Strain identifier
BacDive ID: 12009
Type strain: 
Species: Bhargavaea beijingensis
Strain Designation: ge10
Strain history: <- F. Qiu, College of Life Sci., Capital Normal Univ., Beijing, China; ge10
NCBI tax ID(s): 426756 (species)
version 8.1 (current version)
General
@ref: 7856
BacDive-ID: 12009
DSM-Number: 19037
keywords: genome sequence, 16S sequence, Bacteria, aerobe, mesophilic, Gram-positive, coccus-shaped
description: Bhargavaea beijingensis ge10 is an aerobe, mesophilic, Gram-positive bacterium that was isolated from ginseng roots, internal tissue.
NCBI tax id
- NCBI tax id: 426756
- Matching level: species
strain history
- @ref: 7856
- history: <- F. Qiu, College of Life Sci., Capital Normal Univ., Beijing, China; ge10
doi: 10.13145/bacdive12009.20230509.8.1
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 beijingensis
- full scientific name: Bhargavaea beijingensis (Qiu et al. 2009) Verma et al. 2012
synonyms
- @ref: 20215
- synonym: Bacillus beijingensis
@ref: 7856
domain: Bacteria
phylum: Firmicutes
class: Bacilli
order: Bacillales
family: Caryophanaceae
genus: Bhargavaea
species: Bhargavaea beijingensis
full scientific name: Bhargavaea beijingensis (Qiu et al. 2009) Verma et al. 2012
strain designation: ge10
type strain: yes
Morphology
cell morphology
| @ref | gram stain | cell length | cell width | cell shape | motility | confidence |
|---|---|---|---|---|---|---|
| 32659 | positive | 1.25 µm | 0.65 µm | coccus-shaped | no | |
| 69480 | positive | 100 |
pigmentation
- @ref: 32659
- production: yes
Culture and growth conditions
culture medium
- @ref: 7856
- 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
| @ref | growth | type | temperature | range |
|---|---|---|---|---|
| 7856 | positive | growth | 30 | mesophilic |
| 32659 | positive | growth | 07-45 | |
| 32659 | positive | optimum | 30 | mesophilic |
culture pH
| @ref | ability | type | pH | PH range |
|---|---|---|---|---|
| 32659 | positive | growth | 5.5-11 | alkaliphile |
| 32659 | positive | optimum | 7.5 |
Physiology and metabolism
oxygen tolerance
- @ref: 32659
- oxygen tolerance: aerobe
spore formation
| @ref | spore formation | confidence |
|---|---|---|
| 32659 | no | |
| 69481 | no | 100 |
| 69480 | yes | 99.999 |
halophily
- @ref: 32659
- salt: NaCl
- growth: positive
- tested relation: growth
- concentration: <12 %
murein
- @ref: 7856
- murein short key: A11.33
- type: A4alpha L-Lys-D-Glu
metabolite utilization
| @ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
|---|---|---|---|---|
| 32659 | 30089 | acetate | + | carbon source |
| 32659 | 21217 | L-alaninamide | + | carbon source |
| 32659 | 16449 | alanine | + | carbon source |
| 32659 | 28644 | 2-oxopentanoate | + | carbon source |
| 32659 | 22599 | arabinose | + | carbon source |
| 32659 | 18403 | L-arabitol | + | carbon source |
| 32659 | 23652 | dextrin | + | carbon source |
| 32659 | 28757 | fructose | + | carbon source |
| 32659 | 5291 | gelatin | + | carbon source |
| 32659 | 29987 | glutamate | + | carbon source |
| 32659 | 17754 | glycerol | + | carbon source |
| 32659 | 28087 | glycogen | + | carbon source |
| 32659 | 17596 | inosine | + | carbon source |
| 32659 | 25115 | malate | + | carbon source |
| 32659 | 17306 | maltose | + | carbon source |
| 32659 | 37657 | methyl D-glucoside | + | carbon source |
| 32659 | 506227 | N-acetylglucosamine | + | carbon source |
| 32659 | 17148 | putrescine | + | carbon source |
| 32659 | 15361 | pyruvate | + | carbon source |
| 32659 | 51850 | methyl pyruvate | + | carbon source |
| 32659 | 17822 | serine | + | carbon source |
| 32659 | 30031 | succinate | + | carbon source |
| 32659 | 17748 | thymidine | + | carbon source |
| 32659 | 53423 | tween 40 | + | carbon source |
| 32659 | 16704 | uridine | + | carbon source |
| 32659 | 17151 | xylitol | + | carbon source |
| 32659 | 4853 | esculin | + | hydrolysis |
| 32659 | 17632 | nitrate | + | reduction |
enzymes
| @ref | value | activity | ec |
|---|---|---|---|
| 32659 | catalase | + | 1.11.1.6 |
| 32659 | cytochrome oxidase | + | 1.9.3.1 |
Isolation, sampling and environmental information
isolation
- @ref: 7856
- sample type: ginseng roots, internal tissue
- geographic location: Beijing
- country: China
