Strain identifier

BacDive ID: 14245

Type strain: Yes

Species: Sphingomonas soli

Strain Designation: T5-04, T5-04,52.101

Strain history: CIP <- 2006, IAM <- S.-T. Lee: strain T5-04

NCBI tax ID(s): 1219055 (strain), 266127 (species)

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General

@ref: 7497

BacDive-ID: 14245

DSM-Number: 18313

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

description: Sphingomonas soli T5-04 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from soil of ginseng field.

NCBI tax id

NCBI tax idMatching level
1219055strain
266127species

strain history

@refhistory
7497<- KCTC <- W.-T. Im, KAIST, Korea
374762006, IAM
67770IAM 15213 <-- S.-T. Lee T5-04.
67771<- ST Lee, KAIST
122664CIP <- 2006, IAM <- S.-T. Lee: strain T5-04

doi: 10.13145/bacdive14245.20230509.8.1

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 soli
  • full scientific name: Sphingomonas soli Yang et al. 2006

@ref: 7497

domain: Bacteria

phylum: Proteobacteria

class: Alphaproteobacteria

order: Sphingomonadales

family: Sphingomonadaceae

genus: Sphingomonas

species: Sphingomonas soli

full scientific name: Sphingomonas soli Yang et al. 2006

strain designation: T5-04, T5-04,52.101

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
31577negative1 µm1 µmrod-shapedno
67771negative
69480negative99.898
122664negativerod-shapedno

pigmentation

  • @ref: 31577
  • production: yes

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
7497R2A 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
37476MEDIUM 72- for trypto casein soja agaryesDistilled water make up to (1000.000 ml);Trypto casein soy agar (40.000 g)
122664CIP Medium 566yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=566
122664CIP Medium 72yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72

culture temp

@refgrowthtypetemperaturerange
7497positivegrowth30mesophilic
31577positivegrowth15-37
31577positiveoptimum30mesophilic
37476positivegrowth25mesophilic
67770positivegrowth30mesophilic
67771positivegrowth30mesophilic

culture pH

@refabilitytypepH
31577positivegrowth6.8-7.5
31577positiveoptimum6.8-7.5

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
31577aerobe
67771aerobe
122664microaerophile

spore formation

@refspore formationconfidence
31577no
69481no97
69480no99.954

observation

@refobservation
31577aggregates in chains
67771quinones: Q-10

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3157730089acetate+carbon source
3157722599arabinose+carbon source
3157717992sucrose+carbon source
68371Potassium 5-ketogluconate-builds acid from
68371Potassium 2-ketogluconate-builds acid from
6837124265gluconate-builds acid from
6837118403L-arabitol-builds acid from
6837118333D-arabitol-builds acid from
6837118287L-fucose-builds acid from
6837128847D-fucose-builds acid from
6837116443D-tagatose-builds acid from
6837162318D-lyxose-builds acid from
6837132528turanose-builds acid from
6837128066gentiobiose-builds acid from
6837117151xylitol-builds acid from
6837128087glycogen-builds acid from
6837128017starch-builds acid from
6837116634raffinose-builds acid from
683716731melezitose-builds acid from
6837115443inulin-builds acid from
6837127082trehalose-builds acid from
6837117992sucrose-builds acid from
6837128053melibiose-builds acid from
6837117716lactose-builds acid from
6837117306maltose-builds acid from
6837117057cellobiose-builds acid from
6837117814salicin-builds acid from
683714853esculin+builds acid from
6837118305arbutin-builds acid from
6837127613amygdalin-builds acid from
6837159640N-acetylglucosamine-builds acid from
68371320061methyl alpha-D-glucopyranoside-builds acid from
6837143943methyl alpha-D-mannoside-builds acid from
6837117924D-sorbitol-builds acid from
6837116899D-mannitol-builds acid from
6837117268myo-inositol-builds acid from
6837116813galactitol-builds acid from
6837162345L-rhamnose-builds acid from
6837117266L-sorbose-builds acid from
6837116024D-mannose-builds acid from
6837115824D-fructose-builds acid from
6837117634D-glucose-builds acid from
6837112936D-galactose-builds acid from
6837174863methyl beta-D-xylopyranoside-builds acid from
6837115963ribitol-builds acid from
6837165328L-xylose-builds acid from
6837165327D-xylose-builds acid from
6837116988D-ribose-builds acid from
6837130849L-arabinose-builds acid from
6837117108D-arabinose-builds acid from
6837117113erythritol-builds acid from
6837117754glycerol-builds acid from
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
12266417632nitrate-reduction
12266416301nitrite-reduction

