Strain identifier
BacDive ID: 134290
Type strain:
Species: Methylobacterium platani
Strain Designation: PMB02
Strain history: <- W Park, Korea Univ.
NCBI tax ID(s): 1295136 (strain), 427683 (species)
General
@ref: 32286
BacDive-ID: 134290
keywords: genome sequence, 16S sequence, Bacteria, aerobe, Gram-negative, motile, rod-shaped
description: Methylobacterium platani PMB02 is an aerobe, Gram-negative, motile bacterium that was isolated from plant associated.
NCBI tax id
NCBI tax id | Matching level |
---|---|
1295136 | strain |
427683 | species |
strain history
@ref | history |
---|---|
67770 | W. Park PMB02 <-- H.-D. Shin. |
67771 | <- W Park, Korea Univ. |
doi: 10.13145/bacdive134290.20230509.8.1
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 platani
- full scientific name: Methylobacterium platani Kang et al. 2007
@ref: 32286
domain: Bacteria
phylum: Proteobacteria
class: Alphaproteobacteria
order: Hyphomicrobiales
family: Methylobacteriaceae
genus: Methylobacterium
species: Methylobacterium platani
strain designation: PMB02
type strain: yes
Morphology
cell morphology
@ref | gram stain | cell length | cell width | cell shape | motility | confidence |
---|---|---|---|---|---|---|
32286 | negative | 4.25 µm | 1.45 µm | rod-shaped | yes | |
67771 | negative | |||||
69480 | negative | 91.174 |
pigmentation
- @ref: 32286
- production: yes
Culture and growth conditions
culture temp
@ref | growth | type | temperature | range |
---|---|---|---|---|
32286 | positive | growth | 20-30 | |
32286 | positive | optimum | 27.5 | mesophilic |
67770 | positive | growth | 30 | mesophilic |
67771 | positive | growth | 30 | mesophilic |
culture pH
@ref | ability | type | pH |
---|---|---|---|
32286 | positive | growth | 6.0-8.0 |
32286 | positive | optimum | 6.5 |
Physiology and metabolism
oxygen tolerance
@ref | oxygen tolerance |
---|---|
32286 | aerobe |
67771 | aerobe |
spore formation
@ref | spore formation | confidence |
---|---|---|
32286 | no | |
69480 | no | 99.995 |
halophily
- @ref: 32286
- salt: NaCl
- growth: positive
- tested relation: growth
- concentration: <1 %
observation
@ref | observation |
---|---|
32286 | aggregates in clumps |
67770 | quinones: Q-10 |
67771 | quinones: Q-10 |
metabolite utilization
@ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
---|---|---|---|---|
32286 | 30089 | acetate | + | carbon source |
32286 | 22599 | arabinose | + | carbon source |
32286 | 35391 | aspartate | + | carbon source |
32286 | 15740 | formate | + | carbon source |
32286 | 28757 | fructose | + | carbon source |
32286 | 24175 | galacturonate | + | carbon source |
32286 | 24265 | gluconate | + | carbon source |
32286 | 29987 | glutamate | + | carbon source |
32286 | 24996 | lactate | + | carbon source |
32286 | 51850 | methyl pyruvate | + | carbon source |
32286 | 26271 | proline | + | carbon source |
32286 | 17272 | propionate | + | carbon source |
32286 | 26490 | quinate | + | carbon source |
32286 | 30031 | succinate | + | carbon source |
32286 | 26986 | threonine | + | carbon source |
enzymes
@ref | value | activity | ec |
---|---|---|---|
32286 | catalase | + | 1.11.1.6 |
32286 | cytochrome oxidase | + | 1.9.3.1 |
Isolation, sampling and environmental information
isolation
@ref | sample type | host species | geographic location | country | origin.country | continent |
---|---|---|---|---|---|---|
32286 | plant associated | |||||
67770 | Leaf of Platanus orientalis tree at Korea University | Platanus orientalis | Seoul | Republic of Korea | KOR | Asia |
67771 | From leaf, plane trees | Republic of Korea | KOR | Asia |
isolation source categories
- Cat1: #Host
- Cat2: #Plants
taxonmaps
- @ref: 69479
- File name: preview.99_1774.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_15368;96_262;97_289;98_1400;99_1774&stattab=map
- Last taxonomy: Methylobacterium platani
- 16S sequence: EF426729
- Sequence Identity:
- Total samples: 1659
- soil counts: 351
- aquatic counts: 302
- animal counts: 744
- plant counts: 262
Sequence information
16S sequences
- @ref: 32286
- description: Methylobacterium platani strain PMB02 16S ribosomal RNA gene, partial sequence
- accession: EF426729
- length: 1432
- database: nuccore
- NCBI tax ID: 427683
Genome sequences
@ref | description | accession | assembly level | database | NCBI tax ID |
---|---|---|---|---|---|
66792 | Methylobacterium platani JCM 14648 | GCA_001312265 | contig | ncbi | 1295136 |
66792 | Methylobacterium platani JCM 14648 | 1295136.3 | wgs | patric | 1295136 |
66792 | Methylobacterium platani JCM 14648 | 1295136.4 | wgs | patric | 1295136 |
66792 | Methylobacterium platani JCM 14648 | 2728369717 | draft | img | 1295136 |
66792 | Methylobacterium platani PMB02 | 2855953901 | draft | img | 427683 |
66792 | Methylobacterium platani JCM 14648 | 2651869728 | draft | img | 1295136 |
67770 | Methylobacterium platani JCM 14648 | GCA_001043885 | contig | ncbi | 1295136 |
67770 | Methylobacterium platani PMB02 | GCA_001653715 | scaffold | ncbi | 427683 |
