Strain identifier

BacDive ID: 14200

Type strain: Yes

Species: Sphingomonas echinoides

Strain history: CIP <- 1989, DSM <- ICBB <- W. Heumann

NCBI tax ID(s): 1112212 (strain), 59803 (species)

« back to strain detail view
For citation purpose refer to the digital object identifier (doi) of the current version.
Archive
version 8.1 (current version):
version 8:
version 7.1:
version 7:
version 6:
version 5:
version 4.1:
version 4:
version 3:
version 2.1:
version 2:
version 1:
version 8.1 (current version)

General

@ref: 662

BacDive-ID: 14200

DSM-Number: 1805

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

description: Sphingomonas echinoides DSM 1805 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from contaminant of a nutrient agar plate.

NCBI tax id

NCBI tax idMatching level
59803species
1112212strain

strain history

@refhistory
662<- ICPB <- W. Heumann
118995CIP <- 1989, DSM <- ICBB <- W. Heumann

doi: 10.13145/bacdive14200.20230509.8.1

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 echinoides
  • full scientific name: Sphingomonas echinoides (Heumann 1962) Denner et al. 1999

  • synonyms

    • @ref: 20215
    • synonym: Pseudomonas echinoides

@ref: 662

domain: Bacteria

phylum: Proteobacteria

class: Alphaproteobacteria

order: Sphingomonadales

family: Sphingomonadaceae

genus: Sphingomonas

species: Sphingomonas echinoides

full scientific name: Sphingomonas echinoides (Heumann 1962) Denner et al. 1999

type strain: yes

Morphology

cell morphology

  • @ref: 118995
  • gram stain: negative
  • cell shape: rod-shaped
  • motility: no

colony morphology

  • @ref: 44598
  • incubation period: 2-3 days

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
662R2A MEDIUM (DSMZ Medium 830)yeshttps://mediadive.dsmz.de/medium/830Name: 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
662NUTRIENT 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
662GLUCOSE YEAST EXTRACT MEDIUM (DSMZ Medium 54)yeshttps://mediadive.dsmz.de/medium/54Name: GLUCOSE YEAST EXTRACT MEDIUM (DSMZ Medium 54) Composition: CaCO3 20.0 g/l Glucose 20.0 g/l Agar 17.0 g/l Yeast extract 10.0 g/l Distilled water
37283MEDIUM 18 - for Hydrogenophaga, Vogesella and Pseudomonas generayesDistilled water make up to (1000.000 ml);Sodium chloride (3.000 g);Agar(12.000 g);Yeast extract (3.000 g);Peptone (0.600 g)
118995CIP Medium 72yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72
118995CIP Medium 18yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=18

culture temp

@refgrowthtypetemperaturerange
662positivegrowth30mesophilic
37283positivegrowth25mesophilic
44598positivegrowth25-30mesophilic

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
44598aerobe
118995obligate aerobe

compound production

  • @ref: 662
  • compound: carotenoid

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
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
11899517632nitrate-reduction
11899516301nitrite-reduction

metabolite production

@refChebi-IDmetaboliteproduction
6836935581indoleno
11899535581indoleno

metabolite tests

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

enzymes

@refvalueactivityec
68369cytochrome oxidase+1.9.3.1
68369gelatinase-
68369beta-glucosidase+3.2.1.21
68369urease-3.5.1.5
68369arginine dihydrolase-3.5.3.6
118995oxidase+
118995catalase+1.11.1.6
118995urease-3.5.1.5
68382alkaline phosphatase+3.1.3.1
68382esterase (C 4)-
68382esterase lipase (C 8)+
68382lipase (C 14)-
68382leucine arylamidase+3.4.11.1
68382valine arylamidase+
68382cystine arylamidase-3.4.11.3
68382trypsin+3.4.21.4
68382alpha-chymotrypsin-3.4.21.1
68382acid phosphatase+3.1.3.2
68382naphthol-AS-BI-phosphohydrolase+
68382alpha-galactosidase-3.2.1.22
68382beta-galactosidase-3.2.1.23
68382beta-glucuronidase+3.2.1.31
68382alpha-glucosidase+3.2.1.20
68382beta-glucosidase+3.2.1.21
68382N-acetyl-beta-glucosaminidase-3.2.1.52
68382alpha-mannosidase-3.2.1.24
68382alpha-fucosidase-3.2.1.51

API zym

@refControlAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
118995-+-+-++-+-++--+++---

API 20NE

@refNO3TRPGLU_ FermADH ArgUREESCGELPNPGGLU_ AssimARAMNEMANNAGMALGNTCAPADIMLTCITPACOX
662-----+-+/-++--+++--+--+

Isolation, sampling and environmental information

isolation

@refsample type
662contaminant of a nutrient agar plate
44598Nutrient agar plate contaminant
118995Other, Contaminant, nutrient agar plate

isolation source categories

Cat1Cat2Cat3
#Engineered#Laboratory#Contaminant
#Engineered#Laboratory#Lab enrichment

taxonmaps

  • @ref: 69479
  • File name: preview.99_3276.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_20;96_348;97_2045;98_2512;99_3276&stattab=map
  • Last taxonomy: Sphingomonas echinoides
  • 16S sequence: AB680957
  • Sequence Identity:
  • Total samples: 12549
  • soil counts: 1433
  • aquatic counts: 3911
  • animal counts: 6153
  • plant counts: 1052

