Strain identifier
BacDive ID: 7172
Type strain: 
Species: Methylorubrum thiocyanatum
Strain Designation: ALL/SCN-P
Strain history: NCIMB 13651 <-- DSM 11490 <-- D. P. Kelly strain ALL/SCN-P.
NCBI tax ID(s): 1236972 (strain), 47958 (species)
version 8.1 (current version)
General
@ref: 4386
BacDive-ID: 7172
DSM-Number: 11490
keywords: genome sequence, 16S sequence, Bacteria, mesophilic, motile
description: Methylorubrum thiocyanatum ALL/SCN-P is a mesophilic, motile bacterium that was isolated from soil around root balls of Allium aflatunense.
NCBI tax id
| NCBI tax id | Matching level |
|---|---|
| 1236972 | strain |
| 47958 | species |
strain history
| @ref | history |
|---|---|
| 4386 | <- D.P. Kelly, strain ALL/SCN-P |
| 67770 | NCIMB 13651 <-- DSM 11490 <-- D. P. Kelly strain ALL/SCN-P. |
doi: 10.13145/bacdive7172.20230509.8.1
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 thiocyanatum
- full scientific name: Methylorubrum thiocyanatum (Wood et al. 1999) Green and Ardley 2018
synonyms
- @ref: 20215
- synonym: Methylobacterium thiocyanatum
@ref: 4386
domain: Bacteria
phylum: Proteobacteria
class: Alphaproteobacteria
order: Rhizobiales
family: Methylobacteriaceae
genus: Methylorubrum
species: Methylorubrum thiocyanatum
full scientific name: Methylorubrum thiocyanatum (Wood et al. 1999) Green and Ardley 2018
strain designation: ALL/SCN-P
type strain: yes
Morphology
cell morphology
| @ref | motility | confidence | gram stain |
|---|---|---|---|
| 69480 | yes | 90.965 | |
| 69480 | 100 | negative |
Culture and growth conditions
culture medium
| @ref | name | growth | link | composition |
|---|---|---|---|---|
| 4386 | METHYLOBACTERIUM THIOCYANATUM MEDIUM (DSMZ Medium 805) | yes | https://mediadive.dsmz.de/medium/805 | Name: METHYLOBACTERIUM THIOCYANATUM MEDIUM (DSMZ Medium 805) Composition: Agar 15.0 g/l Na2HPO4 x 2 H2O 7.9 g/l Glucose 4.5 g/l K2HPO4 1.5 g/l KSCN 0.25 g/l MgSO4 x 7 H2O 0.1 g/l FeSO4 x 7 H2O 0.02 g/l Distilled water |
| 4386 | NUTRIENT AGAR (DSMZ Medium 1) | yes | https://mediadive.dsmz.de/medium/1 | 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 |
|---|---|---|---|---|
| 4386 | 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
isolation
| @ref | sample type | host species | geographic location | country | origin.country | continent |
|---|---|---|---|---|---|---|
| 4386 | soil around root balls of Allium aflatunense | Allium aflatunense | Warwickshire | United Kingdom | GBR | Europe |
| 67770 | Soil from around the roots of Allium aflatunense | Allium aflatunense |
isolation source categories
| Cat1 | Cat2 | Cat3 |
|---|---|---|
| #Environmental | #Terrestrial | #Soil |
| #Host | #Plants | #Herbaceous plants (Grass,Crops) |
| #Host Body-Site | #Plant | #Root (Rhizome) |
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: U58018
- Sequence Identity:
- Total samples: 110728
- soil counts: 23280
- aquatic counts: 23711
- animal counts: 47578
- plant counts: 16159
Safety information
risk assessment
- @ref: 4386
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
| @ref | description | accession | length | database | NCBI tax ID |
|---|---|---|---|---|---|
| 20218 | Methylobacterium thiocyanatum 16S ribosomal RNA gene, complete sequence | U58018 | 1447 | ena | 47958 |
| 20218 | Methylobacterium thiocyanatum gene for 16S ribosomal RNA, partial sequence, strain:DSM 11490 | AB175646 | 1435 | ena | 47958 |
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Methylorubrum thiocyanatum JCM 10893 | GCA_001310875 | contig | ncbi | 1236972 |
| 66792 | Methylobacterium thiocyanatum JCM 10893 | 1236972.3 | wgs | patric | 1236972 |
| 66792 | Methylorubrum thiocyanatum strain DSM 11490 | 47958.4 | wgs | patric | 47958 |
| 66792 | Methylorubrum thiocyanatum JCM 10893 | 2728369660 | draft | img | 1236972 |
| 66792 | Methylobacterium thiocyanatum DSM 11490 | 2861691609 | draft | img | 47958 |
| 66792 | Methylorubrum thiocyanatum JCM 10893 | GCA_022179785 | contig | ncbi | 47958 |
Genome-based predictions
predictions
| trait | prediction | confidence | training_data |
|---|---|---|---|
| spore-forming | no | 100 | no |
| motile | yes | 90.703 | no |
| gram-positive | no | 96.906 | no |
| anaerobic | no | 97.252 | no |
| aerobic | yes | 90.837 | no |
| halophile | no | 93.623 | no |
| spore-forming | no | 94.005 | no |
| glucose-util | yes | 84.891 | no |
| flagellated | no | 69.851 | no |
| thermophile | no | 99.106 | no |
| glucose-ferment | no | 87.22 | no |
External links
@ref: 4386
culture collection no.: DSM 11490, ATCC 700647, JCM 10893, NCIMB 13651, VKM B-2197
straininfo link
- @ref: 76625
- straininfo: 45442
literature
| topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
|---|---|---|---|---|---|---|---|---|
| Metabolism | 9446686 | A novel pink-pigmented facultative methylotroph, Methylobacterium thiocyanatum sp. nov., capable of growth on thiocyanate or cyanate as sole nitrogen sources. | Wood AP, Kelly DP, McDonald IR, Jordan SL, Morgan TD, Khan S, Murrell JC, Borodina E | Arch Microbiol | 10.1007/s002030050554 | 1998 | Cyanates/*metabolism, Gram-Negative Aerobic Rods and Cocci/chemistry/genetics/*growth & development, Thiocyanates/*metabolism | Phylogeny |
| Phylogeny | 24297603 | Methylobacterium pseudosasae sp. nov., a pink-pigmented, facultatively methylotrophic bacterium isolated from the bamboo phyllosphere. | Madhaiyan M, Poonguzhali S | Antonie Van Leeuwenhoek | 10.1007/s10482-013-0085-0 | 2013 | Acyl-Butyrolactones/analysis, Alcohol Oxidoreductases/genetics, Bambusa/*microbiology, Base Composition, Cluster Analysis, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis, Methanol/*metabolism, Methylobacterium/*classification/genetics/*isolation & purification/metabolism, Molecular Sequence Data, Nucleic Acid Hybridization, Phylogeny, Plant Leaves/*microbiology, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA | Enzymology |
| 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 |
Reference
| @id | authors | catalogue | doi/url | title | journal | pubmed |
|---|---|---|---|---|---|---|
| 4386 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 11490) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-11490 | |||
| 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 | |||
| 76625 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID45442.1 | StrainInfo: A central database for resolving microbial strain identifiers |