Strain identifier
BacDive ID: 7178
Type strain: 
Species: Methylobacterium variabile
Strain Designation: GR3
Strain history: <- A. Ventosa <- V. Gallego; GR3 {2003}
NCBI tax ID(s): 298794 (species)
version 8.1 (current version)
General
@ref: 6672
BacDive-ID: 7178
DSM-Number: 16961
keywords: genome sequence, 16S sequence, Bacteria, aerobe, mesophilic, Gram-negative, motile, rod-shaped
description: Methylobacterium variabile GR3 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from drinking water.
NCBI tax id
- NCBI tax id: 298794
- Matching level: species
strain history
- @ref: 6672
- history: <- A. Ventosa <- V. Gallego; GR3 {2003}
doi: 10.13145/bacdive7178.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/pseudomonadota
- domain: Bacteria
- phylum: Pseudomonadota
- class: Alphaproteobacteria
- order: Hyphomicrobiales
- family: Methylobacteriaceae
- genus: Methylobacterium
- species: Methylobacterium variabile
- full scientific name: Methylobacterium variabile Gallego et al. 2005
@ref: 6672
domain: Bacteria
phylum: Proteobacteria
class: Alphaproteobacteria
order: Rhizobiales
family: Methylobacteriaceae
genus: Methylobacterium
species: Methylobacterium variabile
full scientific name: Methylobacterium variabile Gallego et al. 2005
strain designation: GR3
type strain: yes
Morphology
cell morphology
| @ref | gram stain | cell length | cell width | cell shape | motility | confidence |
|---|---|---|---|---|---|---|
| 31454 | negative | 4 µm | 1.25 µm | rod-shaped | yes | |
| 69480 | yes | 93.786 | ||||
| 69480 | negative | 99.999 |
pigmentation
- @ref: 31454
- production: yes
Culture and growth conditions
culture medium
- @ref: 6672
- 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
| @ref | growth | type | temperature | range |
|---|---|---|---|---|
| 6672 | positive | growth | 28 | mesophilic |
| 31454 | positive | growth | 20-30 | |
| 31454 | positive | optimum | 28 | mesophilic |
culture pH
| @ref | ability | type | pH |
|---|---|---|---|
| 31454 | positive | growth | 05-08 |
| 31454 | positive | optimum | 6 |
Physiology and metabolism
oxygen tolerance
| @ref | oxygen tolerance |
|---|---|
| 6672 | aerobe |
| 31454 | aerobe |
spore formation
| @ref | spore formation | confidence |
|---|---|---|
| 31454 | no | |
| 69481 | no | 100 |
| 69480 | no | 99.993 |
halophily
| @ref | salt | growth | tested relation | concentration |
|---|---|---|---|---|
| 31454 | NaCl | positive | growth | <1.0 % |
| 31454 | NaCl | positive | optimum | 0.5 % |
observation
- @ref: 31454
- observation: aggregates in clumps
metabolite utilization
| @ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
|---|---|---|---|---|
| 31454 | 30089 | acetate | + | carbon source |
| 31454 | 22653 | asparagine | + | carbon source |
| 31454 | 35391 | aspartate | + | carbon source |
| 31454 | 16947 | citrate | + | carbon source |
| 31454 | 15740 | formate | + | carbon source |
| 31454 | 28757 | fructose | + | carbon source |
| 31454 | 33984 | fucose | + | carbon source |
| 31454 | 28260 | galactose | + | carbon source |
| 31454 | 24265 | gluconate | + | carbon source |
| 31454 | 17234 | glucose | + | carbon source |
| 31454 | 29987 | glutamate | + | carbon source |
| 31454 | 24996 | lactate | + | carbon source |
| 31454 | 25115 | malate | + | carbon source |
| 31454 | 17272 | propionate | + | carbon source |
| 31454 | 15361 | pyruvate | + | carbon source |
| 31454 | 30031 | succinate | + | carbon source |
| 31454 | 17632 | nitrate | + | reduction |
enzymes
| @ref | value | activity | ec |
|---|---|---|---|
| 31454 | catalase | + | 1.11.1.6 |
| 31454 | urease | + | 3.5.1.5 |
Isolation, sampling and environmental information
isolation
- @ref: 6672
- sample type: drinking water
- geographic location: Seville
- country: Spain
- origin.country: ESP
- continent: Europe
isolation source categories
