Strain identifier

BacDive ID: 14223

Type strain: Yes

Species: Sphingomonas asaccharolytica

Strain Designation: Y-345

Strain history: CIP <- 2002, IFO <- M. Takeuchi, Minist. Agric. Forest. Fish, Japan: strain Y-345

NCBI tax ID(s): 1219040 (strain), 40681 (species)

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General

@ref: 3976

BacDive-ID: 14223

DSM-Number: 10564

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

description: Sphingomonas asaccharolytica Y-345 is an obligate aerobe, mesophilic, Gram-negative bacterium that was isolated from roots of apple tree.

NCBI tax id

NCBI tax idMatching level
1219040strain
40681species

strain history

@refhistory
3976<- IFO <- M. Takeuchi; Y-345
67770IAM 14458 <-- IFO 15499 <-- M. Yasuda Y-345.
116517CIP <- 2002, IFO <- M. Takeuchi, Minist. Agric. Forest. Fish, Japan: strain Y-345

doi: 10.13145/bacdive14223.20230509.8.1

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 asaccharolytica
  • full scientific name: Sphingomonas asaccharolytica Takeuchi et al. 1995

@ref: 3976

domain: Bacteria

phylum: Proteobacteria

class: Alphaproteobacteria

order: Sphingomonadales

family: Sphingomonadaceae

genus: Sphingomonas

species: Sphingomonas asaccharolytica

full scientific name: Sphingomonas asaccharolytica Takeuchi et al. 1995

strain designation: Y-345

type strain: yes

Morphology

cell morphology

@refgram stainconfidencecell shapemotility
69480negative98.883
116517negativerod-shapedyes

pigmentation

  • @ref: 116517
  • production: no
  • name: Pyocyanin

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
3976NUTRIENT 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
39746MEDIUM 328- for nutrient agaryesDistilled water make up to (1000.000 ml);Agar (15.000 g);Peptone (5.000g);Beef extract (3.000 g)
116517CIP Medium 328yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=328

culture temp

@refgrowthtypetemperaturerange
3976positivegrowth30mesophilic
39746positivegrowth30mesophilic
67770positivegrowth30mesophilic
116517positivegrowth25-37mesophilic
116517nogrowth5psychrophilic
116517nogrowth10psychrophilic
116517nogrowth41thermophilic

Physiology and metabolism

oxygen tolerance

  • @ref: 116517
  • oxygen tolerance: obligate aerobe

spore formation

@refspore formationconfidence
69481no100
69480no99.844

halophily

@refsaltgrowthtested relationconcentration
116517NaClpositivegrowth0 %
116517NaClnogrowth2 %
116517NaClnogrowth4 %
116517NaClnogrowth6 %
116517NaClnogrowth8 %
116517NaClnogrowth10 %

observation

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

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
11651716947citrate-carbon source
1165174853esculin+hydrolysis
11651717632nitrate-reduction
11651716301nitrite-reduction
11651717632nitrate-respiration

metabolite production

  • @ref: 116517
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

enzymes

@refvalueactivityec
116517oxidase+
116517beta-galactosidase+3.2.1.23
116517alcohol dehydrogenase-1.1.1.1
116517gelatinase-
116517amylase-
116517DNase-
116517caseinase-3.4.21.50
116517catalase-1.11.1.6
116517tween esterase-
116517lecithinase-
116517lipase-
116517lysine decarboxylase-4.1.1.18
116517ornithine decarboxylase-4.1.1.17
116517protease-
116517tryptophan deaminase-
116517urease-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
116517-+++-++++-++-++++---

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
116517--+---------------+--------------------------------------------------------------------------------

Isolation, sampling and environmental information

isolation

@refsample typecountryorigin.countrycontinentisolation date
3976roots of apple treeJapanJPNAsia
67770Root of apple tree
116517JapanJPNAsia1992

isolation source categories

Cat1Cat2Cat3
#Host#Plants#Tree
#Host Body-Site#Plant#Root (Rhizome)

taxonmaps

  • @ref: 69479
  • File name: preview.99_3642.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_20;96_348;97_388;98_2785;99_3642&stattab=map
  • Last taxonomy: Sphingomonas
  • 16S sequence: Y09639
  • Sequence Identity:
  • Total samples: 2385
  • soil counts: 1345
  • aquatic counts: 484
  • animal counts: 298
  • plant counts: 258

