Strain identifier

BacDive ID: 14224

Type strain: Yes

Species: Sphingomonas mali

Strain Designation: Y-347

Strain history: CIP <- 2002, JCM <- IFO <- M. Yasuda: strain Y-347

NCBI tax ID(s): 1219048 (strain), 40682 (species)

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General

@ref: 3977

BacDive-ID: 14224

DSM-Number: 10565

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

description: Sphingomonas mali Y-347 is a mesophilic, Gram-negative bacterium that was isolated from roots of apple tree.

NCBI tax id

NCBI tax idMatching level
1219048strain
40682species

strain history

@refhistory
3977<- IFO <- M. Takeuchi; Y-347
67770IFO 15500 <-- M. Yasuda Y-347.
120758CIP <- 2002, JCM <- IFO <- M. Yasuda: strain Y-347

doi: 10.13145/bacdive14224.20230509.8.1

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

@ref: 3977

domain: Bacteria

phylum: Proteobacteria

class: Alphaproteobacteria

order: Sphingomonadales

family: Sphingomonadaceae

genus: Sphingomonas

species: Sphingomonas mali

full scientific name: Sphingomonas mali Takeuchi et al. 1995

strain designation: Y-347

type strain: yes

Morphology

cell morphology

@refgram stainconfidencecell shapemotility
69480negative99.838
120758negativerod-shapedyes

pigmentation

  • @ref: 120758
  • production: no
  • name: Pyocyanin

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
3977NUTRIENT 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
33115MEDIUM 72- for trypto casein soja agaryesDistilled water make up to (1000.000 ml);Trypto casein soy agar (40.000 g)
120758CIP Medium 72yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72

culture temp

@refgrowthtypetemperaturerange
3977positivegrowth30mesophilic
33115positivegrowth30mesophilic
67770positivegrowth30mesophilic
120758positivegrowth25-30mesophilic
120758nogrowth5psychrophilic
120758nogrowth10psychrophilic
120758nogrowth37mesophilic
120758nogrowth41thermophilic

Physiology and metabolism

spore formation

@refspore formationconfidence
69481no99
69480no99.914

halophily

@refsaltgrowthtested relationconcentration
120758NaClpositivegrowth0 %
120758NaClnogrowth2 %
120758NaClnogrowth4 %
120758NaClnogrowth6 %
120758NaClnogrowth8 %
120758NaClnogrowth10 %

observation

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

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
12075816947citrate-carbon source
1207584853esculin+hydrolysis
12075817632nitrate-reduction
12075816301nitrite-reduction

antibiotic resistance

  • @ref: 120758
  • metabolite: 0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)
  • is antibiotic: yes
  • is sensitive: no
  • is resistant: yes

metabolite production

  • @ref: 120758
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

enzymes

@refvalueactivityec
120758oxidase+
120758beta-galactosidase+3.2.1.23
120758alcohol dehydrogenase-1.1.1.1
120758gelatinase-
120758catalase+1.11.1.6
120758lysine decarboxylase-4.1.1.18
120758ornithine decarboxylase-4.1.1.17
120758tryptophan deaminase-
120758urease-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
120758-+++-+++--++---+----

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
120758+-++-----++----++-+--+------------------------+-------++---+---------------------------------+-----

Isolation, sampling and environmental information

isolation

@refsample typecountryorigin.countrycontinent
3977roots of apple treeJapanJPNAsia
67770Apple tree roots
120758JapanJPNAsia

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: Y09638
  • 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
39771Risk group (German classification)
1207581Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Sphingomonas mali gene for 16S rRNA, partial sequence, strain: NBRC 15500AB6808841412ena40682
20218Sphingomonas mali gene for 16S rRNA, partial sequence, strain:IFO15500D28575176ena40682
20218Sphingomonas mali gene for 16S rRNA, partial sequence, strain:IFO15500D28576829ena40682
20218S.mali 16S rRNA geneY096381442ena40682
67770Sphingomonas mali gene for 16S rRNA, partial sequence, strain:IFO15500D28574251ena40682

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Sphingomonas mali NBRC 155001219048.3wgspatric1219048
66792Sphingomonas mali NBRC 155002681812977draftimg1219048
67770Sphingomonas mali NBRC 15500GCA_001598415contigncbi1219048

GC content

@refGC-contentmethod
397765.9
6777065.7high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno99no
motileyes70.676no
gram-positiveno97.342no
anaerobicno99.457no
aerobicyes93.318no
halophileno95.293no
spore-formingno94.016no
thermophileno97.474yes
glucose-utilyes92.765no
flagellatedno87.123no
glucose-fermentno89.77no

External links

@ref: 3977

culture collection no.: DSM 10565, IFO 15500, NBRC 15500, JCM 10193, ATCC 51840, CGMCC 1.7044, CIP 107356, IAM 14460, KCTC 2826, LMG 17331

straininfo link

  • @ref: 83383
  • straininfo: 14406

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
Phylogeny16585680Sphingomonas soli sp. nov., a beta-glucosidase-producing bacterium in the family Sphingomonadaceae in the alpha-4 subgroup of the Proteobacteria.Yang DC, Im WT, Kim MK, Ohta H, Lee STInt J Syst Evol Microbiol10.1099/ijs.0.63839-02006Molecular Sequence Data, Nucleic Acid Hybridization, Phylogeny, RNA, Ribosomal, 16S/analysis/genetics, *Soil Microbiology, Sphingomonadaceae/classification, Sphingomonas/*classification/*enzymology/genetics, beta-Glucosidase/*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
Phylogeny17625188Sphingomonas kaistensis sp. nov., a novel alphaproteobacterium containing pufLM genes.Kim MK, Schubert K, Im WT, Kim KH, Lee ST, Overmann JInt J Syst Evol Microbiol10.1099/ijs.0.64579-02007Bacterial Proteins/analysis/*genetics, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis, Genes, rRNA, Korea, Light-Harvesting Protein Complexes/*genetics, Molecular Sequence Data, Photosynthetic Reaction Center Complex Proteins/*genetics, Phylogeny, Pigments, Biological/biosynthesis, Quinones/analysis, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sequence Homology, Nucleic Acid, *Soil Microbiology, Sphingomonas/chemistry/*classification/*genetics/isolation & purificationGenetics
Phylogeny24363294Sphingomonas yantingensis sp. nov., a mineral-weathering bacterium isolated from purplish paddy soil.Huang J, Huang Z, Zhang ZD, He LY, Sheng XFInt J Syst Evol Microbiol10.1099/ijs.0.055954-02013Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Fatty Acids/chemistry, Molecular Sequence Data, Nucleic Acid Hybridization, Oryza/microbiology, Phospholipids/chemistry, *Phylogeny, Pigmentation, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Spermidine/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
Phylogeny28837005Sphingomonas crusticola sp. nov., isolated from biological soil crusts.Zhang K, Tang K, Feng F, Yuan B, Zhang X, Meng JInt J Syst Evol Microbiol10.1099/ijsem.0.0020742017Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Fatty Acids/chemistry, Phospholipids/chemistry, *Phylogeny, Pigmentation, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Spermidine/analogs & derivatives/chemistry, Sphingomonas/*classification/genetics/isolation & purification, Ubiquinone/chemistryTranscriptome

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
3977Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 10565)https://www.dsmz.de/collection/catalogue/details/culture/DSM-10565
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
33115Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/4782
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
83383Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID14406.1StrainInfo: A central database for resolving microbial strain identifiers
120758Curators of the CIPCollection of Institut Pasteur (CIP 107356)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20107356