Strain identifier

BacDive ID: 14258

Type strain: Yes

Species: Sphingomonas astaxanthinifaciens

Strain Designation: TDMA-17

Strain history: <- NBRC <- D. Asker, Nihon Univ., College of Bioresource Sci., Fujisawa, Japan; TDMA-17

NCBI tax ID(s): 1123267 (strain), 407019 (species)

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General

@ref: 16261

BacDive-ID: 14258

DSM-Number: 22298

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

description: Sphingomonas astaxanthinifaciens TDMA-17 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from fresh water.

NCBI tax id

NCBI tax idMatching level
1123267strain
407019species

strain history

  • @ref: 16261
  • history: <- NBRC <- D. Asker, Nihon Univ., College of Bioresource Sci., Fujisawa, Japan; TDMA-17

doi: 10.13145/bacdive14258.20230509.8.1

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 astaxanthinifaciens
  • full scientific name: Sphingomonas astaxanthinifaciens Asker et al. 2008

@ref: 16261

domain: Bacteria

phylum: Proteobacteria

class: Alphaproteobacteria

order: Sphingomonadales

family: Sphingomonadaceae

genus: Sphingomonas

species: Sphingomonas astaxanthinifaciens

full scientific name: Sphingomonas astaxanthinifaciens Asker et al. 2008

strain designation: TDMA-17

type strain: yes

Morphology

cell morphology

  • @ref: 69480
  • gram stain: negative
  • confidence: 99.806

colony morphology

  • @ref: 59943
  • incubation period: 2 days

Culture and growth conditions

culture medium

  • @ref: 16261
  • 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
16261positivegrowth37mesophilic
59943positivegrowth30mesophilic

Physiology and metabolism

oxygen tolerance

  • @ref: 59943
  • oxygen tolerance: aerobe

spore formation

@refspore formationconfidence
69481no98
69480no99.977

compound production

  • @ref: 16261
  • compound: astaxanthin

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

metabolite production

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

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

API 20NE

@refNO3TRPGLU_ FermADH ArgUREESCGELPNPGGLU_ AssimARAMNEMANNAGMALGNTCAPADIMLTCITPACOX
16261------+-+----+-------

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentsampling date
16261fresh waterTottori, MisasaJapanJPNAsia
59943Water,freshTottori,MisasaJapanJPNAsia2000

isolation source categories

  • Cat1: #Environmental
  • Cat2: #Aquatic
  • Cat3: #Freshwater

taxonmaps

  • @ref: 69479
  • File name: preview.99_775.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_20;96_470;97_537;98_618;99_775&stattab=map
  • Last taxonomy: Sphingomonas
  • 16S sequence: AB681719
  • Sequence Identity:
  • Total samples: 2788
  • soil counts: 1316
  • aquatic counts: 998
  • animal counts: 348
  • plant counts: 126

Safety information

risk assessment

  • @ref: 16261
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Sphingomonas astaxanthinifaciens gene for 16S rRNA, partial sequence, strain: NBRC 102146AB6817191412ena1123267
16261Sphingomonas astaxanthinifaciens gene for 16S ribosomal RNA, partial sequenceAB2775831396ena1123267

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Sphingomonas astaxanthinifaciens DSM 22298GCA_000711715contigncbi1123267
66792Sphingomonas astaxanthinifaciens DSM 222981123267.3wgspatric1123267
66792Sphingomonas astaxanthinifaciens DSM 222982565957137draftimg1123267

GC content

  • @ref: 16261
  • GC-content: 67.7

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno98no
motileno80.166no
flagellatedno95.929no
gram-positiveno96.699no
anaerobicno98.969yes
aerobicyes90.915no
halophileno93.326no
spore-formingno96.958no
thermophileno93.056no
glucose-utilyes84.005yes
glucose-fermentno91.368yes