- origin.country: CHN
- continent: Asia
isolation source categories
| Cat1 | Cat2 | Cat3 |
|---|---|---|
| #Host | #Plants | #Herbaceous plants (Grass,Crops) |
| #Host Body-Site | #Plant | #Root (Rhizome) |
taxonmaps
- @ref: 69479
- File name: preview.99_5557.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_3;96_2682;97_3294;98_4145;99_5557&stattab=map
- Last taxonomy: Bhargavaea
- 16S sequence: EF371374
- Sequence Identity:
- Total samples: 1707
- soil counts: 871
- aquatic counts: 273
- animal counts: 344
- plant counts: 219
Safety information
risk assessment
- @ref: 7856
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
- @ref: 7856
- description: Bacillus beijingensis strain ge10 16S ribosomal RNA gene, partial sequence
- accession: EF371374
- length: 1512
- database: ena
- NCBI tax ID: 426756
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Bhargavaea beijingensis CGMCC 1.6762 | GCA_900101985 | contig | ncbi | 426756 |
| 66792 | Bhargavaea beijingensis strain CGMCC 1.6762 | 426756.5 | wgs | patric | 426756 |
| 66792 | Bhargavaea beijingensis CGMCC 1.6762 | 2619618820 | draft | img | 426756 |
GC content
| @ref | GC-content | method |
|---|---|---|
| 7856 | 53.1 | thermal denaturation, midpoint method (Tm) |
| 7856 | 49.9 | thermal denaturation, midpoint method (Tm) |
| 32659 | 49.9 |
Genome-based predictions
predictions
| trait | prediction | confidence | training_data |
|---|---|---|---|
| spore-forming | no | 100 | no |
| gram-positive | yes | 94.672 | yes |
| anaerobic | no | 99.382 | yes |
| halophile | yes | 88.498 | no |
| spore-forming | yes | 70.607 | no |
| glucose-util | yes | 86.674 | no |
| aerobic | yes | 95.924 | yes |
| thermophile | no | 97.535 | yes |
| motile | no | 87.56 | yes |
| flagellated | no | 91.804 | no |
| glucose-ferment | no | 90.47 | no |
External links
@ref: 7856
culture collection no.: DSM 19037, CGMCC 1.6762
straininfo link
- @ref: 81228
- straininfo: 362297
literature
| topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
|---|---|---|---|---|---|---|---|---|
| Phylogeny | 19329597 | Bacillus beijingensis sp. nov. and Bacillus ginsengi sp. nov., isolated from ginseng root. | Qiu F, Zhang X, Liu L, Sun L, Schumann P, Song W | Int J Syst Evol Microbiol | 10.1099/ijs.0.65861-0 | 2009 | Bacillus/*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 Acid | Genetics |
| Phylogeny | 22155760 | Reclassification 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 YS | Int J Syst Evol Microbiol | 10.1099/ijs.0.034850-0 | 2011 | Bacillus/*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, DNA | Genetics |
| Phylogeny | 23243092 | Bhargavaea ullalensis sp. nov., isolated from coastal sand. | Glaeser SP, Arun AB, Rekha PD, Prabhu S, Busse HJ, Kampfer P | Int J Syst Evol Microbiol | 10.1099/ijs.0.045062-0 | 2012 | Bacillales/*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/analysis | Genetics |
Reference
| @id | authors | catalogue | doi/url | title | ID_cross_reference | pubmed |
|---|---|---|---|---|---|---|
| 7856 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 19037) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-19037 | |||
| 20215 | Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M. | 10.1099/ijsem.0.004332 | List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ | |||
| 32659 | Barberan A, Caceres Velazquez H, Jones S, Fierer N. | 10.1128/mSphere.00237-17 | Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information | 28870 | 28776041 | |
| 66792 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | https://diaspora-project.de/progress.html#genomes | Automatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) | |||
| 69479 | João 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 | |||
| 69480 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | https://diaspora-project.de/progress.html#genomes | Predictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) | |||
| 69481 | Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch | 10.21203/rs.3.rs-2527258/v1 | Predictions based on the model GenomeNet Sporulation v. 1 | |||
| 81228 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID362297.1 | StrainInfo: A central database for resolving microbial strain identifiers |