Strain identifier

BacDive ID: 14238

Type strain: Yes

Species: Sphingomonas koreensis

Strain history: CIP <- 2002, JCM <- 2001, KCTC <- J.S. Lee: strain JSS26

NCBI tax ID(s): 1219046 (strain), 93064 (species)

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General

@ref: 5904

BacDive-ID: 14238

DSM-Number: 15582

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

description: Sphingomonas koreensis DSM 15582 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from natural mineral water.

NCBI tax id

NCBI tax idMatching level
93064species
1219046strain

strain history

@refhistory
5904<- KCTC <- J.-S. Lee; JSS26
67770KCTC 2882 <-- J.-S. Lee JSS26.
67771<- JS Lee, JSS26
120487CIP <- 2002, JCM <- 2001, KCTC <- J.S. Lee: strain JSS26

doi: 10.13145/bacdive14238.20230509.8.1

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 koreensis
  • full scientific name: Sphingomonas koreensis Lee et al. 2001

@ref: 5904

domain: Bacteria

phylum: Proteobacteria

class: Alphaproteobacteria

order: Sphingomonadales

family: Sphingomonadaceae

genus: Sphingomonas

species: Sphingomonas koreensis

full scientific name: Sphingomonas koreensis Lee et al. 2001

type strain: yes

Morphology

cell morphology

@refgram staincell shapemotility
67771negative
120487negativerod-shapedno

pigmentation

  • @ref: 120487
  • production: no
  • name: Pyocyanin

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
5904CASO AGAR (MERCK 105458) (DSMZ Medium 220)yeshttps://mediadive.dsmz.de/medium/220Name: CASO AGAR (Merck 105458) (DSMZ Medium 220) Composition: Agar 15.0 g/l Casein peptone 15.0 g/l NaCl 5.0 g/l Soy peptone 5.0 g/l Distilled water
39937MEDIUM 72- for trypto casein soja agaryesDistilled water make up to (1000.000 ml);Trypto casein soy agar (40.000 g)
120487CIP Medium 72yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72

culture temp

@refgrowthtypetemperaturerange
5904positivegrowth30mesophilic
39937positivegrowth30mesophilic
67770positivegrowth30mesophilic
67771positivegrowth30mesophilic
120487positivegrowth25-37mesophilic
120487nogrowth5psychrophilic
120487nogrowth10psychrophilic
120487nogrowth41thermophilic

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
67771aerobe
120487obligate aerobe

halophily

@refsaltgrowthtested relationconcentration
120487NaClpositivegrowth0-2 %
120487NaClnogrowth4 %
120487NaClnogrowth6 %
120487NaClnogrowth8 %
120487NaClnogrowth10 %

observation

@refobservation
67770quinones: Q-10
67771quinones: Q-10

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
12048716947citrate-carbon source
1204874853esculin+hydrolysis
12048717632nitrate-reduction
12048716301nitrite-reduction
12048717632nitrate-respiration

antibiotic resistance

  • @ref: 120487
  • 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
12048735581indoleno

metabolite tests

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

enzymes

@refvalueactivityec
68369gelatinase-
68369beta-glucosidase+3.2.1.21
68369urease-3.5.1.5
68369arginine dihydrolase-3.5.3.6
120487oxidase+
120487beta-galactosidase+3.2.1.23
120487alcohol dehydrogenase-1.1.1.1
120487gelatinase+/-
120487amylase-
120487DNase-
120487caseinase-3.4.21.50
120487catalase+1.11.1.6
120487tween esterase+
120487lecithinase-
120487lipase-
120487lysine decarboxylase-4.1.1.18
120487ornithine decarboxylase-4.1.1.17
120487protease-
120487tryptophan deaminase-
120487urease-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
120487-+++-+-+++++----++--

API 20NE

@refNO3TRPGLU_ FermADH ArgUREESCGELPNPGGLU_ AssimARAMNEMANNAGMALGNTCAPADIMLTCITPACOX
5904-----+-++---++---+---
5904-----+--+---++---+--+

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
120487++-+---++++----++-+------------------------------+---------+------------------+++--------++---+----

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
5904natural mineral waterTaejonRepublic of KoreaKORAsia
67770Natural mineral waterTaejon CityRepublic of KoreaKORAsia
67771From natural mineral waterRepublic of KoreaKORAsia
120487Environment, Natural mineral waterTaejonRepublic of KoreaKORAsia

isolation source categories

  • Cat1: #Environmental
  • Cat2: #Aquatic

taxonmaps

  • @ref: 69479
  • File name: preview.99_2401.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_20;96_348;97_1538;98_1872;99_2401&stattab=map
  • Last taxonomy: Sphingomonas
  • 16S sequence: AF131296
  • Sequence Identity:
  • Total samples: 1667
  • soil counts: 259
  • aquatic counts: 981
  • animal counts: 233
  • plant counts: 194

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
59041Risk group (German classification)
1204871Risk group (French classification)

