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, mesophilic, Gram-positive, rod-shaped

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

NCBI tax id

NCBI tax idMatching level
1123262strain
363832species

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/bacdive14088.20230509.8.1

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 shapemotilityconfidence
31958positive2 µmrod-shapedno
67771positive
69480positive99.72

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

@refgrowthtypetemperaturerange
16282positivegrowth28mesophilic
31958positivegrowth25-30mesophilic
67770positivegrowth28mesophilic
67771positivegrowth28mesophilic

culture pH

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

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
31958aerobe
67771aerobe

spore formation

@refspore formationconfidence
31958no
69480no93.069

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: ena
  • 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

traitpredictionconfidencetraining_data
spore-formingyes88no
motileyes54.108yes
flagellatedno89.356no
gram-positiveyes82.733yes
anaerobicno98.492yes
aerobicyes87.24yes
halophileno94.365yes
spore-formingno79.526yes
thermophileno98.003yes
glucose-utilyes86.762yes
glucose-fermentno85.815no

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)
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