Strain identifier

BacDive ID: 23282

Type strain: No

Species: Sphingopyxis panaciterrulae

Variant: Isotype of BacDive ID 14286

Strain history: <- KCTC <- S. Srinivasan, Korean Ginseng Center and Ginseng Genetic Resource Bank, Gyeonggi; DC34

NCBI tax ID(s): 462372 (species)

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General

@ref: 19106

BacDive-ID: 23282

DSM-Number: 27163

keywords: genome sequence, Bacteria, Gram-negative

description: Sphingopyxis panaciterrulae DSM 27163 is a Gram-negative bacterium that was isolated from soil of ginseng field.

NCBI tax id

  • NCBI tax id: 462372
  • Matching level: species

strain history

  • @ref: 19106
  • history: <- KCTC <- S. Srinivasan, Korean Ginseng Center and Ginseng Genetic Resource Bank, Gyeonggi; DC34

doi: 10.13145/bacdive23282.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Alphaproteobacteria
  • order: Sphingomonadales
  • family: Sphingomonadaceae
  • genus: Sphingopyxis
  • species: Sphingopyxis panaciterrulae
  • full scientific name: Sphingopyxis panaciterrulae Srinivasan et al. 2010

@ref: 19106

domain: Bacteria

phylum: Proteobacteria

class: Alphaproteobacteria

order: Sphingomonadales

family: Sphingomonadaceae

genus: Sphingopyxis

species: Sphingopyxis panaciterrulae

full scientific name: Sphingopyxis panaciterrulae Srinivasan et al. 2010

variant: Isotype of BacDive ID 14286

type strain: no

Morphology

cell morphology

  • @ref: 69480
  • gram stain: negative
  • confidence: 99.98

multimedia

  • @ref: 19106
  • multimedia content: https://www.dsmz.de/microorganisms/photos/DSM_27163.jpg
  • intellectual property rights: © Leibniz-Institut DSMZ

Physiology and metabolism

spore formation

@refspore formationconfidence
69481no99
69480no99.98

Isolation, sampling and environmental information

isolation

  • @ref: 19106
  • sample type: soil of ginseng field
  • geographic location: Daejeon
  • country: Republic of Korea
  • origin.country: KOR
  • continent: Asia

isolation source categories

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

Sequence information

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Sphingopyxis panaciterrulae DSM 27163GCA_014199295contigncbi462372
66792Sphingopyxis panaciterrulae strain DSM 27163462372.3wgspatric462372
66792Sphingopyxis panaciterrulae DSM 271632828386659draftimg462372

GC content

  • @ref: 19106
  • GC-content: 62.3
  • method: high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno99no
gram-positiveno96.501no
anaerobicno99.331no
halophileno93.128no
spore-formingno93.882no
glucose-utilyes88.988no
aerobicyes93.28no
flagellatedno87.688no
thermophileno97.544no
motileyes62.7no
glucose-fermentno93.298no

External links

@ref: 19106

culture collection no.: DSM 27163, DCY 34

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny19933588Sphingopyxis panaciterrulae sp. nov., isolated from soil of a ginseng field.Srinivasan S, Kim MK, Sathiyaraj G, Veena V, Mahalakshmi M, Kalaiselvi S, Kim YJ, Yang DCInt J Syst Evol Microbiol10.1099/ijs.0.019414-02009Bacterial Typing Techniques, Cluster Analysis, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis, Korea, Locomotion, Molecular Sequence Data, Panax/*microbiology, Phospholipids/analysis, Phylogeny, Quinones/analysis, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Sphingomonadaceae/chemistry/*classification/genetics/*isolation & purificationGenetics
Phylogeny23125320Sphingopyxis indica sp. nov., isolated from a high dose point hexachlorocyclohexane (HCH)-contaminated dumpsite.Jindal S, Dua A, Lal RInt J Syst Evol Microbiol10.1099/ijs.0.040840-02012Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/analysis, *Hexachlorocyclohexane, India, Molecular Sequence Data, Nucleic Acid Hybridization, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, *Soil Pollutants, Spermidine/analysis, Sphingomonadaceae/*classification/genetics/isolation & purification, Ubiquinone/analysisGenetics

Reference

@idauthorscataloguedoi/urltitle
19106Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 27163)https://www.dsmz.de/collection/catalogue/details/culture/DSM-27163
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