Strain identifier
BacDive ID: 7142
Type strain: 
Species: Methylorubrum extorquens
Strain Designation: TK 0001
Strain history: T. Urakami TK 0001 <-- NCIB 9399 <-- C. Bassalik.
NCBI tax ID(s): 408 (species)
version 8.1 (current version)
General
@ref: 527
BacDive-ID: 7142
DSM-Number: 1337
keywords: genome sequence, 16S sequence, Bacteria, mesophilic, Gram-negative
description: Methylorubrum extorquens TK 0001 is a mesophilic, Gram-negative bacterium of the family Methylobacteriaceae.
NCBI tax id
- NCBI tax id: 408
- Matching level: species
strain history
| @ref | history |
|---|---|
| 527 | <- NCIB (Pseudomonas extorquens) <- L. Janota (Flavobacterium extorquens) |
| 67770 | T. Urakami TK 0001 <-- NCIB 9399 <-- C. Bassalik. |
doi: 10.13145/bacdive7142.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/pseudomonadota
- domain: Bacteria
- phylum: Pseudomonadota
- class: Alphaproteobacteria
- order: Hyphomicrobiales
- family: Methylobacteriaceae
- genus: Methylorubrum
- species: Methylorubrum extorquens
- full scientific name: Methylorubrum extorquens (Urakami and Komagata 1984 ex Bassalik 1913) Green and Ardley 2018
synonyms
@ref synonym 20215 Protomonas extorquens 20215 Methylobacterium extorquens
@ref: 527
domain: Bacteria
phylum: Proteobacteria
class: Alphaproteobacteria
order: Rhizobiales
family: Methylobacteriaceae
genus: Methylorubrum
species: Methylorubrum extorquens
full scientific name: Methylorubrum extorquens (Urakami and Komagata 1984) Green and Ardley 2018
strain designation: TK 0001
type strain: yes
Morphology
cell morphology
- @ref: 69480
- gram stain: negative
- confidence: 100
Culture and growth conditions
culture medium
- @ref: 527
- name: NUTRIENT AGAR (DSMZ Medium 1)
- growth: yes
- link: https://mediadive.dsmz.de/medium/1
- composition: Name: NUTRIENT AGAR (DSMZ Medium 1; with strain-specific modifications) Composition: Agar 15.0 g/l Methanol 10.0 g/l Peptone 5.0 g/l Meat extract 3.0 g/l Distilled water
culture temp
| @ref | growth | type | temperature | range |
|---|---|---|---|---|
| 527 | positive | growth | 30 | mesophilic |
| 67770 | positive | growth | 30 | mesophilic |
Physiology and metabolism
spore formation
| @ref | spore formation | confidence |
|---|---|---|
| 69481 | no | 100 |
| 69480 | no | 99.999 |
observation
- @ref: 67770
- observation: quinones: Q-10
Isolation, sampling and environmental information
taxonmaps
- @ref: 69479
- File name: preview.99_253.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_15368;96_177;97_192;98_215;99_253&stattab=map
- Last taxonomy: Methylorubrum
- 16S sequence: D32224
- Sequence Identity:
- Total samples: 110728
- soil counts: 23280
- aquatic counts: 23711
- animal counts: 47578
- plant counts: 16159
Safety information
risk assessment
- @ref: 527
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
| @ref | description | accession | length | database | NCBI tax ID |
|---|---|---|---|---|---|
| 20218 | Methylobacterium extorquens gene for 16S ribosomal RNA, partial sequence, strain:IAM 12631 | AB175632 | 1435 | ena | 408 |
| 20218 | Methylobacterium extorquens partial 16S rRNA gene, strain IAM 12631 | AJ400915 | 741 | ena | 408 |
| 20218 | Methylobacterium extorquens gene for 16S rRNA, strain: JCM 2802 | D32224 | 1407 | ena | 408 |
| 20218 | Methylobacterium extorquens gene for 16S ribosomal RNA, partial sequence, strain:NCIMB 9399 | AB175633 | 1435 | ena | 408 |
| 20218 | Methylobacterium extorquens 16S ribosomal RNA sequence | L20847 | 1317 | ena | 408 |
Genome sequences
- @ref: 66792
- description: Methylobacterium extorquens strain TK0001_PRJEB23178
- accession: 408.23
- assembly level: complete
- database: patric
- NCBI tax ID: 408
GC content
- @ref: 67770