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
39761Risk group (German classification)
1165171Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Sphingomonas asaccharolytica gene for 16S rRNA, partial sequence, strain: NBRC 15499AB6808831412ena40681
20218Sphingomonas asaccharolytica gene for 16S rRNA, partial sequence, strain:IFO15499D28572176ena40681
20218Sphingomonas asaccharolytica gene for 16S rRNA, partial sequence, strain:IFO15499D28573829ena40681
20218Sphingomonas asaccharolytica partial 16S rRNA gene, strain IFO 15499-TY096391442ena40681
67770Sphingomonas asaccharolytica gene for 16S rRNA, partial sequence, strain:IFO15499D28571251ena40681

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Sphingomonas asaccharolytica NBRC 154991219040.3wgspatric1219040
66792Sphingomonas asaccharolytica NBRC 154992731957698draftimg1219040
67770Sphingomonas asaccharolytica NBRC 15499GCA_001598355contigncbi1219040

GC content

@refGC-contentmethod
397664.8
6777064.8high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileyes69.454no
gram-positiveno96.827no
anaerobicno99.372no
halophileno94.526no
spore-formingno92.813no
thermophileno98.072no
glucose-utilyes90.517no
flagellatedno89.688no
aerobicyes94.24no
glucose-fermentno90.932no

External links

@ref: 3976

culture collection no.: DSM 10564, IFO 15499, NBRC 15499, NCIMB 13747, JCM 21229, ATCC 51839, CIP 107363, IAM 14458, KCTC 2825, LMG 17539, NRRL B-4261

