Strain identifier

BacDive ID: 14240

Type strain: Yes

Species: Sphingomonas oligophenolica

Strain Designation: S213

Strain history: CIP <- 2003, H. Ohta, Ibaraki Univ., Ibaraki, Japan: strain S213 <- T. Hattori

NCBI tax ID(s): 301154 (species)

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General

@ref: 6761

BacDive-ID: 14240

DSM-Number: 17107

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

description: Sphingomonas oligophenolica S213 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from paddy field soil.

NCBI tax id

  • NCBI tax id: 301154
  • Matching level: species

strain history

@refhistory
6761<- H. Ohta; S213
67770H. Ohta S213 <-- T. Hattori.
121416CIP <- 2003, H. Ohta, Ibaraki Univ., Ibaraki, Japan: strain S213 <- T. Hattori

doi: 10.13145/bacdive14240.20230509.8.1

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 oligophenolica
  • full scientific name: Sphingomonas oligophenolica Ohta et al. 2004

@ref: 6761

domain: Bacteria

phylum: Proteobacteria

class: Alphaproteobacteria

order: Sphingomonadales

family: Sphingomonadaceae

genus: Sphingomonas

species: Sphingomonas oligophenolica

full scientific name: Sphingomonas oligophenolica Ohta et al. 2004

strain designation: S213

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotility
30117negative1.25 µm0.5 µmrod-shapedno
121416negativerod-shapedno

pigmentation

  • @ref: 30117
  • production: yes

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
6761R2A 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
37290MEDIUM 479 - for Sphingomonas oligophenolicayesDistilled water make up to (1000.000 ml);Sodium chloride (0.250 g);Peptone (0.500 g);Beef extract (0.500 g)
121416CIP Medium 479yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=479

culture temp

@refgrowthtypetemperaturerange
6761positivegrowth28mesophilic
30117positivegrowth04-37
30117positiveoptimum20.5psychrophilic
37290positivegrowth30mesophilic
67770positivegrowth30mesophilic
121416positivegrowth25-30mesophilic
121416nogrowth5psychrophilic
121416nogrowth10psychrophilic
121416nogrowth37mesophilic
121416nogrowth41thermophilic

Physiology and metabolism

oxygen tolerance

  • @ref: 30117
  • oxygen tolerance: aerobe

spore formation

  • @ref: 30117
  • spore formation: no

halophily

@refsaltgrowthtested relationconcentration
30117NaClpositivegrowth0-0.5 %
121416NaClpositivegrowth0 %
121416NaClnogrowth2 %
121416NaClnogrowth4 %
121416NaClnogrowth6 %
121416NaClnogrowth8 %
121416NaClnogrowth10 %

observation

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

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3011730089acetate+carbon source
3011722599arabinose+carbon source
3011717057cellobiose+carbon source
3011728260galactose+carbon source
3011724265gluconate+carbon source
3011717234glucose+carbon source
3011724996lactate+carbon source
3011717716lactose+carbon source
3011717306maltose+carbon source
3011737684mannose+carbon source
3011715361pyruvate+carbon source
3011716634raffinose+carbon source
3011718222xylose+carbon source
3011717632nitrate+reduction
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
12141616947citrate-carbon source
1214164853esculin-hydrolysis
12141617632nitrate-reduction
12141616301nitrite-reduction

antibiotic resistance

  • @ref: 121416
  • metabolite: 0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)
  • is antibiotic: yes
  • is sensitive: no
  • is resistant: yes

metabolite production

@refChebi-IDmetaboliteproduction
6836935581indoleno
12141635581indoleno

metabolite tests

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

enzymes

@refvalueactivityec
30117catalase+1.11.1.6
30117cytochrome oxidase+1.9.3.1
68369cytochrome oxidase+1.9.3.1
68369gelatinase-
68369beta-glucosidase+3.2.1.21
68369urease-3.5.1.5
68369arginine dihydrolase-3.5.3.6
121416oxidase+
121416beta-galactosidase-3.2.1.23
121416alcohol dehydrogenase-1.1.1.1
121416gelatinase-
121416catalase+1.11.1.6
121416lysine decarboxylase-4.1.1.18
121416ornithine decarboxylase-4.1.1.17
121416tryptophan deaminase-
121416urease-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
121416-+++-+-+--++-+-+-+--