- GC-content: 65.6
- method: thermal denaturation, midpoint method (Tm)
Genome-based predictions
predictions
| trait | prediction | confidence | training_data |
|---|---|---|---|
| spore-forming | no | 100 | no |
| gram-positive | no | 97.464 | no |
| anaerobic | no | 97.117 | no |
| halophile | no | 92.794 | no |
| spore-forming | no | 92.454 | no |
| glucose-util | yes | 89.828 | no |
| aerobic | yes | 88.672 | no |
| flagellated | no | 65.915 | no |
| thermophile | no | 98.993 | no |
| motile | yes | 88.994 | no |
| glucose-ferment | no | 87.771 | no |
External links
@ref: 527
culture collection no.: DSM 1337, ATCC 43645, NCIMB 9399, IAM 12631, JCM 2802, BCRC 12234, CCUG 2084, IFO 15687, IMET 11113, NBRC 15687, VKM B-2064
straininfo link
- @ref: 76596
- straininfo: 46061
literature
| topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
|---|---|---|---|---|---|---|---|---|
| Phylogeny | 16314683 | Reclassification of Methylobacterium chloromethanicum and Methylobacterium dichloromethanicum as later subjective synonyms of Methylobacterium extorquens and of Methylobacterium lusitanum as a later subjective synonym of Methylobacterium rhodesianum. | Kato Y, Asahara M, Arai D, Goto K, Yokota A | J Gen Appl Microbiol | 10.2323/jgam.51.287 | 2005 | Bacterial Typing Techniques, Base Composition, DNA, Bacterial/analysis, DNA, Ribosomal, Fatty Acids/analysis, Methylobacterium/chemistry/*classification/genetics/metabolism, Methylobacterium extorquens/chemistry/*classification/genetics/metabolism, Molecular Sequence Data, Nucleic Acid Hybridization, Phylogeny, RNA, Ribosomal, 16S/genetics, Ribotyping, Sequence Analysis, DNA | Metabolism |
| Metabolism | 16821716 | Identification of oxalotrophic bacteria by neural network analysis of numerical phenetic data. | Sahin N, Aydin S | Folia Microbiol (Praha) | 10.1007/BF02932161 | 2006 | Gram-Negative Aerobic Bacteria/*classification/metabolism, *Neural Networks, Computer, Oxalates/metabolism | Phylogeny |
| Genetics | 29472323 | Complete Genome Sequence of the Facultative Methylotroph Methylobacterium extorquens TK 0001 Isolated from Soil in Poland. | Belkhelfa S, Labadie K, Cruaud C, Aury JM, Roche D, Bouzon M, Salanoubat M, Doring V | Genome Announc | 10.1128/genomeA.00018-18 | 2018 | Phylogeny | |
| Phylogeny | 30024371 | Review of the genus Methylobacterium and closely related organisms: a proposal that some Methylobacterium species be reclassified into a new genus, Methylorubrum gen. nov. | Green PN, Ardley JK | Int J Syst Evol Microbiol | 10.1099/ijsem.0.002856 | 2018 | Bacterial Typing Techniques, DNA, Bacterial/genetics, Methylobacterium/*classification, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA | Transcriptome |
| 31281294 | Continuous Culture Adaptation of Methylobacterium extorquens AM1 and TK 0001 to Very High Methanol Concentrations. | Belkhelfa S, Roche D, Dubois I, Berger A, Delmas VA, Cattolico L, Perret A, Labadie K, Perdereau AC, Darii E, Pateau E, de Berardinis V, Salanoubat M, Bouzon M, Doring V | Front Microbiol | 10.3389/fmicb.2019.01313 | 2019 |
Reference
| @id | authors | catalogue | doi/url | title | journal | pubmed |
|---|---|---|---|---|---|---|
| 527 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 1337) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-1337 | |||
| 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 | |
| 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) | |||
| 67770 | Curators of the JCM | https://jcm.brc.riken.jp/en/ | ||||
| 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 | |||
| 76596 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID46061.1 | StrainInfo: A central database for resolving microbial strain identifiers |