetics/*isolation & purification/metabolismPathogenicity10.1016/j.jgar.2017.10.011
Phylogeny35637321Diversity of the culturable lichen-derived actinobacteria and the taxonomy of Streptomyces parmotrematis sp. nov.Somphong A, Poengsungnoen V, Buaruang K, Suriyachadkun C, Sripreechasak P, Tanasupawat S, Phongsopitanun WAntonie Van Leeuwenhoek202210.1007/s10482-022-01744-6

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
9479Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 40356)https://www.dsmz.de/collection/catalogue/details/culture/DSM-40356
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)
66794Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg10.1093/nar/gkaa1025BRENDA, the ELIXIR core data resource in 2021: new developments and updatesNucleic Acids Res. 49: D498-D508 202033211880
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
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
85099Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID5018.1StrainInfo: A central database for resolving microbial strain identifiers