Strain identifier

BacDive ID: 16484

Type strain: Yes

Species: Streptomyces spongiae

Strain Designation: Sp080513SC-24

Strain history: <- T. Tamura, NBRC; NBRC 106415 <- S. T. Khan; Sp080513SC-24

NCBI tax ID(s): 565072 (species)

For citation purpose refer to the digital object identifier (doi) of the current version.
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General

@ref: 17547

BacDive-ID: 16484

DSM-Number: 42031

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

description: Streptomyces spongiae Sp080513SC-24 is a spore-forming, mesophilic, Gram-positive bacterium that was isolated from marine sponge, Haliclona sp..

NCBI tax id

  • NCBI tax id: 565072
  • Matching level: species

strain history

  • @ref: 17547
  • history: <- T. Tamura, NBRC; NBRC 106415 <- S. T. Khan; Sp080513SC-24

doi: 10.13145/bacdive16484.20230509.8.1

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 spongiae
  • full scientific name: Streptomyces spongiae Khan et al. 2011

@ref: 17547

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Streptomycetaceae

genus: Streptomyces

species: Streptomyces spongiae

full scientific name: Streptomyces spongiae Khan et al. 2011

strain designation: Sp080513SC-24

type strain: yes

Morphology

cell morphology

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

Culture and growth conditions

culture medium

  • @ref: 17547
  • name: YEAST EXTRACT-STARCH AGAR(50% MARINE WATER) (DSMZ Medium 1274)
  • growth: yes
  • link: https://mediadive.dsmz.de/medium/1274
  • composition: Name: YEAST EXTRACT-STARCH AGAR (50% MARINE WATER) (DSMZ Medium 1274) Composition: Agar 15.0 g/l Starch 10.0 g/l Yeast extract 2.0 g/l Sea water Distilled water

culture temp

  • @ref: 17547
  • growth: positive
  • type: growth
  • temperature: 28
  • range: mesophilic

Physiology and metabolism

spore formation

@refspore formationconfidence
69481yes100
69480yes100

Isolation, sampling and environmental information

isolation

  • @ref: 17547
  • sample type: marine sponge, Haliclona sp.
  • host species: Haliclona
  • geographic location: Chiba, Tateyama
  • country: Japan
  • origin.country: JPN
  • continent: Asia

isolation source categories

Cat1Cat2Cat3
#Environmental#Aquatic#Marine
#Host#Invertebrates (Other)#Porifera (Sponges)

Safety information

risk assessment

  • @ref: 17547
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 17547
  • description: Streptomyces spongiae gene for 16S rRNA, partial sequence
  • accession: AB498741
  • length: 1472
  • database: ena
  • NCBI tax ID: 565072

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Streptomyces spongiae NBRC 106415GCA_009377185contigncbi565072
66792Streptomyces spongiae strain NBRC 106415565072.3wgspatric565072

GC content

  • @ref: 17547
  • GC-content: 72
  • method: high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingyes100no
gram-positiveyes84.931no
anaerobicno98.888no
halophileno93.382no
spore-formingyes93.559no
glucose-utilyes89.979no
thermophileno97.994no
flagellatedno98.1no
motileno94.722no
aerobicyes92.953no
glucose-fermentno88.636no

External links

@ref: 17547

culture collection no.: DSM 42031, NBRC 106415

straininfo link

  • @ref: 85519
  • straininfo: 404610

literature

  • topic: Phylogeny
  • Pubmed-ID: 32139879
  • title: Streptomyces acidicola sp. nov., isolated from a peat swamp forest in Thailand.
  • authors: Lipun K, Chantavorakit T, Mingma R, Duangmal K
  • journal: J Antibiot (Tokyo)
  • DOI: 10.1038/s41429-020-0294-5
  • year: 2020
  • mesh: Amino Acids, Diamino/genetics, Bacterial Typing Techniques/methods, Base Composition/genetics, DNA, Bacterial/genetics, Diaminopimelic Acid, Fatty Acids/genetics, Forests, Galactose/genetics, Glucose/genetics, Mannose/genetics, Nucleic Acid Hybridization/genetics, Phospholipids/genetics, Phylogeny, RNA, Ribosomal, 16S/genetics, Ribose/genetics, Soil, Soil Microbiology, Streptomyces/genetics/*isolation & purification, Thailand, Wetlands
  • topic2: Enzymology

Reference

@idauthorscataloguedoi/urltitle
17547Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 42031)https://www.dsmz.de/collection/catalogue/details/culture/DSM-42031
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
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)
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
85519Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID404610.1StrainInfo: A central database for resolving microbial strain identifiers