Strain identifier

BacDive ID: 14088

Type strain: Yes

Species: Solirubrobacter soli

Strain history: <- ST Lee, KAIST

NCBI tax ID(s): 1123262 (strain), 363832 (species)

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General

@ref: 16282

BacDive-ID: 14088

DSM-Number: 22325

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

description: Solirubrobacter soli DSM 22325 is an aerobe, Gram-positive, rod-shaped bacterium that was isolated from soil from a ginseng field.

NCBI tax id

NCBI tax idMatching level
363832species
1123262strain

strain history

@refhistory
16282<- LMG; LMG 23485 <- S.-T. Lee, KAIST <- W.-T. Im
67770LMG 23485 <-- D.-C. Yang Gsoil 355.
67771<- ST Lee, KAIST

doi: 10.13145/bacdive14088.20240916.9.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/actinomycetota
  • domain: Bacteria
  • phylum: Actinomycetota
  • class: Thermoleophilia
  • order: Solirubrobacterales
  • family: Solirubrobacteraceae
  • genus: Solirubrobacter
  • species: Solirubrobacter soli
  • full scientific name: Solirubrobacter soli Kim et al. 2007

@ref: 16282

domain: Bacteria

phylum: Actinobacteria

class: Thermoleophilia

order: Solirubrobacterales

family: Solirubrobacteraceae

genus: Solirubrobacter

species: Solirubrobacter soli

full scientific name: Solirubrobacter soli Kim et al. 2007

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell shapemotility
31958positive2 µmrod-shapedno
67771positive

colony morphology

  • @ref: 16282
  • incubation period: 8-14 days

Culture and growth conditions

culture medium

  • @ref: 16282
  • name: R2A MEDIUM (DSMZ Medium 830)
  • growth: yes
  • link: https://mediadive.dsmz.de/medium/830
  • composition: Name: 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

culture temp

@refgrowthtypetemperature
16282positivegrowth28
31958positivegrowth25-30
67770positivegrowth28
67771positivegrowth28

culture pH

@refabilitytypepHPH range
31958positivegrowth5.0-11alkaliphile
31958positiveoptimum8

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
31958aerobe
67771aerobe

spore formation

  • @ref: 31958
  • spore formation: no

halophily

@refsaltgrowthtested relationconcentration
31958NaClpositivegrowth0.0-1.5 %
31958NaClpositiveoptimum0.75 %

observation

  • @ref: 67770
  • observation: quinones: MK-7(H4)

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3195817128adipate+carbon source
3195822599arabinose+carbon source
3195833984fucose+carbon source
3195824265gluconate+carbon source
3195817234glucose+carbon source
3195817306maltose+carbon source
3195828053melibiose+carbon source
3195817268myo-inositol+carbon source
31958506227N-acetylglucosamine+carbon source
3195826271proline+carbon source
3195826546rhamnose+carbon source
3195833942ribose+carbon source
3195817814salicin+carbon source
3195817992sucrose+carbon source

enzymes

@refvalueactivityec
31958acid phosphatase+3.1.3.2
31958alkaline phosphatase+3.1.3.1
31958catalase+1.11.1.6
31958gelatinase+
31958cytochrome oxidase+1.9.3.1

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
16282soil from a ginseng fieldDaejeonRepublic of KoreaKORAsia
67770Soil of a ginseng fieldRepublic of KoreaKORAsia
67771From soilKAISTRepublic 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_8039.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_373;96_1692;97_2026;98_5859;99_8039&stattab=map
  • Last taxonomy: Solirubrobacter soli subclade
  • 16S sequence: AB245334
  • Sequence Identity:
  • Total samples: 1390
  • soil counts: 998
  • aquatic counts: 81
  • animal counts: 85
  • plant counts: 226

Safety information

risk assessment

  • @ref: 16282
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 16282
  • description: Solirubrobacter soli gene for 16S rRNA, partial sequence
  • accession: AB245334
  • length: 1495
  • database: nuccore
  • NCBI tax ID: 363832