metabolite production

@refChebi-IDmetaboliteproduction
6836935581indoleno
12266435581indoleno

metabolite tests

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

enzymes

@refvalueactivityec
31577catalase+1.11.1.6
31577cytochrome 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
122664oxidase+
122664alcohol dehydrogenase-1.1.1.1
122664catalase+1.11.1.6
122664lysine decarboxylase-4.1.1.18
122664ornithine decarboxylase-4.1.1.17
122664urease-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
122664-+++-++-+-++----+---

API 20NE

@refNO3TRPGLU_ FermADH ArgUREESCGELPNPGGLU_ AssimARAMNEMANNAGMALGNTCAPADIMLTCITPACOX
7497-----+--+++---------+

API 50CHac

@refGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
122664------------------------+------------------------

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
7497soil of ginseng fieldDaejeonRepublic of KoreaKORAsia
67770Soil
67771From compostRepublic of KoreaKORAsia
122664Environment, Soil of a ginseng fieldDaejeonRepublic of KoreaKORAsia

isolation source categories

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

taxonmaps

  • @ref: 69479
  • File name: preview.99_6924.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_20;96_348;97_2009;98_5093;99_6924&stattab=map
  • Last taxonomy: Sphingomonas soli subclade
  • 16S sequence: AB166883
  • Sequence Identity:
  • Total samples: 99
  • soil counts: 41
  • aquatic counts: 23
  • animal counts: 22
  • plant counts: 13

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
74971Risk group (German classification)
1226641Risk group (French classification)

Sequence information

16S sequences

  • @ref: 7497
  • description: Sphingomonas soli gene for 16S rRNA, partial sequence
  • accession: AB166883
  • length: 1422
  • database: ena
  • NCBI tax ID: 266127

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Sphingomonas soli NBRC 1008011219055.3wgspatric1219055
66792Sphingomonas soli NBRC 1008012731957634draftimg1219055
67770Sphingomonas soli NBRC 100801GCA_001591025contigncbi1219055

GC content

@refGC-contentmethod
749763.9high performance liquid chromatography (HPLC)
3157763.9

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno97no
motileyes60.776yes
gram-positiveno97.026no
anaerobicno97.405yes
aerobicyes86.646yes
halophileno95.408no
spore-formingno94.382yes
thermophileno96.274yes
glucose-utilyes83.158yes
flagellatedno88.642yes
glucose-fermentno90.674no

External links

@ref: 7497

culture collection no.: DSM 18313, IAM 15213, KCTC 12210, NBRC 10081, JCM 21668, NBRC 100801, CIP 109210

straininfo link

  • @ref: 83404
  • straininfo: 122342

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
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
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

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmed
7497Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 18313)https://www.dsmz.de/collection/catalogue/details/culture/DSM-18313
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
31577Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2786628776041
37476Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/6926
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/
67771Curators of the KCTChttps://kctc.kribb.re.kr/En/Kctc
68369Automatically annotated from API 20NE
68371Automatically annotated from API 50CH acid
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
83404Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID122342.1StrainInfo: A central database for resolving microbial strain identifiers
122664Curators of the CIPCollection of Institut Pasteur (CIP 109210)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20109210