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
6621Risk group (German classification)
1189951Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Sphingomonas echinoides gene for 16S rRNA, strain: ATCC 14820AB0213701463ena59803
20218Sphingomonas echinoides 16S rRNA gene, strain DSM 1805-TAJ0124611437ena1112212
20218Pseudomonas echinoides DSM1805 16S ribosomal RNA gene, partial sequenceU96454509ena1112212
20218Sphingomonas echinoides gene for 16S rRNA, partial sequence, strain: NBRC 15742AB6809571410ena59803

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Sphingomonas echinoides ATCC 14820GCA_000241465scaffoldncbi1112212
66792Sphingomonas echinoides ATCC 148201112212.3wgspatric1112212
66792Sphingomonas echinoides ATCC 148202547132141draftimg1112212

GC content

  • @ref: 662
  • GC-content: 65.8
  • method: thermal denaturation, midpoint method (Tm)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
motileyes74.601no
flagellatedno88.53no
gram-positiveno96.538no
anaerobicno99.327yes
aerobicyes90.784no
halophileno94.146no
spore-formingno91.138no
thermophileno98.922yes
glucose-utilyes91.098yes
glucose-fermentno91.975no

External links

@ref: 662

culture collection no.: DSM 1805, ATCC 14820, DSM 50409, DSM 7240, ICPB 2835, NCIB 9420, CCUG 2870, LMG 7462, ATCC 17833, CIP 103301, LMG 2181, JCM 10637, NCIMB 9420

straininfo link

  • @ref: 83359
  • straininfo: 4046

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny10425767Reclassification of Pseudomonas echinoides Heumann 1962, 343AL, in the genus Sphingomonas as Sphingomonas echinoides comb. nov.Denner EB, Kampfer P, Busse HJ, Moore ERInt J Syst Bacteriol10.1099/00207713-49-3-11031999Bacterial Typing Techniques, Base Composition, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis, Genes, rRNA, Gram-Negative Aerobic Rods and Cocci/chemistry/*classification/genetics, Molecular Sequence Data, Phenotype, Phylogeny, Pseudomonas/chemistry/*classification/genetics, RNA, Ribosomal, 16S/*genetics, Sequence Analysis, DNAGenetics
Phylogeny15545456Sphingomonas oligophenolica sp. nov., a halo- and organo-sensitive oligotrophic bacterium from paddy soil that degrades phenolic acids at low concentrations.Ohta H, Hattori R, Ushiba Y, Mitsui H, Ito M, Watanabe H, Tonosaki A, Hattori TInt J Syst Evol Microbiol10.1099/ijs.0.02959-02004Aerobiosis, Bacteria, Bacterial Typing Techniques, Calcium Chloride/metabolism, Coenzymes, DNA, Bacterial/chemistry/isolation & purification, DNA, Ribosomal/chemistry/isolation & purification, Fatty Acids/analysis/isolation & purification, Genes, rRNA, Gentian Violet, Glycosphingolipids/analysis/isolation & purification, Growth Inhibitors/pharmacology, Hydroxybenzoates/*metabolism, Molecular Sequence Data, Movement, Nucleic Acid Hybridization, Phenazines, Phylogeny, Pigments, Biological/biosynthesis, Quinones/analysis/isolation & purification, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Sodium Chloride/pharmacology, *Soil Microbiology, Sphingomonadaceae/*classification/cytology/*isolation & purification/physiology, Ubiquinone/*analogs & derivatives/isolation & purificationEnzymology
Phylogeny20382784Sphingomonas glacialis sp. nov., a psychrophilic bacterium isolated from alpine glacier cryoconite.Zhang DC, Busse HJ, Liu HC, Zhou YG, Schinner F, Margesin RInt J Syst Evol Microbiol10.1099/ijs.0.023135-02010Bacterial Typing Techniques, Base Composition, Cluster Analysis, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis, Glycolipids/analysis, Ice Cover/*microbiology, Molecular Sequence Data, Nucleic Acid Hybridization, Phospholipids/analysis, Phylogeny, Polyamines/analysis, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sphingomonas/*classification/genetics/*isolation & purification/physiology, Ubiquinone/analysisGenetics
Genetics22408244Draft genome sequence of Sphingomonas echinoides ATCC 14820.Shin SC, Kim SJ, Ahn DH, Lee JK, Park HJ Bacteriol10.1128/JB.00046-122012Base Sequence, *Genome, Bacterial, Molecular Sequence Data, Phylogeny, Sphingomonas/*geneticsPhylogeny

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
662Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 1805)https://www.dsmz.de/collection/catalogue/details/culture/DSM-1805
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
37283Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/15083
44598Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 2870)https://www.ccug.se/strain?id=2870
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)
68369Automatically annotated from API 20NE
68382Automatically annotated from API zym
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
83359Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID4046.1StrainInfo: A central database for resolving microbial strain identifiers
118995Curators of the CIPCollection of Institut Pasteur (CIP 103301)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20103301