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Solirubrobacter soli DSM 223251123262.3wgspatric1123262
66792Solirubrobacter soli DSM 223252524023148draftimg1123262
67770Solirubrobacter soli DSM 22325GCA_000423665scaffoldncbi1123262

GC content

@refGC-contentmethod
1628271.5high performance liquid chromatography (HPLC)
3195871.5

Genome-based predictions

predictions

@reftraitmodeldescriptionpredictionconfidencetraining_data
69481spore-formingspore-formingAbility to form endo- or exosporesyes88no
69480gram-positivegram-positivePositive reaction to Gram-stainingyes71.876yes
69480anaerobicanaerobicAbility to grow under anoxygenic conditions (including facultative anaerobes)no85.077no
69480spore-formingspore-formingAbility to form endo- or exosporesyes55.959no
69480aerobicaerobicAbility to grow under oxygenic conditions (including facultative aerobes)yes83.982yes
69480thermophilicthermophileAbility to grow at temperatures above or equal to 45°Cno94.111yes
69480flagellatedmotile2+Ability to perform flagellated movementno56.131no

External links

@ref: 16282

culture collection no.: DSM 22325, JCM 14923, KCTC 12628, LMG 23485, Gsoil 355

straininfo link

  • @ref: 83256
  • straininfo: 309492

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny17625174Solirubrobacter soli sp. nov., isolated from soil of a ginseng field.Kim MK, Na JR, Lee TH, Im WT, Soung NK, Yang DCInt J Syst Evol Microbiol10.1099/ijs.0.64715-02007Actinobacteria/chemistry/*classification/*isolation & purification/physiology, Base Composition, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis, Genes, rRNA, Korea, Locomotion, Molecular Sequence Data, Panax, Phylogeny, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sequence Homology, Nucleic Acid, *Soil Microbiology, Spores, Bacterial, Vitamin K 2/analysisGenetics
Phylogeny21148679Solirubrobacter ginsenosidimutans sp. nov., isolated from soil of a ginseng field.An DS, Wang L, Kim MS, Bae HM, Lee ST, Im WTInt J Syst Evol Microbiol10.1099/ijs.0.028431-02010Actinobacteria/*classification/genetics/*isolation & purification/metabolism, Base Composition, China, DNA, Bacterial/genetics, DNA, Ribosomal/genetics, Fatty Acids/metabolism, Ginsenosides/metabolism, Molecular Sequence Data, Panax/*microbiology, Phylogeny, RNA, Ribosomal, 16S/genetics, *Soil MicrobiologyMetabolism
Phylogeny24254741Solirubrobacter phytolaccae sp. nov., an endophytic bacterium isolated from roots of Phytolacca acinosa Roxb.Wei L, Ouyang S, Wang Y, Shen X, Zhang LInt J Syst Evol Microbiol10.1099/ijs.0.057554-02013Actinobacteria/*classification/genetics/isolation & purification, Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Fatty Acids/chemistry, Molecular Sequence Data, Nucleic Acid Hybridization, *Phylogeny, Phytolacca/*microbiology, Plant Roots/microbiology, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Vitamin K 2/analogs & derivatives/chemistryGenetics
Phylogeny24846053Solirubrobacter taibaiensis sp. nov., isolated from a stem of Phytolacca acinosa Roxb.Zhang L, Zhu L, Si M, Li C, Zhao L, Wei Y, Shen XAntonie Van Leeuwenhoek10.1007/s10482-014-0194-42014Actinobacteria/*classification/genetics/*isolation & purification/physiology, Aerobiosis, Bacterial Typing Techniques, Base Composition, China, Cluster Analysis, Cytosol/chemistry, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis, Hydrogen-Ion Concentration, Molecular Sequence Data, Nucleic Acid Hybridization, Phylogeny, Phytolacca/*microbiology, Plant Stems/microbiology, Quinones/analysis, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sodium Chloride/metabolism, TemperatureGenetics

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmed
16282Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 22325)https://www.dsmz.de/collection/catalogue/details/culture/DSM-22325
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
31958Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2821428776041
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
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
83256Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID309492.1StrainInfo: A central database for resolving microbial strain identifiers