Strain identifier

BacDive ID: 13470

Type strain: No

Species: Saccharopolyspora kobensis

Strain Designation: W12

Strain history: J. Zhang W12.

NCBI tax ID(s): 146035 (species)

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

@ref: 17642

BacDive-ID: 13470

DSM-Number: 45556

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

description: Saccharopolyspora kobensis W12 is an aerobe, spore-forming, mesophilic bacterium that was isolated from soil from a field of grass.

NCBI tax id

  • NCBI tax id: 146035
  • Matching level: species

strain history

@refhistory
17642<- JCM <- J. Zhang; W12
67770J. Zhang W12.

doi: 10.13145/bacdive13470.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/actinomycetota
  • domain: Bacteria
  • phylum: Actinomycetota
  • class: Actinomycetes
  • order: Pseudonocardiales
  • family: Pseudonocardiaceae
  • genus: Saccharopolyspora
  • species: Saccharopolyspora kobensis
  • full scientific name: Saccharopolyspora kobensis (Lacey 1989 ex Iwasake and Mori 1979) Nouioui et al. 2018
  • synonyms

    @refsynonym
    20215Saccharopolyspora jiangxiensis
    20215Saccharopolyspora hirsuta subsp. kobensis

@ref: 17642

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Pseudonocardiaceae

genus: Saccharopolyspora

species: Saccharopolyspora kobensis

full scientific name: Saccharopolyspora kobensis (Lacey 1989) Nouioui et al. 2018

strain designation: W12

type strain: no

Morphology

cell morphology

@refgram staincell shapemotilityconfidence
32660positiverod-shapedno
69480positive100

Culture and growth conditions

culture medium

  • @ref: 17642
  • name: GYM STREPTOMYCES MEDIUM (DSMZ Medium 65)
  • growth: yes
  • link: https://mediadive.dsmz.de/medium/65
  • composition: Name: 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

culture temp

@refgrowthtypetemperaturerange
17642positivegrowth28mesophilic
32660positivegrowth15-45
32660positiveoptimum30mesophilic
67770positivegrowth28mesophilic

culture pH

@refabilitytypepHPH range
32660positivegrowth5.5-9.5alkaliphile
32660positiveoptimum7.5

Physiology and metabolism

oxygen tolerance

  • @ref: 32660
  • oxygen tolerance: aerobe

spore formation

@refspore formationconfidence
32660yes
69481yes100
69480yes100

halophily

  • @ref: 32660
  • salt: NaCl
  • growth: positive
  • tested relation: growth
  • concentration: <11 %

observation

@refobservation
32660aggregates in chains
67770quinones: MK-9(H4), MK-10(H2)

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3266030089acetate+carbon source
3266015963ribitol+carbon source
3266022599arabinose+carbon source
3266016947citrate+carbon source
3266023652dextrin+carbon source
3266028757fructose+carbon source
3266028260galactose+carbon source
3266017234glucose+carbon source
3266017754glycerol+carbon source
3266017716lactose+carbon source
3266025115malate+carbon source
3266017306maltose+carbon source
3266029864mannitol+carbon source
3266037684mannose+carbon source
3266037657methyl D-glucoside+carbon source
3266017268myo-inositol+carbon source
3266016634raffinose+carbon source
3266026546rhamnose+carbon source
3266033942ribose+carbon source
3266030911sorbitol+carbon source
3266030031succinate+carbon source
3266017992sucrose+carbon source
3266027082trehalose+carbon source
3266018222xylose+carbon source
326604853esculin+hydrolysis
3266017632nitrate+reduction

enzymes

@refvalueactivityec
32660catalase+1.11.1.6
32660urease+3.5.1.5

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
17642soil from a field of grassJiangxi ProvinceChinaCHNAsia
67770Soil from a field of grassJiangxi ProvinceChinaCHNAsia

isolation source categories

Cat1Cat2Cat3
#Engineered#Agriculture#Field
#Environmental#Terrestrial#Soil
#Host#Plants#Herbaceous plants (Grass,Crops)

taxonmaps

  • @ref: 69479
  • File name: preview.99_35945.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_10;96_5246;97_19583;98_26504;99_35945&stattab=map
  • Last taxonomy: Saccharopolyspora
  • 16S sequence: EF143926
  • Sequence Identity:
  • Total samples: 136
  • soil counts: 112
  • aquatic counts: 3
  • animal counts: 15
  • plant counts: 6

Safety information

risk assessment

  • @ref: 17642
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 17642
  • description: Saccharopolyspora jiangxiensis strain W12 16S ribosomal RNA gene, partial sequence
  • accession: EF143926
  • length: 1419
  • database: ena
  • NCBI tax ID: 418522

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Saccharopolyspora jiangxiensis strain CGMCC 4.3529418522.7wgspatric146035
66792Saccharopolyspora jiangxiensis CGMCC 4.35292667527438draftimg418522
67770Saccharopolyspora kobensis CGMCC 4.3529GCA_900112555scaffoldncbi146035

GC content

@refGC-contentmethod
1764270.3thermal denaturation, midpoint method (Tm)
3266070.3

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingyes100no
gram-positiveyes90.06yes
anaerobicno98.935no
halophileyes56.13yes
spore-formingyes92.668yes
glucose-utilyes87.429yes
aerobicyes90.561yes
flagellatedno97.429yes
thermophileno96.667no
motileno90.887no
glucose-fermentno91.673no

External links

@ref: 17642

culture collection no.: DSM 45556, CGMCC 4.3529, JCM 14613

straininfo link

  • @ref: 82662
  • straininfo: 400005

literature

  • topic: Phylogeny
  • Pubmed-ID: 19406796
  • title: Saccharopolyspora jiangxiensis sp. nov., isolated from grass-field soil.
  • authors: Zhang J, Wu D, Liu Z
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijs.0.65863-0
  • year: 2009
  • mesh: Bacterial Typing Techniques, China, DNA, Bacterial/analysis/genetics, Genes, rRNA, Genotype, Molecular Sequence Data, Phenotype, Phylogeny, *Poaceae, RNA, Ribosomal, 16S/genetics, Saccharopolyspora/*classification/genetics/isolation & purification/physiology, Sequence Analysis, DNA, *Soil Microbiology, Species Specificity
  • topic2: Genetics

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmed
17642Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 45556)https://www.dsmz.de/collection/catalogue/details/culture/DSM-45556
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
32660Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2887128776041
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
82662Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID400005.1StrainInfo: A central database for resolving microbial strain identifiers