Strain identifier

BacDive ID: 14257

Type strain: Yes

Species: Sphingomonas insulae

Strain Designation: DS-28

Strain history: CIP <- 2012, JCM <- 2007, J.H. Yoon: strain DS-28

NCBI tax ID(s): 424800 (species)

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General

@ref: 15956

BacDive-ID: 14257

DSM-Number: 21792

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

description: Sphingomonas insulae DS-28 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from soil.

NCBI tax id

  • NCBI tax id: 424800
  • Matching level: species

strain history

@refhistory
15956<- KCTC <- J.-H. Yoon, KRIBB
67770J.-H. Yoon DS-28.
67771<- JH Yoon, KRIBB
120141CIP <- 2012, JCM <- 2007, J.H. Yoon: strain DS-28

doi: 10.13145/bacdive14257.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Alphaproteobacteria
  • order: Sphingomonadales
  • family: Sphingomonadaceae
  • genus: Sphingomonas
  • species: Sphingomonas insulae
  • full scientific name: Sphingomonas insulae Yoon et al. 2008

@ref: 15956

domain: Bacteria

phylum: Proteobacteria

class: Alphaproteobacteria

order: Sphingomonadales

family: Sphingomonadaceae

genus: Sphingomonas

species: Sphingomonas insulae

full scientific name: Sphingomonas insulae Yoon et al. 2008

strain designation: DS-28

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
32175negative3 µm0.45 µmrod-shapedyes
67771negative
69480negative99.966
120141negativerod-shapedyes

pigmentation

  • @ref: 32175
  • production: yes

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
15956NUTRIENT AGAR (DSMZ Medium 1)yeshttps://mediadive.dsmz.de/medium/1Name: NUTRIENT AGAR (DSMZ Medium 1) Composition: Agar 15.0 g/l Peptone 5.0 g/l Meat extract 3.0 g/l Distilled water
36905MEDIUM 328- for nutrient agaryesDistilled water make up to (1000.000 ml);Agar (15.000 g);Peptone (5.000g);Beef extract (3.000 g)
120141CIP Medium 328yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=328

culture temp

@refgrowthtypetemperaturerange
15956positivegrowth28mesophilic
32175positivegrowth04-34
32175positiveoptimum25mesophilic
36905positivegrowth25mesophilic
67770positivegrowth25mesophilic
67771positivegrowth25mesophilic

culture pH

@refabilitytypepHPH range
32175positivegrowth5-8.5alkaliphile
32175positiveoptimum6.5

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
32175aerobe
67771aerobe

spore formation

@refspore formationconfidence
69481no96
69480no99.988

halophily

@refsaltgrowthtested relationconcentration
32175NaClpositivegrowth0-2 %
32175NaClpositiveoptimum0.25 %

observation

  • @ref: 67770
  • observation: quinones: Q-10

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3217522599arabinose+carbon source
3217517057cellobiose+carbon source
3217516947citrate+carbon source
3217528757fructose+carbon source
3217528260galactose+carbon source
3217517234glucose+carbon source
3217517754glycerol+carbon source
3217525115malate+carbon source
3217517306maltose+carbon source
3217537684mannose+carbon source
3217528053melibiose+carbon source
32175506227N-acetylglucosamine+carbon source
3217516634raffinose+carbon source
3217526546rhamnose+carbon source
3217517814salicin+carbon source
3217517992sucrose+carbon source
3217527082trehalose+carbon source
3217518222xylose+carbon source
321754853esculin+hydrolysis
6836925115malate+assimilation
6836917128adipate-assimilation
6836927689decanoate-assimilation
6836924265gluconate-assimilation
6836917306maltose-assimilation
6836959640N-acetylglucosamine+assimilation
6836916899D-mannitol-assimilation
6836916024D-mannose+assimilation
6836930849L-arabinose+assimilation
6836917634D-glucose+assimilation
683695291gelatin-hydrolysis
683694853esculin+hydrolysis
6836916199urea-hydrolysis
6836929016arginine-hydrolysis
6836917634D-glucose-fermentation
6836927897tryptophan-energy source
6836917632nitrate-reduction

metabolite production

  • @ref: 68369
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

metabolite tests

  • @ref: 68369
  • Chebi-ID: 35581
  • metabolite: indole
  • indole test: -

enzymes

@refvalueactivityec
32175acid phosphatase+3.1.3.2
32175alkaline phosphatase+3.1.3.1
32175catalase+1.11.1.6
68369cytochrome oxidase+1.9.3.1
68369gelatinase-
68369beta-glucosidase+3.2.1.21
68369urease-3.5.1.5
68369arginine dihydrolase-3.5.3.6

