Strain identifier

BacDive ID: 7515

Type strain: Yes

Species: Gryllotalpicola ginsengisoli

Strain history: <- DC Yang, Kyunghee Univ.

NCBI tax ID(s): 1121372 (strain), 444608 (species)

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General

@ref: 16095

BacDive-ID: 7515

DSM-Number: 22003

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

description: Gryllotalpicola ginsengisoli DSM 22003 is an aerobe, mesophilic, Gram-positive bacterium that was isolated from Surface soil of a ginseng field.

NCBI tax id

NCBI tax idMatching level
444608species
1121372strain

strain history

@refhistory
16095<- JCM/RIKEN <- D.-C. Yang, Kyung Hee University, Giheung-gu Yongin, South Korea; DCY26
67770D.-C. Yang DCY26.
67771<- DC Yang, Kyunghee Univ.

doi: 10.13145/bacdive7515.20241212.9.2

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/actinomycetota
  • domain: Bacteria
  • phylum: Actinomycetota
  • class: Actinomycetes
  • order: Micrococcales
  • family: Microbacteriaceae
  • genus: Gryllotalpicola
  • species: Gryllotalpicola ginsengisoli
  • full scientific name: Gryllotalpicola ginsengisoli (Kim et al. 2008) Kim et al. 2012

  • synonyms

    • @ref: 20215
    • synonym: Curtobacterium ginsengisoli

@ref: 16095

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Microbacteriaceae

genus: Gryllotalpicola

species: Gryllotalpicola ginsengisoli

full scientific name: Gryllotalpicola ginsengisoli (Kim et al. 2008) Kim et al. 2012

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
32503positive0.5-0.8 µm0.3-0.6 µmrod-shapedno
67771positive
69480positive90.573
69480no96.5

pigmentation

  • @ref: 32503
  • production: yes

Culture and growth conditions

culture medium

  • @ref: 16095
  • 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
16095positivegrowth28
32503positivegrowth25-42
32503positiveoptimum30-37
67770positivegrowth28
67771positivegrowth30

culture pH

@refabilitytypepHPH range
32503positivegrowth05-11alkaliphile
32503positiveoptimum7

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
32503aerobe
67771aerobe

spore formation

@refspore formationconfidence
32503no
69481no95

observation

@refobservation
32503aggregates in chains
67770quinones: MK-9, MK-11, MK-10
67771quinones: MK-9

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3250322599arabinose+carbon source
3250317234glucose+carbon source
3250317306maltose+carbon source
3250326546rhamnose+carbon source
3250317992sucrose+carbon source

enzymes

@refvalueactivityec
32503acid phosphatase+3.1.3.2
32503alkaline phosphatase+3.1.3.1
32503catalase+1.11.1.6
32503cytochrome oxidase+1.9.3.1

Isolation, sampling and environmental information

isolation

@refsample typecountryorigin.countrycontinent
16095Surface soil of a ginseng fieldRepublic of KoreaKORAsia
67770Surface soil of a ginseng fieldRepublic of KoreaKORAsia
67771From soil. ginseng fieldRepublic 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_7352.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_9;96_3440;97_4222;98_5395;99_7352&stattab=map
  • Last taxonomy: Gryllotalpicola ginsengisoli subclade
  • 16S sequence: EF587758
  • Sequence Identity:
  • Total samples: 302
  • soil counts: 42
  • aquatic counts: 8
  • animal counts: 42
  • plant counts: 210

Safety information

risk assessment

  • @ref: 16095
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 16095
  • description: Gryllotalpicola ginsengisoli DSM 22003 16S ribosomal RNA gene, partial sequence
  • accession: EF587758
  • length: 1390
  • database: nuccore
  • NCBI tax ID: 1121372

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Curtobacterium ginsengisoli DSM 220031121372.3wgspatric1121372
66792Gryllotalpicola ginsengisoli DSM 220032523533581draftimg1121372
67770Gryllotalpicola ginsengisoli DSM 22003GCA_000419445scaffoldncbi1121372

GC content

@refGC-contentmethod
1609565.8high performance liquid chromatography (HPLC)
6777071.6high performance liquid chromatography (HPLC)
6777165.8

Genome-based predictions

predictions

@reftraitmodeldescriptionpredictionconfidencetraining_data
69481spore-formingspore-formingAbility to form endo- or exosporesno95no
69480gram-positivegram-positivePositive reaction to Gram-stainingyes90.573yes
69480anaerobicanaerobicAbility to grow under anoxygenic conditions (including facultative anaerobes)no98.395yes
69480spore-formingspore-formingAbility to form endo- or exosporesno82.37yes
69480aerobicaerobicAbility to grow under oxygenic conditions (including facultative aerobes)yes82.214no
69480thermophilicthermophileAbility to grow at temperatures above or equal to 45°Cno95yes
69480flagellatedmotile2+Ability to perform flagellated movementno96.5no

External links

@ref: 16095

culture collection no.: DSM 22003, JCM 14773, KCTC 13163, DCY 26

straininfo link

  • @ref: 76960
  • straininfo: 407938

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny18842862Curtobacterium ginsengisoli sp. nov., isolated from soil of a ginseng field.Kim MK, Kim YJ, Kim HB, Kim SY, Yi TH, Yang DCInt J Syst Evol Microbiol10.1099/ijs.0.65591-02008Actinomycetales/chemistry/*classification/*genetics/isolation & purification, Agriculture, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Genes, Bacterial, Genes, rRNA, Korea, Molecular Sequence Data, Panax/*microbiology, Phenotype, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil MicrobiologyGenetics
Phylogeny22140167Gryllotalpicola gen. nov., with descriptions of Gryllotalpicola koreensis sp. nov., Gryllotalpicola daejeonensis sp. nov. and Gryllotalpicola kribbensis sp. nov. from the gut of the African mole cricket, Gryllotalpa africana, and reclassification of Curtobacterium ginsengisoli as Gryllotalpicola ginsengisoli comb. nov.Kim H, Park DS, Oh HW, Lee KH, Chung DH, Park HY, Park HM, Bae KSInt J Syst Evol Microbiol10.1099/ijs.0.034678-02011Actinomycetales/*classification/genetics/isolation & purification, Animals, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/analysis, Gastrointestinal Tract/*microbiology, Gryllidae/*microbiology, Molecular Sequence Data, *Phylogeny, Quinones/analysis, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNAGenetics

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmed
16095Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 22003)https://www.dsmz.de/collection/catalogue/details/culture/DSM-22003
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
32503Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2872328776041
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
76960Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID407938.1StrainInfo: A central database for resolving microbial strain identifiers