Strain identifier

BacDive ID: 12010

Type strain: Yes

Species: Bhargavaea ginsengi

Strain Designation: ge14

Strain history: <- F. Qiu, College of Life Sci., Capital Normal Univ., Beijing , PR China; ge14

NCBI tax ID(s): 426757 (species)

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General

@ref: 7857

BacDive-ID: 12010

DSM-Number: 19038

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

description: Bhargavaea ginsengi ge14 is an aerobe, Gram-positive, rod-shaped bacterium that was isolated from Ginseng roots, internal tissue.

NCBI tax id

  • NCBI tax id: 426757
  • Matching level: species

strain history

  • @ref: 7857
  • history: <- F. Qiu, College of Life Sci., Capital Normal Univ., Beijing , PR China; ge14

doi: 10.13145/bacdive12010.20240916.9.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/bacillota
  • domain: Bacteria
  • phylum: Bacillota
  • class: Bacilli
  • order: Caryophanales
  • family: Caryophanaceae
  • genus: Bhargavaea
  • species: Bhargavaea ginsengi
  • full scientific name: Bhargavaea ginsengi (Qiu et al. 2009) Verma et al. 2012

  • synonyms

    • @ref: 20215
    • synonym: Bacillus ginsengi

@ref: 7857

domain: Bacteria

phylum: Firmicutes

class: Bacilli

order: Bacillales

family: Caryophanaceae

genus: Bhargavaea

species: Bhargavaea ginsengi

full scientific name: Bhargavaea ginsengi (Qiu et al. 2009) Verma et al. 2012

strain designation: ge14

type strain: yes

Morphology

cell morphology

  • @ref: 32659
  • gram stain: positive
  • cell length: 1.3 µm
  • cell width: 1.1 µm
  • cell shape: rod-shaped
  • motility: no

pigmentation

  • @ref: 32659
  • production: yes

Culture and growth conditions

culture medium

  • @ref: 7857
  • name: CASO AGAR (MERCK 105458) (DSMZ Medium 220)
  • growth: yes
  • link: https://mediadive.dsmz.de/medium/220
  • composition: Name: 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

culture temp

@refgrowthtypetemperature
7857positivegrowth30
32659positivegrowth04-45
32659positiveoptimum30

culture pH

@refabilitytypepHPH range
32659positivegrowth06-11alkaliphile
32659positiveoptimum7.5

Physiology and metabolism

oxygen tolerance

  • @ref: 32659
  • oxygen tolerance: aerobe

spore formation

@refspore formationconfidence
32659no
69481no99

halophily

  • @ref: 32659
  • salt: NaCl
  • growth: positive
  • tested relation: growth
  • concentration: <10 %

murein

  • @ref: 7857
  • murein short key: A11.33
  • type: A4alpha L-Lys-D-Glu

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3265930089acetate+carbon source
3265921217L-alaninamide+carbon source
3265916449alanine+carbon source
32659286442-oxopentanoate+carbon source
3265922653asparagine+carbon source
3265928757fructose+carbon source
326595291gelatin+carbon source
3265929987glutamate+carbon source
3265917754glycerol+carbon source
3265928087glycogen+carbon source
3265917596inosine+carbon source
3265925115malate+carbon source
3265937684mannose+carbon source
32659506227N-acetylglucosamine+carbon source
3265917272propionate+carbon source
3265915361pyruvate+carbon source
3265951850methyl pyruvate+carbon source
3265917822serine+carbon source
3265930031succinate+carbon source
3265917748thymidine+carbon source
3265953423tween 40+carbon source
3265916704uridine+carbon source
326594853esculin+hydrolysis
3265917632nitrate+reduction

metabolite production

  • @ref: 32659
  • Chebi-ID: 35581
  • metabolite: indole
  • production: yes

metabolite tests

  • @ref: 32659
  • Chebi-ID: 35581
  • metabolite: indole
  • indole test: +

enzymes

@refvalueactivityec
32659catalase+1.11.1.6
32659cytochrome oxidase+1.9.3.1

Isolation, sampling and environmental information

isolation

  • @ref: 7857
  • sample type: Ginseng roots, internal tissue
  • geographic location: Beijing
  • country: China
  • origin.country: CHN
  • continent: Asia

isolation source categories

Cat1Cat2Cat3
#Host#Plants#Herbaceous plants (Grass,Crops)
#Host Body-Site#Plant#Root (Rhizome)

taxonmaps

  • @ref: 69479
  • File name: preview.99_28944.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_3;96_2682;97_3294;98_4145;99_28944&stattab=map
  • Last taxonomy: Bhargavaea
  • 16S sequence: EF371375
  • Sequence Identity:
  • Total samples: 282
  • soil counts: 187
  • aquatic counts: 40
  • animal counts: 47
  • plant counts: 8

