Strain identifier
BacDive ID: 24174
Type strain: 
Species: Methylobacterium brachythecii
Strain Designation: 99b
Strain history: <- A. Tani, Okayama University, Japan; 99b
NCBI tax ID(s): 1176177 (species)
version 9.1 (current version)
General
@ref: 20649
BacDive-ID: 24174
DSM-Number: 24105
keywords: genome sequence, 16S sequence, Bacteria, aerobe, Gram-negative, motile, rod-shaped
description: Methylobacterium brachythecii 99b is an aerobe, Gram-negative, motile bacterium that was isolated from rusty feather-moss Brachythecium plumosum.
NCBI tax id
- NCBI tax id: 1176177
- Matching level: species
strain history
- @ref: 20649
- history: <- A. Tani, Okayama University, Japan; 99b
doi: 10.13145/bacdive24174.20240916.9.1
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 brachythecii
- full scientific name: Methylobacterium brachythecii Tani and Sahin 2013
@ref: 20649
domain: Bacteria
phylum: Proteobacteria
class: Alphaproteobacteria
order: Rhizobiales
family: Methylobacteriaceae
genus: Methylobacterium
species: Methylobacterium brachythecii
full scientific name: Methylobacterium brachythecii Tani and Sahin 2013
strain designation: 99b
type strain: yes
Morphology
cell morphology
| @ref | gram stain | cell length | cell width | cell shape | motility | confidence |
|---|---|---|---|---|---|---|
| 30947 | negative | 2.5 µm | 1.2 µm | rod-shaped | yes | |
| 69480 | negative | 98 |
colony morphology
- @ref: 20649
- incubation period: 2-3 days
pigmentation
- @ref: 30947
- production: yes
Culture and growth conditions
culture medium
- @ref: 20649
- 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: 20649
- growth: positive
- type: growth
- temperature: 28
Physiology and metabolism
oxygen tolerance
- @ref: 30947
- oxygen tolerance: aerobe
spore formation
| @ref | spore formation | confidence |
|---|---|---|
| 30947 | no | |
| 69481 | no | 100 |
metabolite utilization
| @ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
|---|---|---|---|---|
| 30947 | 30089 | acetate | + | carbon source |
| 30947 | 22599 | arabinose | + | carbon source |
| 30947 | 22653 | asparagine | + | carbon source |
| 30947 | 35391 | aspartate | + | carbon source |
| 30947 | 23652 | dextrin | + | carbon source |
| 30947 | 15740 | formate | + | carbon source |
| 30947 | 17234 | glucose | + | carbon source |
| 30947 | 29987 | glutamate | + | carbon source |
| 30947 | 17754 | glycerol | + | carbon source |
| 30947 | 28087 | glycogen | + | carbon source |
| 30947 | 24996 | lactate | + | carbon source |
| 30947 | 15792 | malonate | + | carbon source |
| 30947 | 51850 | methyl pyruvate | + | carbon source |
| 30947 | 17272 | propionate | + | carbon source |
| 30947 | 30031 | succinate | + | carbon source |
| 30947 | 17632 | nitrate | + | reduction |
enzymes
| @ref | value | activity | ec |
|---|---|---|---|
| 30947 | catalase | + | 1.11.1.6 |
| 30947 | cytochrome oxidase | + | 1.9.3.1 |
| 30947 | urease | + | 3.5.1.5 |
Isolation, sampling and environmental information
isolation
- @ref: 20649
- sample type: rusty feather-moss Brachythecium plumosum
- host species: Brachythecium plumosum
- geographic location: premises of the Institute of Plant Science and Resources, Okayama University
- country: Japan
- origin.country: JPN
- continent: Asia
isolation source categories
- Cat1: #Host
- Cat2: #Plants
- Cat3: #Moss
Safety information
risk assessment
- @ref: 20649
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
- @ref: 20649
- description: Methylobacterium brachythecii gene for 16S rRNA, partial sequence, strain: 99b
- accession: AB703239
- length: 1444
- database: nuccore
- NCBI tax ID: 1176177
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Methylobacterium brachythecii DSM 24105 | GCA_014196345 | contig | ncbi | 1176177 |
| 66792 | Methylobacterium brachythecii strain DSM 24105 | 1176177.3 | wgs | patric | 1176177 |
| 66792 | Methylobacterium brachythecii DSM 24105 | 2829871319 | draft | img | 1176177 |
GC content
| @ref | GC-content | method |
|---|---|---|
| 20649 | 66.5 | thermal denaturation, midpoint method (Tm) |
| 30947 | 66.5 |
Genome-based predictions
predictions
| @ref | trait | model | description | prediction | confidence | training_data |
|---|---|---|---|---|---|---|
| 69481 | spore-forming | spore-forming | Ability to form endo- or exospores | no | 100 | no |
| 69480 | gram-positive | gram-positive | Positive reaction to Gram-staining | no | 98 | yes |
| 69480 | anaerobic | anaerobic | Ability to grow under anoxygenic conditions (including facultative anaerobes) | no | 93.101 | no |
| 69480 | spore-forming | spore-forming | Ability to form endo- or exospores | no | 86.35 | yes |
| 69480 | aerobic | aerobic | Ability to grow under oxygenic conditions (including facultative aerobes) | yes | 86.858 | yes |
| 69480 | thermophilic | thermophile | Ability to grow at temperatures above or equal to 45°C | no | 97.399 | yes |
| 69480 | flagellated | motile2+ | Ability to perform flagellated movement | yes | 72.097 | no |
External links
@ref: 20649
culture collection no.: DSM 24105, NBRC 107710
straininfo link
- @ref: 88129
- straininfo: 397582
literature
- topic: Phylogeny
- Pubmed-ID: 23475343
- title: Methylobacterium haplocladii sp. nov. and Methylobacterium brachythecii sp. nov., isolated from bryophytes.
- authors: Tani A, Sahin N
- journal: Int J Syst Evol Microbiol
- DOI: 10.1099/ijs.0.048215-0
- year: 2013
- mesh: Bacterial Typing Techniques, Base Composition, Bryophyta/*microbiology, DNA, Bacterial/genetics, Fatty Acids/analysis, Japan, Methylobacterium/*classification/genetics/isolation & purification, Molecular Sequence Data, Nucleic Acid Hybridization, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization, Ubiquinone/analogs & derivatives/analysis
- topic2: Genetics
Reference
| @id | authors | title | doi/url | catalogue | ID_cross_reference | pubmed |
|---|---|---|---|---|---|---|
| 20215 | Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M. | List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ | 10.1099/ijsem.0.004332 | |||
| 20649 | Curators of the DSMZ | https://www.dsmz.de/collection/catalogue/details/culture/DSM-24105 | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 24105) | |||
| 30947 | Barberan A, Caceres Velazquez H, Jones S, Fierer N. | Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information | 10.1128/mSphere.00237-17 | 27277 | 28776041 | |
| 66792 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | Automatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) | https://diaspora-project.de/progress.html#genomes | |||
| 69480 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | Predictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) | https://diaspora-project.de/progress.html#genomes | |||
| 69481 | Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch | Predictions based on the model GenomeNet Sporulation v. 1 | 10.21203/rs.3.rs-2527258/v1 | |||
| 88129 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | StrainInfo: A central database for resolving microbial strain identifiers | 10.60712/SI-ID397582.1 |