Strain identifier
BacDive ID: 24175
Type strain: 
Species: Methylobacterium haplocladii
Strain Designation: 87e
Strain history: <- A. Tani, Okayama University, Japan; 87e
NCBI tax ID(s): 1176176 (species)
version 8.1 (current version)
General
@ref: 20650
BacDive-ID: 24175
DSM-Number: 24195
keywords: genome sequence, 16S sequence, Bacteria, aerobe, mesophilic, Gram-negative, motile, rod-shaped
description: Methylobacterium haplocladii 87e is an aerobe, mesophilic, Gram-negative bacterium that was isolated from epilithic moss Haplocladium microphyllum.
NCBI tax id
- NCBI tax id: 1176176
- Matching level: species
strain history
- @ref: 20650
- history: <- A. Tani, Okayama University, Japan; 87e
doi: 10.13145/bacdive24175.20230509.8.1
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 haplocladii
- full scientific name: Methylobacterium haplocladii Tani and Sahin 2013
@ref: 20650
domain: Bacteria
phylum: Proteobacteria
class: Alphaproteobacteria
order: Rhizobiales
family: Methylobacteriaceae
genus: Methylobacterium
species: Methylobacterium haplocladii
full scientific name: Methylobacterium haplocladii Tani and Sahin 2013
strain designation: 87e
type strain: yes
Morphology
cell morphology
| @ref | gram stain | cell length | cell width | cell shape | motility | confidence |
|---|---|---|---|---|---|---|
| 30947 | negative | 2.5 µm | 1.1 µm | rod-shaped | yes | |
| 69480 | yes | 97.231 | ||||
| 69480 | negative | 99.999 |
colony morphology
- @ref: 20650
- incubation period: 3-7 days
pigmentation
- @ref: 30947
- production: yes
Culture and growth conditions
culture medium
- @ref: 20650
- 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: 20650
- growth: positive
- type: growth
- temperature: 28
- range: mesophilic
Physiology and metabolism
oxygen tolerance
- @ref: 30947
- oxygen tolerance: aerobe
spore formation
| @ref | spore formation | confidence |
|---|---|---|
| 30947 | no | |
| 69481 | no | 99 |
| 69480 | no | 99.965 |
metabolite utilization
| @ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
|---|---|---|---|---|
| 30947 | 15740 | formate | + | carbon source |
| 30947 | 17234 | glucose | + | carbon source |
| 30947 | 17754 | glycerol | + | carbon source |
| 30947 | 24996 | lactate | + | carbon source |
| 30947 | 15792 | malonate | + | carbon source |
| 30947 | 51850 | methyl pyruvate | + | carbon source |
| 30947 | 17272 | propionate | + | carbon source |
| 30947 | 26546 | rhamnose | + | carbon source |
enzymes
- @ref: 30947
- value: catalase
- activity: +
- ec: 1.11.1.6
Isolation, sampling and environmental information
isolation
- @ref: 20650
- sample type: epilithic moss Haplocladium microphyllum
- host species: Haplocladium microphyllum
- geographic location: premises of the Institute of Plant Science and Resources, Okayama University
- country: Japan
- origin.country: JPN
- continent: Asia
isolation source categories
| Cat1 | Cat2 | Cat3 |
|---|---|---|
| #Environmental | #Terrestrial | #Geologic |
| #Host | #Plants | #Moss |
Safety information
risk assessment
- @ref: 20650
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
- @ref: 20650
- description: Methylobacterium haplocladii gene for 16S ribosomal RNA, partial sequence, strain: 87e
- accession: AB698691
- length: 1446
- database: ena
- NCBI tax ID: 1176176
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Methylobacterium haplocladii NBRC 107714 | GCA_007992175 | contig | ncbi | 1176176 |
| 66792 | Methylobacterium haplocladii strain NBRC 107714 | 1176176.3 | wgs | patric | 1176176 |
| 66792 | Methylobacterium haplocladii NBRC 107714 | 2900261899 | draft | img | 1176176 |
| 66792 | Methylobacterium haplocladii DSM 24195 | GCA_022179265 | contig | ncbi | 1176176 |
GC content
| @ref | GC-content | method |
|---|---|---|
| 20650 | 67.3 | thermal denaturation, midpoint method (Tm) |
| 30947 | 67.3 |
Genome-based predictions
predictions
| trait | prediction | confidence | training_data |
|---|---|---|---|
| spore-forming | no | 99 | no |
| motile | yes | 88.411 | no |
| gram-positive | no | 97.693 | yes |
| anaerobic | no | 97.26 | no |
| halophile | no | 90.841 | no |
| spore-forming | no | 93.388 | no |
| flagellated | no | 75.83 | no |
| thermophile | no | 98.754 | no |
| glucose-util | yes | 89.618 | yes |
| aerobic | yes | 89.257 | yes |
| glucose-ferment | no | 91.568 | no |
External links
@ref: 20650
culture collection no.: DSM 24195, NBRC 107714
straininfo link
- @ref: 88130
- straininfo: 400225
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 | journal |
|---|---|---|---|---|---|---|---|
| 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 | ||||
| 20650 | Curators of the DSMZ | https://www.dsmz.de/collection/catalogue/details/culture/DSM-24195 | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 24195) | ||||
| 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 | ||||
| 66794 | Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg | BRENDA, the ELIXIR core data resource in 2021: new developments and updates | 10.1093/nar/gkaa1025 | 33211880 | Nucleic Acids Res. 49: D498-D508 2020 | ||
| 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 | ||||
| 88130 | 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-ID400225.1 |