Safety information

risk assessment

  • @ref: 7857
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 7857
  • description: Bacillus ginsengi strain ge14 16S ribosomal RNA gene, partial sequence
  • accession: EF371375
  • length: 1512
  • database: nuccore
  • NCBI tax ID: 426757

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Bhargavaea ginsengi CGMCC 1.6763GCA_900109165scaffoldncbi426757
66792Bhargavaea ginsengi strain CGMCC 1.6763426757.4wgspatric426757
66792Bhargavaea ginsengi CGMCC 1.67632617270926draftimg426757

GC content

@refGC-contentmethod
785750.2thermal denaturation, midpoint method (Tm)
785749.6thermal denaturation, midpoint method (Tm)
3265949.6

Genome-based predictions

predictions

@reftraitmodeldescriptionpredictionconfidencetraining_data
69481spore-formingspore-formingAbility to form endo- or exosporesno99no
69480gram-positivegram-positivePositive reaction to Gram-stainingyes84.34yes
69480anaerobicanaerobicAbility to grow under anoxygenic conditions (including facultative anaerobes)no97.794yes
69480aerobicaerobicAbility to grow under oxygenic conditions (including facultative aerobes)yes80.519no
69480spore-formingspore-formingAbility to form endo- or exosporesno55.008yes
69480thermophilicthermophileAbility to grow at temperatures above or equal to 45°Cno91.891no
69480flagellatedmotile2+Ability to perform flagellated movementno70.939yes

External links

@ref: 7857

culture collection no.: DSM 19038, CGMCC 1.6763

straininfo link

  • @ref: 81229
  • straininfo: 362296

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny19329597Bacillus beijingensis sp. nov. and Bacillus ginsengi sp. nov., isolated from ginseng root.Qiu F, Zhang X, Liu L, Sun L, Schumann P, Song WInt J Syst Evol Microbiol10.1099/ijs.0.65861-02009Bacillus/*classification/genetics/*isolation & purification/physiology, Bacterial Typing Techniques, Base Composition, Cell Wall/chemistry, Cluster Analysis, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis, Molecular Sequence Data, Nucleic Acid Hybridization, Panax/*microbiology, Peptidoglycan/analysis, Phospholipids/analysis, Phylogeny, Plant Roots/*microbiology, Quinones/analysis, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sequence Homology, Nucleic AcidGenetics
Phylogeny22155760Reclassification of Bacillus beijingensis Qiu et al. 2009 and Bacillus ginsengi Qiu et al. 2009 as Bhargavaea beijingensis comb. nov. and Bhargavaea ginsengi comb. nov. and emended description of the genus Bhargavaea.Verma P, Pandey PK, Gupta AK, Seong CN, Park SC, Choe HN, Baik KS, Patole MS, Shouche YSInt J Syst Evol Microbiol10.1099/ijs.0.034850-02011Bacillus/*classification/genetics/metabolism, Bacterial Typing Techniques, Base Composition, DNA Gyrase/genetics, DNA, Bacterial/genetics, Fatty Acids/analysis, Genes, Bacterial, Molecular Sequence Data, Nucleic Acid Hybridization, Peptidoglycan/analysis, *Phylogeny, Quinones/analysis, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNAGenetics
Phylogeny23243092Bhargavaea ullalensis sp. nov., isolated from coastal sand.Glaeser SP, Arun AB, Rekha PD, Prabhu S, Busse HJ, Kampfer PInt J Syst Evol Microbiol10.1099/ijs.0.045062-02012Bacillales/*classification/genetics/isolation & purification, Bacterial Typing Techniques, DNA, Bacterial/genetics, Fatty Acids/analysis, Genes, Bacterial, India, Molecular Sequence Data, Nucleic Acid Hybridization, Peptidoglycan/analysis, *Phylogeny, Polyamines/analysis, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Silicon Dioxide, Vitamin K 2/analogs & derivatives/analysisGenetics

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmed
7857Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 19038)https://www.dsmz.de/collection/catalogue/details/culture/DSM-19038
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
32659Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2887028776041
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)
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
81229Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID362296.1StrainInfo: A central database for resolving microbial strain identifiers