Strain identifier

BacDive ID: 16061

Type strain: Yes

Species: Streptomyces umbrinus

Strain history: KCC S-0521 <-- IFO 13091 <-- SAJ <-- ISP 5278 <-- INA 1703/53.

NCBI tax ID(s): 67370 (species)

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General

@ref: 9429

BacDive-ID: 16061

DSM-Number: 40278

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

description: Streptomyces umbrinus DSM 40278 is a spore-forming, mesophilic, Gram-positive bacterium that was isolated from soil.

NCBI tax id

  • NCBI tax id: 67370
  • Matching level: species

strain history

@refhistory
9429<- E.B. Shirling, ISP <- G.F. Gauze INA
67770KCC S-0521 <-- IFO 13091 <-- SAJ <-- ISP 5278 <-- INA 1703/53.

doi: 10.13145/bacdive16061.20230509.8.1

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 umbrinus
  • full scientific name: Streptomyces umbrinus (Sveshnikova 1957) Pridham et al. 1958 (Approved Lists 1980)
  • synonyms

    • @ref: 20215
    • synonym: Actinomyces umbrinus

@ref: 9429

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Streptomycetaceae

genus: Streptomyces

species: Streptomyces umbrinus

full scientific name: Streptomyces umbrinus (Sveshnikova 1957) Pridham et al. 1958

type strain: yes

Morphology

cell morphology

  • @ref: 69480
  • gram stain: positive
  • confidence: 100

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
9429GYM 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
9429ISP 5 MEDIUM (DSMZ Medium 993)yeshttps://www.dsmz.de/microorganisms/medium/pdf/DSMZ_Medium993.pdf

culture temp

@refgrowthtypetemperaturerange
9429positivegrowth28mesophilic
67770positivegrowth28mesophilic

Physiology and metabolism

spore formation

@refspore formationconfidence
69481yes100
69480yes100

observation

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

Isolation, sampling and environmental information

isolation

@refsample typecountrycontinentorigin.country
9429soilUSSRAsia
67770SoilRussiaRUS

isolation source categories

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

Safety information

risk assessment

  • @ref: 9429
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Streptomyces umbrinus gene for 16S ribosomal RNA, partial sequence, strain: JCM 4521D44209120ena67370
20218Streptomyces umbrinus gene for 16S rRNA, partial sequence, strain: NBRC 13091AB1843051479ena67370
20218Streptomyces umbrinus strain NRRL B-2572T 16S ribosomal RNA gene, partial sequenceDQ4425491538ena67370

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Streptomyces umbrinus strain JCM 452167370.3wgspatric67370
67770Streptomyces umbrinus JCM 4521GCA_014650195scaffoldncbi67370

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingyes100no
gram-positiveyes86.508no
anaerobicno99.168no
halophileno94.217no
spore-formingyes93.547no
glucose-utilyes91.353no
thermophileno98.991yes
flagellatedno97.882no
motileno93.235no
aerobicyes91.689no
glucose-fermentno88.334no

External links

@ref: 9429

culture collection no.: DSM 40278, ATCC 19929, ATCC 25503, CBS 645.69, IFO 13091, INA 1703, ISP 5278, NBRC 13091, RIA 1283, JCM 4521, BCRC 15129, CGMCC 4.1791, INA 1703/53, NRRL B-2572, VKM Ac-1747

straininfo link

  • @ref: 85134
  • straininfo: 389294

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny28382471Two new species of the genus Streptomyces: Streptomyces camponoti sp. nov. and Streptomyces cuticulae sp. nov. isolated from the cuticle of Camponotus japonicus Mayr.Piao C, Zheng W, Li Y, Liu C, Jin L, Song W, Yan K, Wang X, Xiang WArch Microbiol10.1007/s00203-017-1353-62017Animals, Ants/*microbiology, Bacterial Typing Techniques, China, DNA Gyrase/genetics, DNA, Bacterial/genetics, DNA, Ribosomal/genetics, Fatty Acids/analysis, Nucleic Acid Hybridization, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Streptomyces/classification/genetics/isolation & purificationTranscriptome
Phylogeny35471105Streptomyces liliifuscus sp. nov and an anti-ginger plague agent Streptomyces liliiviolaceus sp. nov, two novel species isolated from soil of Lilium lancifolium.Li K, Man Y, Liu J, Liu Z, Ma H, Zhu H, Zhou Y, Zhang C, Zhou XInt J Syst Evol Microbiol10.1099/ijsem.0.0053402022Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, *Ginger/genetics, *Lilium/genetics, Phylogeny, *Plague, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Soil, Soil Microbiology, *StreptomycesTranscriptome

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
9429Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 40278)https://www.dsmz.de/collection/catalogue/details/culture/DSM-40278
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/
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
85134Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID389294.1StrainInfo: A central database for resolving microbial strain identifiers