Strain identifier

BacDive ID: 14252

Type strain: Yes

Species: Sphingomonas jaspsi

Strain Designation: TDMA-16

Strain history: CIP <- 2007, CCUG

NCBI tax ID(s): 1123268 (strain), 392409 (species)

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General

@ref: 7547

BacDive-ID: 14252

DSM-Number: 18422

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

description: Sphingomonas jaspsi TDMA-16 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from fresh water.

NCBI tax id

NCBI tax idMatching level
1123268strain
392409species

strain history

@refhistory
7547<- K. Ueda, Nihon Univers., Fujisawa, Japan
368262007, CCUG
120322CIP <- 2007, CCUG

doi: 10.13145/bacdive14252.20230509.8.1

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 jaspsi
  • full scientific name: Sphingomonas jaspsi Asker et al. 2007

@ref: 7547

domain: Bacteria

phylum: Proteobacteria

class: Alphaproteobacteria

order: Sphingomonadales

family: Sphingomonadaceae

genus: Sphingomonas

species: Sphingomonas jaspsi

full scientific name: Sphingomonas jaspsi Asker et al. 2007

strain designation: TDMA-16

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
32024negative0.85 µm0.45 µmrod-shapedyes
69480negative99.956
120322negativerod-shapedno

pigmentation

  • @ref: 32024
  • production: yes

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
7547NUTRIENT 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
7547R2A 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
36826MEDIUM 328- for nutrient agaryesDistilled water make up to (1000.000 ml);Agar (15.000 g);Peptone (5.000g);Beef extract (3.000 g)
120322CIP Medium 328yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=328

culture temp

@refgrowthtypetemperaturerange
7547positivegrowth37mesophilic
32024positivegrowth20-40
32024positiveoptimum36mesophilic
36826positivegrowth37mesophilic

culture pH

@refabilitytypepHPH range
32024positivegrowth6.0-9.0alkaliphile
32024positiveoptimum6.5

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
32024aerobe
120322obligate aerobe

spore formation

@refspore formationconfidence
32024no
69481no100
69480no99.992

compound production

  • @ref: 7547
  • compound: carotenoids

halophily

  • @ref: 32024
  • salt: NaCl
  • growth: positive
  • tested relation: growth
  • concentration: 0.0-0.25 %

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3202417234glucose+carbon source
3202417306maltose+carbon source
3202453426tween 80+carbon source
12032217632nitrate-reduction
12032216301nitrite-reduction

metabolite production

  • @ref: 120322
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

enzymes

@refvalueactivityec
32024catalase+1.11.1.6
32024gelatinase+
32024cytochrome oxidase+1.9.3.1
120322oxidase+
120322catalase+1.11.1.6
120322urease-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
120322-+++-++++-++---+----

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentsampling date
7547fresh waterMisasa, TottoriJapanJPNAsia
59942Tottori,MisasaJapanJPNAsia2000
120322Environment, Fresh water sampleMisassa, TottoriJapanJPNAsia

isolation source categories

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

taxonmaps

  • @ref: 69479
  • File name: preview.99_5228.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_20;96_470;97_3104;98_3899;99_5228&stattab=map
  • Last taxonomy: Sphingomonas jaspsi subclade
  • 16S sequence: AB681706
  • Sequence Identity:
  • Total samples: 1130
  • soil counts: 743
  • aquatic counts: 208
  • animal counts: 20
  • plant counts: 159

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
75471Risk group (German classification)
1203221Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Sphingomonas jaspsi gene for 16S rRNA, partial sequence, strain: NBRC 102120AB6817061408ena392409
7547Sphingomonas jaspsi gene for 16S rRNA, partial sequenceAB2641311383ena392409

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Sphingomonas jaspsi DSM 18422GCA_000585415scaffoldncbi1123268
66792Sphingomonas jaspsi DSM 184221123268.4wgspatric1123268
66792Sphingomonas jaspsi DSM 184222524614649draftimg1123268

GC content

  • @ref: 32024
  • GC-content: 63.3

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileno79.208yes
flagellatedno96.814no
gram-positiveno96.437yes
anaerobicno98.736yes
halophileno92.224yes
spore-formingno95.702yes
glucose-utilyes82.257no
aerobicyes88.416yes
glucose-fermentno89.56no
thermophileno93.875yes

External links

@ref: 7547

culture collection no.: DSM 18422, CCUG 53607, NBRC 102120, CIP 109619

straininfo link

  • @ref: 83411
  • straininfo: 309502

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny17625171Sphingomonas jaspsi sp. nov., a novel carotenoid-producing bacterium isolated from Misasa, Tottori, Japan.Asker D, Beppu T, Ueda KInt J Syst Evol Microbiol10.1099/ijs.0.64828-02007Aerobiosis, Bacterial Typing Techniques, Base Composition, Carotenoids/*biosynthesis, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis, Fresh Water/*microbiology, Gamma Rays, Genes, rRNA, Glycolipids/analysis, Japan, Locomotion, Molecular Sequence Data, Phospholipids/analysis, Phylogeny, Pigments, Biological/biosynthesis, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sequence Homology, Nucleic Acid, Sphingomonas/chemistry/*classification/genetics/*isolation & purification, Ubiquinone/analysisGenetics
Phylogeny21057052Sphingomonas oryziterrae sp. nov. and Sphingomonas jinjuensis sp. nov. isolated from rhizosphere soil of rice (Oryza sativa L.).Chung EJ, Jo EJ, Yoon HS, Song GC, Jeon CO, Chung YRInt J Syst Evol Microbiol10.1099/ijs.0.023846-02010Bacterial Typing Techniques, Base Composition, Cluster Analysis, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis, Hydrogen-Ion Concentration, Korea, Molecular Sequence Data, Oryza/growth & development, Phospholipids/analysis, Phylogeny, Pigments, Biological/metabolism, Quinones/analysis, RNA, Ribosomal, 16S/genetics, Rhizosphere, Sequence Analysis, DNA, *Soil Microbiology, Sphingomonas/*classification/genetics/*isolation & purification/physiology, TemperatureGenetics
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
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
Phylogeny31596192Sphingomonas edaphi sp. nov., a novel species isolated from beach soil in the Republic of Korea.Kim H, Chhetri G, Seo TInt J Syst Evol Microbiol10.1099/ijsem.0.0037802020Bacterial Typing Techniques, Base Composition, *Bathing Beaches, DNA, Bacterial/genetics, Fatty Acids/chemistry, Glycolipids/chemistry, Nucleic Acid Hybridization, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, Sequence Analysis, DNA, *Soil Microbiology, Spermidine/analogs & derivatives/chemistry, Sphingomonas/*classification/isolation & purification, Ubiquinone/analogs & derivatives/chemistryTranscriptome
Phylogeny33146742Sphingomonas xanthus sp. nov., Isolated from Beach Soil.Kim H, Chhetri G, Seo TCurr Microbiol10.1007/s00284-020-02273-z2020Bacterial Typing Techniques, DNA, Bacterial/genetics, Fatty Acids/analysis, Phospholipids, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Soil, Soil Microbiology, *Sphingomonas/geneticsTranscriptome

Reference

@idauthorscataloguedoi/urltitlejournalpubmedID_cross_reference
7547Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 18422)https://www.dsmz.de/collection/catalogue/details/culture/DSM-18422
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
32024Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2877604128276
36826Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/7383
59942Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 53607)https://www.ccug.se/strain?id=53607
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)
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
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
83411Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID309502.1StrainInfo: A central database for resolving microbial strain identifiers
120322Curators of the CIPCollection of Institut Pasteur (CIP 109619)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20109619