API 20NE

@refNO3TRPGLU_ FermADH ArgUREESCGELPNPGGLU_ AssimARAMNEMANNAGMALGNTCAPADIMLTCITPACOX
6761+----+-+--------+-+++

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentisolation date
6761paddy field soilnear SendaiJapanJPNAsia
67770Paddy soil
121416Environment, Paddy field soilKasimadaiJapanJPNAsia1976

isolation source categories

Cat1Cat2Cat3
#Engineered#Agriculture#Field
#Environmental#Terrestrial#Soil
#Host#Plants#Herbaceous plants (Grass,Crops)
#Condition#Anoxic (anaerobic)
#Condition#Humid

taxonmaps

  • @ref: 69479
  • File name: preview.99_52004.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_20;96_348;97_2045;98_37314;99_52004&stattab=map
  • Last taxonomy: Sphingomonas
  • 16S sequence: AB018439
  • Sequence Identity:
  • Total samples: 256
  • soil counts: 67
  • aquatic counts: 55
  • animal counts: 47
  • plant counts: 87

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
67611Risk group (German classification)
1214161Risk group (French classification)

Sequence information

16S sequences

  • @ref: 6761
  • description: Sphingomonas oligophenolica gene for 16S rRNA, partial sequence
  • accession: AB018439
  • length: 1306
  • database: ena
  • NCBI tax ID: 301154

GC content

  • @ref: 30117
  • GC-content: 64.2

External links

@ref: 6761

culture collection no.: DSM 17107, CIP 107926, JCM 12082, CCUG 56448

straininfo link

  • @ref: 83399
  • straininfo: 134451

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
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
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
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
Phylogeny23456806Prosthecate sphingomonads: proposal of Sphingomonas canadensis sp. nov.Abraham WR, Estrela AB, Rohde M, Smit J, Vancanneyt MInt J Syst Evol Microbiol10.1099/ijs.0.048678-02013Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/analysis, Molecular Sequence Data, Nucleic Acid Hybridization, *Phylogeny, Polyamines/analysis, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Spermidine/analogs & derivatives/analysis, Sphingomonas/*classification/genetics/isolation & purification, Ubiquinone/analogs & derivatives/analysisGenetics
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
Phylogeny26286474Sphingomonas hylomeconis sp. nov., isolated from the stem of Hylomecon japonica.Akbar A, Chen C, Zhu L, Xin K, Cheng J, Yang Q, Zhao L, Zhang L, Shen XInt J Syst Evol Microbiol10.1099/ijsem.0.0005322015Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Fatty Acids/chemistry, Papaveraceae/*microbiology, Phospholipids/chemistry, *Phylogeny, Pigmentation, Plant Stems/*microbiology, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Spermidine/analogs & derivatives/chemistry, Sphingomonas/*classification/genetics/isolation & purification, Ubiquinone/chemistryTranscriptome
Phylogeny26676296Sphingomonas qilianensis sp. nov., Isolated from Surface Soil in the Permafrost Region of Qilian Mountains, China.Piao AL, Feng XM, Nogi Y, Han L, Li Y, Lv JCurr Microbiol10.1007/s00284-015-0957-92015Base Composition, China, *Environment, Permafrost/*microbiology, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Sphingomonas/chemistry/*classification/genetics/isolation & purificationTranscriptome
Phylogeny27902288Sphingomonas aquatica sp. nov., isolated from tap water.Choi GM, Jo JH, Kang MS, Kim MS, Lee SY, Im WTInt J Syst Evol Microbiol10.1099/ijsem.0.0016822017Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Drinking Water/*microbiology, Fatty Acids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, Sequence Analysis, DNA, Spermidine/chemistry, Sphingomonas/*classification/genetics/isolation & purification, Ubiquinone/analogs & derivatives/chemistryTranscriptome
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
Phylogeny31671048Sphingomonas paeninsulae sp. nov., isolated from soil sampled at Fildes Peninsula, Antarctica.Geng Y, Zhang Y, Qin K, Liu J, Tian J, Huang Y, Wei Z, Zhang F, Peng FInt J Syst Evol Microbiol10.1099/ijsem.0.0035042019Antarctic Regions, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Spermidine/analogs & derivatives/chemistry, Sphingomonas/*classification/isolation & purification, Ubiquinone/analogs & derivatives/chemistryTranscriptome

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmedjournal
6761Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 17107)https://www.dsmz.de/collection/catalogue/details/culture/DSM-17107
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
30117Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2647228776041
37290Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/5491
66794Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg10.1093/nar/gkaa1025BRENDA, the ELIXIR core data resource in 2021: new developments and updates33211880Nucleic Acids Res. 49: D498-D508 2020
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
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
83399Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID134451.1StrainInfo: A central database for resolving microbial strain identifiers
121416Curators of the CIPCollection of Institut Pasteur (CIP 107926)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20107926