Strain identifier
BacDive ID: 23092
Type strain:
Species: Methylobacterium oxalidis
Strain Designation: 35a
Strain history: <- A. Tani, Okayama University, Institute of Plant Science and Resources, Japan; strain 35a
NCBI tax ID(s): 944322 (species)
General
@ref: 19152
BacDive-ID: 23092
DSM-Number: 24028
keywords: genome sequence, 16S sequence, Bacteria, aerobe, mesophilic, Gram-negative, motile, rod-shaped
description: Methylobacterium oxalidis 35a is an aerobe, mesophilic, Gram-negative bacterium that was isolated from leaves of the sorrel Oxalis corniculata.
NCBI tax id
- NCBI tax id: 944322
- Matching level: species
strain history
- @ref: 19152
- history: <- A. Tani, Okayama University, Institute of Plant Science and Resources, Japan; strain 35a
doi: 10.13145/bacdive23092.20230509.8.1
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 oxalidis
- full scientific name: Methylobacterium oxalidis Tani et al. 2012
@ref: 19152
domain: Bacteria
phylum: Proteobacteria
class: Alphaproteobacteria
order: Rhizobiales
family: Methylobacteriaceae
genus: Methylobacterium
species: Methylobacterium oxalidis
full scientific name: Methylobacterium oxalidis Tani et al. 2012
strain designation: 35a
type strain: yes
Morphology
cell morphology
@ref | gram stain | cell length | cell width | cell shape | motility | confidence |
---|---|---|---|---|---|---|
30303 | negative | 1.8 µm | 1.3 µm | rod-shaped | yes | |
69480 | yes | 92.828 | ||||
69480 | negative | 100 |
colony morphology
- @ref: 19152
- incubation period: 3-7 days
pigmentation
- @ref: 30303
- production: yes
Culture and growth conditions
culture medium
- @ref: 19152
- 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 |
---|---|---|---|---|
19152 | positive | growth | 28 | mesophilic |
30303 | positive | growth | 28-35 | mesophilic |
Physiology and metabolism
oxygen tolerance
- @ref: 30303
- oxygen tolerance: aerobe
spore formation
@ref | spore formation | confidence |
---|---|---|
30303 | no | |
69481 | no | 99 |
69480 | no | 99.998 |
halophily
- @ref: 30303
- salt: NaCl
- growth: positive
- tested relation: growth
- concentration: <2 %
metabolite utilization
@ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
---|---|---|---|---|
30303 | 30089 | acetate | + | carbon source |
30303 | 15740 | formate | + | carbon source |
30303 | 28757 | fructose | + | carbon source |
30303 | 29987 | glutamate | + | carbon source |
30303 | 24996 | lactate | + | carbon source |
30303 | 15792 | malonate | + | carbon source |
30303 | 51850 | methyl pyruvate | + | carbon source |
30303 | 17272 | propionate | + | carbon source |
30303 | 30031 | succinate | + | carbon source |
enzymes
- @ref: 30303
- value: catalase
- activity: +
- ec: 1.11.1.6
Isolation, sampling and environmental information
isolation
- @ref: 19152
- sample type: leaves of the sorrel Oxalis corniculata
- host species: Oxalis corniculata
- 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) |
taxonmaps
- @ref: 69479
- File name: preview.99_62296.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_15368;96_6152;97_28745;98_44137;99_62296&stattab=map
- Last taxonomy: Methylobacterium oxalidis subclade
- 16S sequence: AB607860
- Sequence Identity:
- Total samples: 6895
- soil counts: 3583
- aquatic counts: 701
- animal counts: 1775
- plant counts: 836
Safety information
risk assessment
- @ref: 19152
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
- @ref: 19152
- description: Methylobacterium oxalidis gene for 16S ribosomal RNA, partial sequence
- accession: AB607860
- length: 1446
- database: ena
- NCBI tax ID: 944322
Genome sequences
@ref | description | accession | assembly level | database | NCBI tax ID |
---|---|---|---|---|---|
66792 | Methylobacterium oxalidis NBRC 107715 | GCA_007992195 | contig | ncbi | 944322 |
66792 | Methylobacterium oxalidis strain NBRC 107715 | 944322.3 | wgs | patric | 944322 |
66792 | Methylobacterium oxalidis DSM 24028 | GCA_022179505 | contig | ncbi | 944322 |
GC content
@ref | GC-content | method |
---|---|---|
19152 | 70.2 | thermal denaturation, midpoint method (Tm) |
30303 | 70.2 |
Genome-based predictions
predictions
trait | prediction | confidence | training_data |
---|---|---|---|
spore-forming | no | 99 | no |
motile | yes | 88.071 | yes |
flagellated | no | 83.604 | no |
gram-positive | no | 97.135 | yes |
anaerobic | no | 98.155 | yes |
halophile | no | 90.496 | no |
spore-forming | no | 94.083 | no |
glucose-util | yes | 82.199 | no |
aerobic | yes | 92.232 | yes |
thermophile | no | 98.559 | yes |
glucose-ferment | no | 91.053 | no |
External links
@ref: 19152
culture collection no.: DSM 24028, NBRC 107715
straininfo link
- @ref: 87330
- straininfo: 380589
literature
topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
---|---|---|---|---|---|---|---|---|
Phylogeny | 21908681 | Methylobacterium oxalidis sp. nov., isolated from leaves of Oxalis corniculata. | Tani A, Sahin N, Kimbara K | Int J Syst Evol Microbiol | 10.1099/ijs.0.033019-0 | 2011 | Bacterial Typing Techniques, Cluster Analysis, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis, Ferns/*microbiology, Locomotion, Methylobacterium/*classification/genetics/*isolation & purification/physiology, Molecular Sequence Data, Nucleic Acid Hybridization, Phylogeny, Pigments, Biological/metabolism, Plant Leaves/microbiology, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA | Genetics |
Phylogeny | 31796988 | Methylobacterium segetis sp. nov., a novel member of the family Methylobacteriaceae isolated from soil on Jeju Island. | Ten LN, Li W, Elderiny NS, Kim MK, Lee SY, Rooney AP, Jung HY | Arch Microbiol | 10.1007/s00203-019-01784-z | 2019 | Base Composition, Fatty Acids/chemistry, Methylobacterium/*classification/genetics, Nucleic Acid Hybridization, Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, Sequence Analysis, DNA, *Soil Microbiology, Species Specificity | Transcriptome |
Reference
@id | authors | catalogue | doi/url | title | ID_cross_reference | pubmed |
---|---|---|---|---|---|---|
19152 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 24028) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-24028 | |||
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 | |||
30303 | 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 | 26644 | 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 | |||
87330 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID380589.1 | StrainInfo: A central database for resolving microbial strain identifiers |