Strain identifier

BacDive ID: 14281

Type strain: Yes

Species: Sphingopyxis granuli

Strain Designation: Kw07

Strain history: <- ST Lee, KAIST

NCBI tax ID(s): 1219060 (strain), 267128 (species)

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General

@ref: 7201

BacDive-ID: 14281

DSM-Number: 17810

keywords: genome sequence, 16S sequence, Bacteria, aerobe, mesophilic, Gram-negative

description: Sphingopyxis granuli Kw07 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from granules from a wastewater treatment plant of a brewery.

NCBI tax id

NCBI tax idMatching level
267128species
1219060strain

strain history

@refhistory
7201<- S.-T. Lee, KAIST <- W.-T. Im, KAIST; Kw07
67771<- ST Lee, KAIST

doi: 10.13145/bacdive14281.20230509.8.1

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 granuli
  • full scientific name: Sphingopyxis granuli Kim et al. 2011

@ref: 7201

domain: Bacteria

phylum: Proteobacteria

class: Alphaproteobacteria

order: Sphingomonadales

family: Sphingomonadaceae

genus: Sphingopyxis

species: Sphingopyxis granuli

full scientific name: Sphingopyxis granuli Kim et al. 2011

strain designation: Kw07

type strain: yes

Morphology

cell morphology

  • @ref: 67771
  • gram stain: negative

Culture and growth conditions

culture medium

  • @ref: 7201
  • name: R2A MEDIUM (DSMZ Medium 830)
  • growth: yes
  • link: https://mediadive.dsmz.de/medium/830
  • composition: Name: R2A MEDIUM (DSMZ Medium 830) Composition: Agar 15.0 g/l Casamino acids 0.5 g/l Starch 0.5 g/l Glucose 0.5 g/l Proteose peptone 0.5 g/l Yeast extract 0.5 g/l K2HPO4 0.3 g/l Na-pyruvate 0.3 g/l MgSO4 x 7 H2O 0.05 g/l Distilled water

culture temp

@refgrowthtypetemperaturerange
7201positivegrowth28mesophilic
59720positivegrowth30-37mesophilic
67771positivegrowth30mesophilic

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
59720aerobe
67771aerobe

observation

  • @ref: 67771
  • observation: quinones: Q-10

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
7201granules from a wastewater treatment plant of a breweryKwang-JuRepublic of KoreaKORAsia
67771From granule sludgeRepublic of KoreaKORAsia

isolation source categories

Cat1Cat2Cat3
#Engineered#Waste#Activated sludge
#Engineered#Waste#Water treatment plant

taxonmaps

  • @ref: 69479
  • File name: preview.99_2844.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_20;96_1020;97_1190;98_1749;99_2844&stattab=map
  • Last taxonomy: Sphingopyxis granuli
  • 16S sequence: AB681243
  • Sequence Identity:
  • Total samples: 92
  • soil counts: 38
  • aquatic counts: 35
  • animal counts: 11
  • plant counts: 8

Safety information

risk assessment

  • @ref: 7201
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Sphingomonas sp. Kw07 gene for 16S rRNA, partial sequence, strain:Kw07AB1875871422ena267128
20218Sphingopyxis granuli gene for 16S rRNA, partial sequence, strain: NBRC 100800AB6812431414ena1219060
7201Sphingopyxis granuli strain Kw07 16S ribosomal RNA gene, partial sequenceAY5630341422ena1219060

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Sphingopyxis granuli NBRC 100800GCA_001591045contigncbi1219060
66792Sphingopyxis granuli NBRC 1008001219060.3wgspatric1219060
66792Sphingopyxis granuli NBRC 1008002731957635draftimg1219060

GC content

  • @ref: 7201
  • GC-content: 63.7

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
motileyes66.588no
gram-positiveno96.49yes
anaerobicno98.913yes
aerobicyes90.551no
halophileno94.903no
spore-formingno95.28no
thermophileno93.867yes
glucose-utilyes73.364no
flagellatedno84.033no
glucose-fermentno91.545no

External links

@ref: 7201

culture collection no.: DSM 17810, KCTC 12209, NBRC 100800, CCUG 52902

straininfo link

  • @ref: 83436
  • straininfo: 132667

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny15880090Sphingopyxis granuli sp. nov., a beta-glucosidase-producing bacterium in the family Sphingomonadaceae in alpha-4 subclass of the Proteobacteria.Kim MK, Im WT, Ohta H, Lee M, Lee STJ Microbiol21692005Base Composition, Nucleic Acid Hybridization, Phylogeny, Sphingomonadaceae/*classification/enzymology/genetics, beta-Glucosidase/*biosynthesisEnzymology
Phylogeny23264504Sphingopyxis italica sp. nov., isolated from Roman catacombs.Alias-Villegas C, Jurado V, Laiz L, Saiz-Jimenez CInt J Syst Evol Microbiol10.1099/ijs.0.046573-02012Bacterial Typing Techniques, DNA, Bacterial/genetics, Fatty Acids/analysis, Molecular Sequence Data, Nucleic Acid Hybridization, *Phylogeny, RNA, Ribosomal, 16S/genetics, Rome, Sequence Analysis, DNA, *Soil Microbiology, Sphingomonadaceae/*classification/genetics/isolation & purification, Ubiquinone/analogs & derivatives/analysisGenetics
Phylogeny30394866Sphingopyxis lindanitolerans sp. nov. strain WS5A3p(T) enriched from a pesticide disposal site.Kaminski MA, Sobczak A, Spolnik G, Danikiewicz W, Dziembowski A, Lipinski LInt J Syst Evol Microbiol10.1099/ijsem.0.0030942018Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, *Hazardous Waste, Nucleic Acid Hybridization, *Pesticides, Phospholipids/chemistry, *Phylogeny, Poland, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Sphingomonadaceae/*classification/genetics/isolation & purification, Ubiquinone/analogs & derivatives/chemistryTranscriptome

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
7201Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 17810)https://www.dsmz.de/collection/catalogue/details/culture/DSM-17810
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
20218Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P.10.1016/j.syapm.2013.11.002StrainInfo introduces electronic passports for microorganisms.Syst Appl Microbiol. 37: 42-50 201424321274
59720Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 52902)https://www.ccug.se/strain?id=52902
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 updatesNucleic Acids Res. 49: D498-D508 202033211880
67771Curators of the KCTChttps://kctc.kribb.re.kr/En/Kctc
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
83436Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID132667.1StrainInfo: A central database for resolving microbial strain identifiers