Strain identifier

BacDive ID: 15604

Type strain: Yes

Species: Streptomyces somaliensis

Strain history: NCTC 11332 <-- R. Gordon IMRU 1274 <-- F. Mariat IP733.

NCBI tax ID(s): 1134445 (strain), 78355 (species)

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General

@ref: 9741

BacDive-ID: 15604

DSM-Number: 40738

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

description: Streptomyces somaliensis DSM 40738 is a spore-forming, mesophilic bacterium that was isolated from mycetoma on foot of 20-year old male.

NCBI tax id

NCBI tax idMatching level
78355species
1134445strain

strain history

@refhistory
9741<- R.E. Gordon, IMRU <- F. Mariat, IP 733
67770NCTC 11332 <-- R. Gordon IMRU 1274 <-- F. Mariat IP733.

doi: 10.13145/bacdive15604.20230509.8.1

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 somaliensis
  • full scientific name: Streptomyces somaliensis (Brumpt 1906) Waksman and Henrici 1948 (Approved Lists 1980)

  • synonyms

    • @ref: 20215
    • synonym: Indiella somaliensis

@ref: 9741

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Streptomycetaceae

genus: Streptomyces

species: Streptomyces somaliensis

full scientific name: Streptomyces somaliensis (Brumpt 1906) Waksman and Henrici 1948 emend. Nouioui et al. 2018

type strain: yes

Morphology

cell morphology

@refmotilityconfidencegram stain
69480no93.951
69480100positive

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
9741GYM 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
9741SPORULATION-AGAR (SA) (DSMZ Medium 555)yeshttps://mediadive.dsmz.de/medium/555Name: SPORULATION-AGAR (SA) (DSMZ Medium 555) Composition: Agar 15.0 g/l Glucose 10.0 g/l Tryptone peptone 2.0 g/l Beef extract 1.0 g/l Yeast extract 1.0 g/l FeSO4 Distilled water

culture temp

@refgrowthtypetemperaturerange
9741positivegrowth28mesophilic
67770positivegrowth28mesophilic

Physiology and metabolism

spore formation

@refspore formationconfidence
69481yes100
69480yes99.515

Isolation, sampling and environmental information

isolation

@refsample typecountryorigin.countrycontinent
9741mycetoma on foot of 20-year old maleSomaliaSOMAfrica
67770Mycetoma on foot of a 20-year-old maleSomaliaSOMAfrica

isolation source categories

Cat1Cat2Cat3
#Infection#Disease
#Infection#Patient
#Host Body-Site#Limb#Foot
#Host#Human#Male

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: AJ007403
  • Sequence Identity:
  • Total samples: 775
  • soil counts: 538
  • aquatic counts: 41
  • animal counts: 100
  • plant counts: 96

Safety information

risk assessment

  • @ref: 9741
  • biosafety level: 2
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Streptomyces somaliensis clone E2 16S ribosomal RNA gene, partial sequenceAY262297504ena1134445
20218Streptomyces somaliensis strain DSM 40738, 16S rRNA geneAJ0074031483ena1134445
20218Streptomyces somaliensis DSM 40738 16S ribosomal RNA gene, partial sequenceAY9997311450ena1134445

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Streptomyces somaliensis DSM 407381134445.8wgspatric1134445
66792Streptomyces somaliensis DSM 407381134445.3wgspatric1134445
66792Streptomyces somaliensis DSM 407382548876818draftimg1134445
67770Streptomyces somaliensis DSM 40738GCA_000258595contigncbi1134445
67770Streptomyces somaliensis DSM 40738GCA_012396115contigncbi1134445
66792Streptomyces somaliensis DSM 40738GCA_024349285scaffoldncbi1134445

GC content

  • @ref: 67770
  • GC-content: 74.1
  • method: genome sequence analysis

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingyes100no
motileno94.272no
flagellatedno98.619no
gram-positiveyes91.558no
anaerobicno98.542no
aerobicyes92.085no
halophileno94.792no
spore-formingyes89.988no
thermophileno92.34yes
glucose-utilyes88.936no
glucose-fermentno88.805no

External links

@ref: 9741

culture collection no.: DSM 40738, ATCC 33201, IMRU 1274, IP 733, JCM 12659, KCTC 9044, NCTC 11332, NRRL B-12077, RIA 1188, VKM Ac-1898

straininfo link

  • @ref: 84691
  • straininfo: 360119

literature

  • topic: Genetics
  • Pubmed-ID: 22689234
  • title: Draft genome sequence of the human pathogen Streptomyces somaliensis, a significant cause of actinomycetoma.
  • authors: Kirby R, Sangal V, Tucker NP, Zakrzewska-Czerwinska J, Wierzbicka K, Herron PR, Chu CJ, Chandra G, Fahal AH, Goodfellow M, Hoskisson PA
  • journal: J Bacteriol
  • DOI: 10.1128/JB.00534-12
  • year: 2012
  • mesh: Actinomycetales Infections/*microbiology, Foot Diseases/*microbiology, *Genome, Bacterial, Humans, Male, Molecular Sequence Data, Mycetoma/*microbiology, *Sequence Analysis, DNA, Streptomyces/classification/*genetics/isolation & purification, Young Adult
  • topic2: Pathogenicity

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
9741Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 40738)https://www.dsmz.de/collection/catalogue/details/culture/DSM-40738
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/
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
84691Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID360119.1StrainInfo: A central database for resolving microbial strain identifiers