Strain identifier

BacDive ID: 13469

Type strain: Yes

Species: Saccharopolyspora shandongensis

Strain Designation: strain 88

Strain history: J. Zhang 88.

NCBI tax ID(s): 418495 (species)

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General

@ref: 15828

BacDive-ID: 13469

DSM-Number: 45244

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

description: Saccharopolyspora shandongensis strain 88 is an aerobe, spore-forming, Gram-positive bacterium that was isolated from wheat-field soil sample.

NCBI tax id

  • NCBI tax id: 418495
  • Matching level: species

strain history

@refhistory
15828<- JCM/RIKEN; JCM 14614 <- J. Zhang; strain 88
67770J. Zhang 88.

doi: 10.13145/bacdive13469.20240916.9.1

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 shandongensis
  • full scientific name: Saccharopolyspora shandongensis Zhang et al. 2008

@ref: 15828

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Pseudonocardiaceae

genus: Saccharopolyspora

species: Saccharopolyspora shandongensis

full scientific name: Saccharopolyspora shandongensis Zhang et al. 2008

strain designation: strain 88

type strain: yes

Morphology

cell morphology

@refgram stainmotilityconfidence
32456positiveno
69480positive90.368

pigmentation

  • @ref: 32456
  • production: yes

multimedia

  • @ref: 15828
  • multimedia content: https://www.dsmz.de/microorganisms/photos/DSM_45244.jpg
  • caption: Medium 554 28°C
  • intellectual property rights: © Leibniz-Institut DSMZ

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
15828GYM 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
15828N-Z-AMINE-MEDIUM (DSMZ Medium 554)yeshttps://mediadive.dsmz.de/medium/554Name: N-Z-AMINE-MEDIUM (DSMZ Medium 554) Composition: Starch 20.0 g/l Agar 20.0 g/l Glucose 10.0 g/l N-Z amine 5.0 g/l Yeast extract 5.0 g/l CaCO3 1.0 g/l Distilled water

culture temp

@refgrowthtypetemperature
15828positivegrowth28
32456positivegrowth15-38
67770positivegrowth28

culture pH

  • @ref: 32456
  • ability: positive
  • type: growth
  • pH: 5.5-9.5
  • PH range: alkaliphile

Physiology and metabolism

oxygen tolerance

  • @ref: 32456
  • oxygen tolerance: aerobe

spore formation

  • @ref: 32456
  • spore formation: yes

halophily

  • @ref: 32456
  • salt: NaCl
  • growth: positive
  • tested relation: growth
  • concentration: <7 %

observation

  • @ref: 67770
  • observation: quinones: MK-9(H4)

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3245630089acetate+carbon source
3245615963ribitol+carbon source
3245622599arabinose+carbon source
3245617057cellobiose+carbon source
3245616947citrate+carbon source
3245628053melibiose+carbon source
3245630911sorbitol+carbon source
3245630031succinate+carbon source
3245627082trehalose+carbon source
324564853esculin+hydrolysis
3245617632nitrate+reduction

enzymes

  • @ref: 32456
  • value: urease
  • activity: +
  • ec: 3.5.1.5

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
15828wheat-field soil sampleShandong ProvinceChinaCHNAsia
67770Wheat-field soil in Shandong ProvinceChinaCHNAsia

isolation source categories

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

taxonmaps

  • @ref: 69479
  • File name: preview.99_150923.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_10;96_1393;97_1660;98_2017;99_150923&stattab=map
  • Last taxonomy: Saccharopolyspora shandongensis
  • 16S sequence: EF104116
  • Sequence Identity:
  • Total samples: 261
  • soil counts: 223
  • aquatic counts: 2
  • animal counts: 23
  • plant counts: 13

Safety information

risk assessment

  • @ref: 15828
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 15828
  • description: Saccharopolyspora shandongensis strain 88 16S ribosomal RNA gene, partial sequence
  • accession: EF104116
  • length: 1417
  • database: nuccore
  • NCBI tax ID: 418495

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Saccharopolyspora shandongensis strain CGMCC 4.3530418495.4wgspatric418495
66792Saccharopolyspora shandongensis CGMCC 4.35302671180068draftimg418495
67770Saccharopolyspora shandongensis CGMCC 4.3530GCA_900106995scaffoldncbi418495

GC content

@refGC-contentmethod
1582870.1
6777070.1thermal denaturation, midpoint method (Tm)

Genome-based predictions

predictions

@reftraitmodeldescriptionpredictionconfidencetraining_data
69480gram-positivegram-positivePositive reaction to Gram-stainingyes90.368yes
69480anaerobicanaerobicAbility to grow under anoxygenic conditions (including facultative anaerobes)no93.894no
69480spore-formingspore-formingAbility to form endo- or exosporesyes86.495yes
69480aerobicaerobicAbility to grow under oxygenic conditions (including facultative aerobes)yes89.37yes
69480thermophilicthermophileAbility to grow at temperatures above or equal to 45°Cno95no
69480flagellatedmotile2+Ability to perform flagellated movementno88yes

External links

@ref: 15828

culture collection no.: DSM 45244, CGMCC 4.3530, JCM 14614

straininfo link

  • @ref: 82661
  • straininfo: 389429

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny18450695Saccharopolyspora shandongensis sp. nov., isolated from wheat-field soil.Zhang J, Wu D, Zhang J, Liu Z, Song FInt J Syst Evol Microbiol10.1099/ijs.0.65521-02008Bacterial Typing Techniques, DNA, Bacterial/analysis/isolation & purification, Genes, rRNA, Genotype, Molecular Sequence Data, Nucleic Acid Hybridization, Phenotype, Phylogeny, RNA, Ribosomal, 16S/genetics, Saccharopolyspora/*classification/genetics/isolation & purification/physiology, Sequence Analysis, DNA, *Soil Microbiology, Species Specificity, *TriticumGenetics
Phylogeny19783611Saccharopolyspora phatthalungensis sp. nov., isolated from rhizosphere soil of Hevea brasiliensis.Duangmal K, Mingma R, Thamchaipenet A, Matsumoto A, Takahashi YInt J Syst Evol Microbiol10.1099/ijs.0.018275-02009DNA, Bacterial/genetics, DNA, Ribosomal/genetics, Fatty Acids/metabolism, Hevea/*microbiology, Molecular Sequence Data, Phylogeny, Plant Roots/microbiology, RNA, Ribosomal, 16S/genetics, Saccharopolyspora/*classification/genetics/*isolation & purification/metabolism, *Soil MicrobiologyMetabolism

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmedjournal
15828Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 45244)https://www.dsmz.de/collection/catalogue/details/culture/DSM-45244
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
32456Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2867828776041
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 updates33211880Nucleic Acids Res. 49: D498-D508 2020
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)
82661Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID389429.1StrainInfo: A central database for resolving microbial strain identifiers