Strain identifier
BacDive ID: 7190
Type strain: 
Species: Methylobacterium komagatae
Strain Designation: 002-079
Strain history: <- Y. Kato, Microbiol. and Analytical Group, Food Res. Lab., Mitsui Norin Co. Ltd., Shizuoka, Japan; 002-079
NCBI tax ID(s): 1122234 (strain), 374425 (species)
version 8.1 (current version)
General
@ref: 8178
BacDive-ID: 7190
DSM-Number: 19563
keywords: genome sequence, 16S sequence, Bacteria, aerobe, mesophilic, Gram-negative, motile, ovoid-shaped
description: Methylobacterium komagatae 002-079 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from water sample in a food factory.
NCBI tax id
| NCBI tax id | Matching level |
|---|---|
| 1122234 | strain |
| 374425 | species |
strain history
- @ref: 8178
- history: <- Y. Kato, Microbiol. and Analytical Group, Food Res. Lab., Mitsui Norin Co. Ltd., Shizuoka, Japan; 002-079
doi: 10.13145/bacdive7190.20230509.8.1
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 komagatae
- full scientific name: Methylobacterium komagatae Kato et al. 2008
@ref: 8178
domain: Bacteria
phylum: Proteobacteria
class: Alphaproteobacteria
order: Rhizobiales
family: Methylobacteriaceae
genus: Methylobacterium
species: Methylobacterium komagatae
full scientific name: Methylobacterium komagatae Kato et al. 2008
strain designation: 002-079
type strain: yes
Morphology
cell morphology
- @ref: 32496
- gram stain: negative
- cell length: 3.6 µm
- cell width: 1.4 µm
- cell shape: ovoid-shaped
- motility: yes
pigmentation
- @ref: 32496
- production: yes
Culture and growth conditions
culture medium
- @ref: 8178
- name: NUTRIENT AGAR (DSMZ Medium 1)
- growth: yes
- link: https://mediadive.dsmz.de/medium/1
- composition: Name: NUTRIENT AGAR (DSMZ Medium 1) Composition: Agar 15.0 g/l Peptone 5.0 g/l Meat extract 3.0 g/l Distilled water
culture temp
| @ref | growth | type | temperature | range |
|---|---|---|---|---|
| 8178 | positive | growth | 28 | mesophilic |
| 32496 | positive | growth | 10-35 | |
| 32496 | positive | optimum | 25 | mesophilic |
Physiology and metabolism
oxygen tolerance
- @ref: 32496
- oxygen tolerance: aerobe
metabolite utilization
| @ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
|---|---|---|---|---|
| 32496 | 30089 | acetate | + | carbon source |
| 32496 | 22599 | arabinose | + | carbon source |
| 32496 | 28757 | fructose | + | carbon source |
| 32496 | 17234 | glucose | + | carbon source |
enzymes
| @ref | value | activity | ec |
|---|---|---|---|
| 32496 | catalase | + | 1.11.1.6 |
| 32496 | cytochrome oxidase | + | 1.9.3.1 |
Isolation, sampling and environmental information
isolation
- @ref: 8178
- sample type: water sample in a food factory
- country: Japan
- origin.country: JPN
- continent: Asia
isolation source categories
| Cat1 | Cat2 | Cat3 |
|---|---|---|
| #Engineered | #Food production | #Food |
| #Engineered | #Industrial | #Plant (Factory) |
| #Environmental | #Aquatic |
taxonmaps
- @ref: 69479
- File name: preview.99_55804.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_15368;96_285;97_11230;98_16861;99_55804&stattab=map
- Last taxonomy: Methylobacterium komagatae
- 16S sequence: AB252201
- Sequence Identity:
- Total samples: 2029
- soil counts: 246
- aquatic counts: 289
- animal counts: 1026
- plant counts: 468
Safety information
risk assessment
- @ref: 8178
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
- @ref: 8178
- description: Methylobacterium komagatae gene for 16S rRNA, partial sequence, strain: 002-079
- accession: AB252201
- length: 1439
- database: ena
- NCBI tax ID: 1122234
Genome sequences
- @ref: 66792
- description: Methylobacterium komagatae DSM 19563
- accession: 2574179709
- assembly level: draft
- database: img
- NCBI tax ID: 1122234
GC content
| @ref | GC-content | method |
|---|---|---|
| 8178 | 68.7 | high performance liquid chromatography (HPLC) |
| 32496 | 68.7 |
External links
@ref: 8178
culture collection no.: DSM 19563, NBRC 103627, NCIMB 14377
straininfo link
- @ref: 76643
- straininfo: 401554
literature
- topic: Phylogeny
- Pubmed-ID: 18450702
- title: Methylobacterium persicinum sp. nov., Methylobacterium komagatae sp. nov., Methylobacterium brachiatum sp. nov., Methylobacterium tardum sp. nov. and Methylobacterium gregans sp. nov., isolated from freshwater.
- authors: Kato Y, Asahara M, Goto K, Kasai H, Yokota A
- journal: Int J Syst Evol Microbiol
- DOI: 10.1099/ijs.0.65583-0
- year: 2008
- mesh: Bacterial Typing Techniques, Base Composition, DNA Gyrase/genetics, DNA, Bacterial/analysis, DNA, Ribosomal/analysis, Fatty Acids/analysis, Food Industry, Fresh Water/*microbiology, Genes, rRNA, Japan, Methylobacterium/chemistry/*classification/genetics/*isolation & purification, Molecular Sequence Data, Phenotype, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Species Specificity
- topic2: Genetics
Reference
| @id | authors | catalogue | doi/url | title | ID_cross_reference | pubmed |
|---|---|---|---|---|---|---|
| 8178 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 19563) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-19563 | |||
| 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 | |||
| 32496 | 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 | 28716 | 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 | |||
| 76643 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID401554.1 | StrainInfo: A central database for resolving microbial strain identifiers |