straininfo link

  • @ref: 83382
  • straininfo: 343906

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny7537068Taxonomic study of bacteria isolated from plants: proposal of Sphingomonas rosa sp. nov., Sphingomonas pruni sp. nov., Sphingomonas asaccharolytica sp. nov., and Sphingomonas mali sp. nov.Takeuchi M, Sakane T, Yanagi M, Yamasato K, Hamana K, Yokota AInt J Syst Bacteriol10.1099/00207713-45-2-3341995DNA, Bacterial/genetics, Gram-Negative Aerobic Bacteria/chemistry/*classification/physiology, Lactose/analogs & derivatives/metabolism, Phylogeny, Plants/*microbiology, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/geneticsMetabolism
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
Phylogeny17267979Sphingomonas molluscorum sp. nov., a novel marine isolate with antimicrobial activity.Romanenko LA, Uchino M, Frolova GM, Tanaka N, Kalinovskaya NI, Latyshev N, Mikhailov VVInt J Syst Evol Microbiol10.1099/ijs.0.64441-02007Aerobiosis, Animals, *Antibiosis, Arcidae/*microbiology, Bacterial Typing Techniques, Carbohydrate Metabolism, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis/chemistry, Genes, rRNA, Glycosphingolipids/analysis/chemistry, Gram-Positive Bacteria/drug effects, Japan, Molecular Sequence Data, Movement, Nucleic Acid Hybridization, Phylogeny, Pigments, Biological/biosynthesis, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sequence Homology, Nucleic Acid, Sphingomonas/*classification/cytology/*isolation & purification/physiologyGenetics
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
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
Phylogeny19502316Sphingomonas aestuarii sp. nov., isolated from tidal flat sediment.Roh SW, Kim KH, Nam YD, Chang HW, Kim MS, Oh HM, Bae JWInt J Syst Evol Microbiol10.1099/ijs.0.65528-02009Bacterial Typing Techniques, DNA, Bacterial/analysis, DNA, Ribosomal/analysis, Genotype, Geologic Sediments/*microbiology, Korea, Molecular Sequence Data, Nucleic Acid Hybridization, Phenotype, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Species Specificity, Sphingomonas/*classification/genetics/isolation & purification/physiologyGenetics
Phylogeny22307515Sphingomonas indica sp. nov., isolated from hexachlorocyclohexane (HCH)-contaminated soil.Niharika N, Jindal S, Kaur J, Lal RInt J Syst Evol Microbiol10.1099/ijs.0.033845-02012Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/analysis, Hexachlorocyclohexane/*analysis, India, Molecular Sequence Data, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Soil Pollutants/*analysis, Spermidine/analogs & derivatives/analysis, Sphingomonas/*classification/genetics/isolation & purification, Ubiquinone/analogs & derivatives/analysisGenetics
Phylogeny24425812Sphingomonas aerophila sp. nov. and Sphingomonas naasensis sp. nov., isolated from air and soil, respectively.Kim SJ, Moon JY, Lim JM, Ahn JH, Weon HY, Ahn TY, Kwon SWInt J Syst Evol Microbiol10.1099/ijs.0.055269-02013*Air Microbiology, Bacterial Typing Techniques, DNA, Bacterial/genetics, Fatty Acids/chemistry, Molecular Sequence Data, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, Sequence Analysis, DNA, *Soil Microbiology, Spermidine/chemistry, Sphingomonas/*classification/genetics/isolation & purification, Ubiquinone/chemistryGenetics
Phylogeny25604345Sphingomonas gei sp. nov., isolated from roots of Geum aleppicum.Zhu L, Si M, Li C, Xin K, Chen C, Shi X, Huang R, Zhao L, Shen X, Zhang LInt J Syst Evol Microbiol10.1099/ijs.0.0000742015Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Fatty Acids/chemistry, Geum/*microbiology, Molecular Sequence Data, Nucleic Acid Hybridization, Phospholipids/chemistry, *Phylogeny, Pigmentation, Plant Roots/microbiology, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Spermidine/analogs & derivatives/chemistry, Sphingomonas/*classification/genetics/isolation & purification, Ubiquinone/chemistryGenetics
Phylogeny26155772Sphingomonas panacis sp. nov., isolated from rhizosphere of rusty ginseng.Singh P, Kim YJ, Hoang VA, Farh Mel-A, Yang DCAntonie Van Leeuwenhoek10.1007/s10482-015-0527-y2015Aerobiosis, Bacterial Typing Techniques, Base Composition, Cluster Analysis, Cytosol/chemistry, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis, Hydrogen-Ion Concentration, Locomotion, Nucleic Acid Hybridization, Panax/*microbiology, Phospholipids/analysis, Phylogeny, Quinones/analysis, RNA, Ribosomal, 16S/genetics, Republic of Korea, Rhizosphere, Sequence Analysis, DNA, *Soil Microbiology, Spermidine/analysis, Sphingomonas/*classification/genetics/*isolation & purification/physiology, TemperatureTranscriptome
Phylogeny26410379Sphingomonas hengshuiensis sp. nov., isolated from lake wetland.Wei S, Wang T, Liu H, Zhang C, Guo J, Wang Q, Liang K, Zhang ZInt J Syst Evol Microbiol10.1099/ijsem.0.0006262015Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Fatty Acids/chemistry, Glycosphingolipids/chemistry, Lakes, Molecular Sequence Data, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Spermidine/analogs & derivatives/chemistry, Sphingomonas/*classification/genetics/isolation & purification, Ubiquinone/chemistry, *WetlandsGenetics
Phylogeny33560200Sphingomonas panacisoli sp. nov., bacterium isolated from soil in South Korea.Maeng S, Liu Q, Park Y, Bai J, Im WTInt J Syst Evol Microbiol10.1099/ijsem.0.0046752021
Phylogeny36477930Sphingomonas liriopis sp. nov., Sphingomonas donggukensis sp. nov., and Sphingomonas tagetis sp. nov., isolated from Liriope platyphylla fruit, soil, and Tagetes patula roots.Kim I, Chhetri G, So Y, Jung Y, Park S, Seo TArch Microbiol10.1007/s00203-022-03360-42022*Tagetes, Soil, *Sphingomonas/genetics, Fruit, RNA, Ribosomal, 16S/genetics, Phylogeny, DNA

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
3976Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 10564)https://www.dsmz.de/collection/catalogue/details/culture/DSM-10564
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
39746Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/4790
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/
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
83382Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID343906.1StrainInfo: A central database for resolving microbial strain identifiers
116517Curators of the CIPCollection of Institut Pasteur (CIP 107363)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20107363