API 20NE

@refNO3TRPGLU_ FermADH ArgUREESCGELPNPGGLU_ AssimARAMNEMANNAGMALGNTCAPADIMLTCITPACOX
15956-----+-++++-+----++-+

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
15956soilDokdoRepublic of KoreaKORAsia
67770Soil
67771From soilDokdoRepublic of KoreaKORAsia
120141Environment, Soil

isolation source categories

  • Cat1: #Environmental
  • Cat2: #Terrestrial
  • Cat3: #Soil

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
159561Risk group (German classification)
1201411Risk group (French classification)

Sequence information

16S sequences

  • @ref: 15956
  • description: Sphingomonas insulae strain DS-28 16S ribosomal RNA gene, partial sequence
  • accession: EF363714
  • length: 1447
  • database: ena
  • NCBI tax ID: 424800

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Sphingomonas insulae KCTC 12872GCA_010450875completencbi424800
66792Sphingomonas insulae strain DSM 21792424800.4wgspatric424800
66792Sphingomonas insulae strain KCTC 12872424800.3completepatric424800
66792Sphingomonas insulae DSM 217922828333980draftimg424800
67770Sphingomonas insulae DSM 21792GCA_011762035scaffoldncbi424800

GC content

@refGC-contentmethod
3217567
6777067high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno96no
motileyes81.383yes
flagellatedno85.68no
gram-positiveno97.091yes
anaerobicno99.347yes
aerobicyes94.717no
halophileno93.46yes
spore-formingno94.755no
glucose-utilyes92.509no
thermophileno99.028yes
glucose-fermentno91.332no

External links

@ref: 15956

culture collection no.: DSM 21792, JCM 14603, KCTC 12872, CIP 110394

straininfo link

  • @ref: 83416
  • straininfo: 323998

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny18175714Sphingomonas insulae sp. nov., isolated from soil.Yoon JH, Kang SJ, Lee SY, Oh TKInt J Syst Evol Microbiol10.1099/ijs.0.65075-02008Bacterial Typing Techniques, Base Composition, DNA, Bacterial/analysis, Genes, rRNA, Korea, Molecular Sequence Data, Nucleic Acid Hybridization, Phenotype, Phylogeny, RNA, Ribosomal, 16S, Sequence Analysis, DNA, *Soil Microbiology, Species Specificity, Sphingomonas/*classification/genetics/*isolation & purificationGenetics
Phylogeny22328613Sphingomonas cynarae sp. nov., a proteobacterium that produces an unusual type of sphingan.Tala A, Lenucci M, Gaballo A, Durante M, Tredici SM, Debowles DA, Pizzolante G, Marcuccio C, Carata E, Piro G, Carpita NC, Mita G, Alifano PInt J Syst Evol Microbiol10.1099/ijs.0.032060-02012Bacterial Typing Techniques, Base Composition, Cynara/*microbiology, DNA, Bacterial/genetics, Fatty Acids/analysis, Molecular Sequence Data, Nucleic Acid Hybridization, *Phylogeny, Polyamines/analysis, Polysaccharides, Bacterial/*biosynthesis, RNA, Ribosomal, 16S/genetics, Sphingomonas/*classification/genetics/isolation & purification, Ubiquinone/analysisGenetics

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmed
15956Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 21792)https://www.dsmz.de/collection/catalogue/details/culture/DSM-21792
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
32175Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2841728776041
36905Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/8249
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/
67771Curators of the KCTChttps://kctc.kribb.re.kr/En/Kctc
68369Automatically annotated from API 20NE
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
83416Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID323998.1StrainInfo: A central database for resolving microbial strain identifiers
120141Curators of the CIPCollection of Institut Pasteur (CIP 110394)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20110394