Strain identifier
BacDive ID: 7200
Type strain: 
Species: Methylobacterium gnaphalii
Strain Designation: 23e
Strain history: <- A. Tani, Okayama University, Institute of Plant Science and Resources, Japan; strain 23e
NCBI tax ID(s): 1010610 (species)
version 8.1 (current version)
General
@ref: 17479
BacDive-ID: 7200
DSM-Number: 24027
keywords: genome sequence, 16S sequence, Bacteria, aerobe, mesophilic, Gram-negative, motile, rod-shaped
description: Methylobacterium gnaphalii 23e is an aerobe, mesophilic, Gram-negative bacterium that was isolated from leaves of Gnaphalium spicatum .
NCBI tax id
- NCBI tax id: 1010610
- Matching level: species
strain history
- @ref: 17479
- history: <- A. Tani, Okayama University, Institute of Plant Science and Resources, Japan; strain 23e
doi: 10.13145/bacdive7200.20230509.8.1
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 gnaphalii
- full scientific name: Methylobacterium gnaphalii Tani et al. 2012
@ref: 17479
domain: Bacteria
phylum: Proteobacteria
class: Alphaproteobacteria
order: Rhizobiales
family: Methylobacteriaceae
genus: Methylobacterium
species: Methylobacterium gnaphalii
full scientific name: Methylobacterium gnaphalii Tani et al. 2012
strain designation: 23e
type strain: yes
Morphology
cell morphology
| @ref | gram stain | cell length | cell width | cell shape | motility | confidence |
|---|---|---|---|---|---|---|
| 30510 | negative | 1.99 µm | 0.9 µm | rod-shaped | yes | |
| 69480 | yes | 92.025 | ||||
| 69480 | negative | 99.997 |
colony morphology
- @ref: 17479
- incubation period: 3-7 days
pigmentation
- @ref: 30510
- production: yes
Culture and growth conditions
culture medium
- @ref: 17479
- 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 |
|---|---|---|---|---|
| 17479 | positive | growth | 28 | mesophilic |
| 30510 | positive | growth | 28-37 | mesophilic |
Physiology and metabolism
oxygen tolerance
- @ref: 30510
- oxygen tolerance: aerobe
spore formation
| @ref | spore formation | confidence |
|---|---|---|
| 69481 | no | 100 |
| 69480 | no | 99.998 |
metabolite utilization
| @ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
|---|---|---|---|---|
| 30510 | 30089 | acetate | + | carbon source |
| 30510 | 22599 | arabinose | + | carbon source |
| 30510 | 15740 | formate | + | carbon source |
| 30510 | 29987 | glutamate | + | carbon source |
| 30510 | 24996 | lactate | + | carbon source |
| 30510 | 15792 | malonate | + | carbon source |
| 30510 | 51850 | methyl pyruvate | + | carbon source |
| 30510 | 17272 | propionate | + | carbon source |
| 30510 | 30031 | succinate | + | carbon source |
| 30510 | 17632 | nitrate | + | reduction |
enzymes
| @ref | value | activity | ec |
|---|---|---|---|
| 30510 | catalase | + | 1.11.1.6 |
| 30510 | urease | + | 3.5.1.5 |
Isolation, sampling and environmental information
isolation
- @ref: 17479
- sample type: leaves of Gnaphalium spicatum (cudweed)
- host species: Gnaphalium spicatum
- geographic location: Okayama, Okayama University at the Institute of Plant Science and Resources
- country: Japan
- origin.country: JPN
- continent: Asia
isolation source categories
| Cat1 | Cat2 | Cat3 |
|---|---|---|
| #Host | #Plants | #Herbaceous plants (Grass,Crops) |
| #Host Body-Site | #Plant | #Leaf (Phyllosphere) |
Safety information
risk assessment
- @ref: 17479
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
- @ref: 17479
- description: Methylobacterium gnaphalii gene for 16S ribosomal RNA, partial sequence
- accession: AB627071
- length: 1445
- database: ena
- NCBI tax ID: 1010610
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Methylobacterium gnaphalii NBRC 107716 | GCA_007992215 | contig | ncbi | 1010610 |
| 66792 | Methylobacterium gnaphalii strain NBRC 107716 | 1010610.3 | wgs | patric | 1010610 |
| 66792 | Methylobacterium gnaphalii DSM 24027 | GCA_022179205 | contig | ncbi | 1010610 |
GC content
| @ref | GC-content | method |
|---|---|---|
| 17479 | 67.2 | thermal denaturation, midpoint method (Tm) |
| 30510 | 67.2 |
Genome-based predictions
predictions
| trait | prediction | confidence | training_data |
|---|---|---|---|
| spore-forming | no | 100 | no |
| motile | yes | 87.696 | no |
| flagellated | no | 77.722 | no |
| gram-positive | no | 97.907 | no |
| anaerobic | no | 98.982 | yes |
| aerobic | yes | 93.265 | yes |
| halophile | no | 92.845 | no |
| spore-forming | no | 93.889 | no |
| thermophile | no | 98.501 | yes |
| glucose-util | yes | 87.297 | no |
| glucose-ferment | no | 90.115 | no |
External links
@ref: 17479
culture collection no.: DSM 24027, NBRC 107716
straininfo link
- @ref: 76653
- straininfo: 397058
literature
- topic: Phylogeny
- Pubmed-ID: 22199216
- title: Methylobacterium gnaphalii sp. nov., isolated from leaves of Gnaphalium spicatum.
- authors: Tani A, Sahin N, Kimbara K
- journal: Int J Syst Evol Microbiol
- DOI: 10.1099/ijs.0.037713-0
- year: 2011
- mesh: Bacterial Typing Techniques, DNA, Bacterial/genetics, Fatty Acids/analysis, Gnaphalium/*microbiology, Methylobacterium/*classification/genetics/isolation & purification, Molecular Sequence Data, Nucleic Acid Hybridization, *Phylogeny, Plant Leaves/microbiology, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization, Ubiquinone/analysis
- topic2: Genetics
Reference
| @id | authors | catalogue | doi/url | title | ID_cross_reference | pubmed |
|---|---|---|---|---|---|---|
| 17479 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 24027) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-24027 | |||
| 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 | |||
| 30510 | 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 | 26842 | 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) | |||
| 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 | |||
| 76653 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID397058.1 | StrainInfo: A central database for resolving microbial strain identifiers |