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, mesophilic, Gram-positive

description: Saccharopolyspora shandongensis strain 88 is an aerobe, spore-forming, mesophilic 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/bacdive13469.20230509.8.1

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 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

  • @ref: 32456
  • gram stain: positive
  • motility: no

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

@refgrowthtypetemperaturerange
15828positivegrowth28mesophilic
32456positivegrowth15-38
67770positivegrowth28mesophilic

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: ena
  • 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

traitpredictionconfidencetraining_data
gram-positiveyes87.972no
anaerobicno98.182yes
halophileno51.02yes
spore-formingyes93.512no
glucose-utilyes86.866no
aerobicyes87.456yes
flagellatedno97.261yes
thermophileno98.233yes
motileno91.707yes
glucose-fermentno91.472no

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
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