External links

@ref: 16261

culture collection no.: DSM 22298, CCUG 53608, NBRC 102146

straininfo link

  • @ref: 83417
  • straininfo: 407095

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny17590230Sphingomonas astaxanthinifaciens sp. nov., a novel astaxanthin-producing bacterium of the family Sphingomonadaceae isolated from Misasa, Tottori, Japan.Asker D, Beppu T, Ueda KFEMS Microbiol Lett10.1111/j.1574-6968.2007.00760.x2007Carotenoids/chemistry/classification, Fresh Water/*microbiology, Japan, Molecular Sequence Data, *Phylogeny, RNA, Ribosomal, 16S/chemistry/classification, Sequence Analysis, DNA, Sphingomonas/*classification/isolation & purification/metabolism, Xanthophylls/biosynthesisGenetics
Phylogeny20437147Sphingomonas humi sp. nov., isolated from soil.Yi TH, Han CK, Srinivasan S, Lee KJ, Kim MKJ Microbiol10.1007/s12275-010-0011-32010Bacterial Typing Techniques, Base Composition, Cluster Analysis, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis, Molecular Sequence Data, Nucleic Acid Hybridization, Phylogeny, Quinones/analysis, RNA, Ribosomal, 16S/genetics, Republic of Korea, Sequence Analysis, DNA, *Soil Microbiology, Sphingomonas/*classification/genetics/*isolation & purification/physiologyGenetics
Phylogeny21887644Sphingomonas rosea sp. nov. and Sphingomonas swuensis sp. nov., rosy colored beta-glucosidase-producing bacteria isolated from soil.Srinivasan S, Lee JJ, Kim MKJ Microbiol10.1007/s12275-011-1017-12011Bacterial Typing Techniques, Base Composition, DNA, Bacterial, Fatty Acids/metabolism, Phylogeny, RNA, Ribosomal, 16S/genetics, *Soil Microbiology, Sphingomonas/*classification/genetics/isolation & purification/ultrastructure, beta-Glucosidase/*biosynthesisMetabolism
Phylogeny22505600Sphingomonas ginsengisoli sp. nov. and Sphingomonas sediminicola sp. nov.An DS, Liu QM, Lee HG, Jung MS, Kim SC, Lee ST, Im WTInt J Syst Evol Microbiol10.1099/ijs.0.039578-02012Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/analysis, Geologic Sediments/*microbiology, Glycosphingolipids/analysis, Molecular Sequence Data, Panax/*microbiology, *Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, Sequence Analysis, DNA, *Soil Microbiology, Sphingomonas/*classification/genetics/isolation & purification, Ubiquinone/analysisGenetics
Phylogeny25336722Parablastomonas arctica gen. nov., sp. nov., isolated from high Arctic glacial till.Ren L, Chang X, Jiang F, Kan W, Qu Z, Qiu X, Fang C, Peng FInt J Syst Evol Microbiol10.1099/ijs.0.067231-02014Arctic Regions, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Ice Cover, Molecular Sequence Data, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Spermidine/chemistry, Sphingomonadaceae/*classification/genetics/isolation & purification, Svalbard, Ubiquinone/chemistryGenetics
Phylogeny25985832Sphingomonas lacus sp. nov., an astaxanthin-dideoxyglycoside-producing species isolated from soil near a pond.Kim JH, Kim SH, Kim KH, Lee PCInt J Syst Evol Microbiol10.1099/ijs.0.0003372015Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Glycosides/biosynthesis, Molecular Sequence Data, Nucleic Acid Hybridization, Phospholipids/chemistry, *Phylogeny, *Ponds, RNA, Ribosomal, 16S/genetics, Republic of Korea, Sequence Analysis, DNA, *Soil Microbiology, Spermidine/chemistry, Sphingomonas/*classification/genetics/isolation & purification, Ubiquinone/chemistry, Xanthophylls/biosynthesisGenetics
Phylogeny29388549Sphingomonas rhizophila sp. nov., isolated from rhizosphere of Hibiscus syriacus.Yan ZF, Lin P, Won KH, Li CT, Park G, Chin B, Kook M, Wang QJ, Yi THInt J Syst Evol Microbiol10.1099/ijsem.0.0025662018Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Glycolipids/chemistry, Hibiscus/*microbiology, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, *Rhizosphere, Sequence Analysis, DNA, *Soil Microbiology, Spermidine/chemistry, Sphingomonas/*classification/genetics/isolation & purification, Ubiquinone/chemistryTranscriptome
Phylogeny30109631Purification and Identification of Astaxanthin and Its Novel Derivative Produced by Radio-tolerant Sphingomonas astaxanthinifaciens.Asker D, Awad TS, Beppu T, Ueda KMethods Mol Biol10.1007/978-1-4939-8742-9_102018Antioxidants/chemistry/isolation & purification/metabolism, Chromatography, High Pressure Liquid, Molecular Structure, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Spectrum Analysis, Sphingomonas/chemistry/*metabolism/*radiation effects/ultrastructure, Xanthophylls/biosynthesis/chemistry/isolation & purificationEnzymology

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
16261Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 22298)https://www.dsmz.de/collection/catalogue/details/culture/DSM-22298
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
59943Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 53608)https://www.ccug.se/strain?id=53608
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
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
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
83417Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID407095.1StrainInfo: A central database for resolving microbial strain identifiers