Sequence information

16S sequences

  • @ref: 5904
  • description: Sphingomonas sp. JSS-26 16S ribosomal RNA gene, partial sequence
  • accession: AF131296
  • length: 1441
  • database: ena
  • NCBI tax ID: 93064

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Sphingomonas koreensis KCTC 2882GCA_003953035contigncbi93064
66792Sphingomonas koreensis NBRC 16723GCA_001598395contigncbi1219046
66792Sphingomonas koreensis NBRC 167231219046.3wgspatric1219046
66792Sphingomonas koreensis strain KCTC 2882 strain not collected93064.57wgspatric93064
66792Sphingomonas koreensis NBRC 167232731957699draftimg1219046

GC content

@refGC-contentmethod
6777066high performance liquid chromatography (HPLC)
6777166.0

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
motileyes75.701no
gram-positiveno97.492yes
anaerobicno99.19yes
halophileno97.87no
spore-formingno93.299no
thermophileno98.382no
glucose-utilyes87.459yes
flagellatedno83.667no
aerobicyes94.44no
glucose-fermentno90.838yes

External links

@ref: 5904

culture collection no.: DSM 15582, KCCM 41069, KCTC 2882, JSS 26, JCM 11456, CIP 107740, IFO 16723, NBRC 16723, KCCM 41067, NBRL 16723

straininfo link

  • @ref: 83397
  • straininfo: 62901

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny11491350Sphingomonas aquatilis sp. nov., Sphingomonas koreensis sp. nov., and Sphingomonas taejonensis sp. nov., yellow-pigmented bacteria isolated from natural mineral water.Lee JS, Shin YK, Yoon JH, Takeuchi M, Pyun YR, Park YHInt J Syst Evol Microbiol10.1099/00207713-51-4-14912001Base Composition, Base Sequence, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/genetics, Fatty Acids/analysis, Fresh Water/*microbiology, Korea, Microscopy, Electron, Molecular Sequence Data, Nucleic Acid Hybridization, Phylogeny, Species Specificity, Sphingomonas/*classification/genetics/*isolation & purification/metabolismGenetics
Phylogeny16280528Description of two novel species, Sphingomonas abaci sp. nov. and Sphingomonas panni sp. nov.Busse HJ, Hauser E, Kampfer PInt J Syst Evol Microbiol10.1099/ijs.0.63872-02005DNA, Bacterial/analysis/genetics, DNA, Ribosomal/genetics, Fatty Acids/analysis, Molecular Sequence Data, Nucleic Acid Hybridization, Phylogeny, RNA, Ribosomal, 16S/*analysis/genetics, Species Specificity, Sphingomonas/*classification/genetics/isolation & purification/metabolismGenetics
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
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
Phylogeny21538244Sphingomonas jejuensis sp. nov., isolated from marine sponge Hymeniacidon flavia.Park S, Yokota A, Itoh T, Park JSJ Microbiol10.1007/s12275-011-0500-z2011Animals, Base Composition, Cluster Analysis, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis, Molecular Sequence Data, Phospholipids/analysis, Phylogeny, Pigments, Biological/metabolism, Porifera/*microbiology, Quinones/analysis, RNA, Ribosomal, 16S/genetics, Republic of Korea, Sequence Analysis, DNA, Sphingomonas/*classification/genetics/*isolation & purification/physiologyGenetics
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
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
Phylogeny24718620Sphingomonas gimensis sp. nov., a novel Gram-negative bacterium isolated from abandoned lead-zinc ore mine.Feng GD, Yang SZ, Wang YH, Zhao GZ, Deng MR, Zhu HHAntonie Van Leeuwenhoek10.1007/s10482-014-0167-72014Bacterial Typing Techniques, Base Composition, China, Cluster Analysis, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Hydrogen-Ion Concentration, Molecular Sequence Data, Nucleic Acid Hybridization, Phylogeny, Pigments, Biological/metabolism, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sodium Chloride/metabolism, *Soil Microbiology, Sphingomonas/*classification/genetics/*isolation & purification/physiology, TemperatureGenetics
Phylogeny30180924Sphingomonas turrisvirgatae sp. nov., an agar-degrading species isolated from freshwater.Thaller MC, D'Andrea MM, Marmo P, Civitareale C, Casu F, Migliore LInt J Syst Evol Microbiol10.1099/ijsem.0.0028962018Agar/metabolism, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Fresh Water/*microbiology, Italy, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Spermidine/chemistry, Sphingomonas/*classification/genetics/isolation & purification, Ubiquinone/analogs & derivatives/chemistry, WetlandsTranscriptome

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
5904Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 15582)https://www.dsmz.de/collection/catalogue/details/culture/DSM-15582
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
39937Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/5209
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)
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 updatesNucleic Acids Res. 49: D498-D508 202033211880
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
67771Curators of the KCTChttps://kctc.kribb.re.kr/En/Kctc
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
83397Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID62901.1StrainInfo: A central database for resolving microbial strain identifiers
120487Curators of the CIPCollection of Institut Pasteur (CIP 107740)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20107740