- Cat1: #Environmental
- Cat2: #Aquatic
- Cat3: #Freshwater
taxonmaps
- @ref: 69479
- File name: preview.99_384.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_15368;96_262;97_289;98_322;99_384&stattab=map
- Last taxonomy: Methylobacterium variabile subclade
- 16S sequence: AJ851087
- Sequence Identity:
- Total samples: 3279
- soil counts: 338
- aquatic counts: 1173
- animal counts: 1485
- plant counts: 283
Safety information
risk assessment
- @ref: 6672
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
| @ref | description | accession | length | database | NCBI tax ID |
|---|---|---|---|---|---|
| 20218 | Methylobacterium variabile gene for 16S rRNA, partial sequence, strain: DSM 16961 | AB302931 | 1436 | ena | 298794 |
| 6672 | Methylobacterium variabile 16S rRNA gene, type strain GR3 | AJ851087 | 1410 | ena | 298794 |
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Methylobacterium variabile DSM 16961 | GCA_001043975 | contig | ncbi | 298794 |
| 66792 | Methylobacterium variabile strain DSM 16961 | 298794.3 | wgs | patric | 298794 |
| 66792 | Methylobacterium variabile DSM 16961 | 2636415936 | draft | img | 298794 |
GC content
- @ref: 6672
- GC-content: 69.2
Genome-based predictions
predictions
| trait | prediction | confidence | training_data |
|---|---|---|---|
| spore-forming | no | 100 | no |
| gram-positive | no | 97.623 | yes |
| anaerobic | no | 97.831 | yes |
| halophile | no | 90.171 | no |
| spore-forming | no | 92.616 | yes |
| glucose-util | yes | 90.149 | yes |
| motile | yes | 89.863 | yes |
| flagellated | no | 71.768 | no |
| aerobic | yes | 92.742 | yes |
| thermophile | no | 99.069 | no |
| glucose-ferment | no | 89.19 | no |
External links
@ref: 6672
culture collection no.: DSM 16961, CCM 7281, CECT 7045
straininfo link
- @ref: 76631
- straininfo: 265402
literature
| topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
|---|---|---|---|---|---|---|---|---|
| Phylogeny | 16014462 | Methylobacterium variabile sp. nov., a methylotrophic bacterium isolated from an aquatic environment. | Gallego V, Garcia MT, Ventosa A | Int J Syst Evol Microbiol | 10.1099/ijs.0.63597-0 | 2005 | Bacterial Typing Techniques, Base Composition, DNA, Bacterial/analysis, Fresh Water/*microbiology, Genes, rRNA, Methylobacterium/*classification/genetics/physiology, Molecular Sequence Data, Nucleic Acid Hybridization, Phenotype, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Spain, *Water Supply | Genetics |
| Phylogeny | 32207677 | Methylobacterium nonmethylotrophicum sp. nov., isolated from tungsten mine tailing. | Feng GD, Chen W, Zhang XJ, Zhang J, Wang SN, Zhu H | Int J Syst Evol Microbiol | 10.1099/ijsem.0.004112 | 2020 | Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Fatty Acids/chemistry, Genes, Bacterial, Methylobacterium/*classification/isolation & purification, *Mining, Nucleic Acid Hybridization, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Tungsten, Ubiquinone/analogs & derivatives/chemistry | Transcriptome |
Reference
| @id | authors | catalogue | doi/url | title | journal | pubmed | ID_cross_reference |
|---|---|---|---|---|---|---|---|
| 6672 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 16961) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-16961 | ||||
| 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 | ||||
| 20218 | Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P. | 10.1016/j.syapm.2013.11.002 | StrainInfo introduces electronic passports for microorganisms. | Syst Appl Microbiol. 37: 42-50 2014 | 24321274 | ||
| 31454 | 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 | 28776041 | 27756 | ||
| 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 | ||||
| 76631 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID265402.1 | StrainInfo: A central database for resolving microbial strain identifiers |