GC content
@ref | GC-content | method |
---|---|---|
32286 | 68.5 | |
67770 | 68.5 | high performance liquid chromatography (HPLC) |
Genome-based predictions
predictions
trait | prediction | confidence | training_data |
---|---|---|---|
spore-forming | no | 87 | no |
motile | yes | 91.895 | yes |
gram-positive | no | 97.51 | yes |
anaerobic | no | 98.682 | no |
aerobic | yes | 94.13 | yes |
halophile | no | 91.786 | no |
spore-forming | no | 94.032 | yes |
thermophile | no | 99.225 | yes |
glucose-util | yes | 93.416 | no |
flagellated | no | 76.93 | no |
glucose-ferment | no | 86.251 | no |
External links
@ref: 32286
culture collection no.: KCTC 12901, JCM 14648
straininfo link
- @ref: 91874
- straininfo: 323252
literature
topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
---|---|---|---|---|---|---|---|---|
Phylogeny | 18048737 | Methylobacterium platani sp. nov., isolated from a leaf of the tree Platanus orientalis. | Kang YS, Kim J, Shin HD, Nam YD, Bae JW, Jeon CO, Park W | Int J Syst Evol Microbiol | 10.1099/ijs.0.65262-0 | 2007 | Aerobiosis, Bacterial Typing Techniques, Catalase/analysis, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Genes, rRNA, Hydrogen-Ion Concentration, Locomotion, Magnoliopsida/*microbiology, Methylobacterium/chemistry/*classification/genetics/*isolation & purification, Molecular Sequence Data, Nucleic Acid Hybridization, Oxidoreductases/analysis, Phylogeny, Pigments, Biological/metabolism, Plant Leaves/*microbiology, Quinones/analysis, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sequence Homology, Nucleic Acid, Sodium Chloride/metabolism, Temperature | Enzymology |
Phylogeny | 23315404 | Methylobacterium tarhaniae sp. nov., isolated from arid soil. | Veyisoglu A, Camas M, Tatar D, Guven K, Sazak A, Sahin N | Int J Syst Evol Microbiol | 10.1099/ijs.0.049551-0 | 2013 | Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/analysis, Methylobacterium/*classification/genetics/isolation & purification, Molecular Sequence Data, Nigeria, Nucleic Acid Hybridization, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Ubiquinone/analogs & derivatives/analysis | Genetics |
Phylogeny | 26776106 | Methylobacterium indicum sp. nov., a facultative methylotrophic bacterium isolated from rice seed. | Chaudhry V, Baindara P, Pal VK, Chawla N, Patil PB, Korpole S | Syst Appl Microbiol | 10.1016/j.syapm.2015.12.006 | 2015 | Bacterial Typing Techniques, DNA, Bacterial/genetics, DNA, Ribosomal/genetics, Endophytes/*classification/genetics/isolation & purification, Fatty Acids/analysis, Methylobacterium/*classification/genetics/*isolation & purification, Nucleic Acid Hybridization, Oryza/*microbiology, Phylogeny, RNA, Ribosomal, 16S/genetics, Seeds/*microbiology, Sequence Analysis, DNA | Enzymology |
Phylogeny | 29160200 | Methylobacterium frigidaeris sp. nov., isolated from an air conditioning system. | Lee Y, Jeon CO | Int J Syst Evol Microbiol | 10.1099/ijsem.0.002500 | 2017 | *Air Conditioning, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Methylobacterium/*classification/genetics/isolation & purification, Nucleic Acid Hybridization, *Phylogeny, Pigmentation, RNA, Ribosomal, 16S/genetics, Republic of Korea, Sequence Analysis, DNA, Ubiquinone/chemistry | Transcriptome |
Phylogeny | 31463788 | Methylobacterium terrae sp. nov., a radiation-resistant bacterium isolated from gamma ray-irradiated soil. | Kim J, Chhetri G, Kim I, Kim H, Kim MK, Seo T | J Microbiol | 10.1007/s12275-019-9007-9 | 2019 | Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, *Gamma Rays, Genotype, Lipids/chemistry, Methylobacterium/*classification/genetics/*isolation & purification/radiation effects, Nucleic Acid Hybridization, *Phylogeny, RNA, Ribosomal, 16S/genetics, *Radiation Tolerance, Republic of Korea, Sequence Analysis, DNA, Soil, *Soil Microbiology, Ubiquinone/analogs & derivatives/chemistry, Whole Genome Sequencing | Genetics |
Phylogeny | 32100693 | Methylobacterium terricola sp. nov., a gamma radiation-resistant bacterium isolated from gamma ray-irradiated soil. | Kim J, Chhetri G, Kim I, Lee B, Jang W, Kim MK, Seo T | Int J Syst Evol Microbiol | 10.1099/ijsem.0.004054 | 2020 | Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, *Gamma Rays, Methylobacterium/*classification/isolation & purification/radiation effects, Nucleic Acid Hybridization, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, Sequence Analysis, DNA, *Soil Microbiology, Ubiquinone/analogs & derivatives/chemistry | Transcriptome |
Phylogeny | 32207677 | Methylobacterium nonmethylotrophicum sp. nov., isolated from tungsten mine tailing. | Feng GD, Chen W, Zhang XJ, Zhang J, Wang SN, Zhu H | Int J Syst Evol Microbiol | 10.1099/ijsem.0.004112 | 2020 | Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Fatty Acids/chemistry, Genes, Bacterial, Methylobacterium/*classification/isolation & purification, *Mining, Nucleic Acid Hybridization, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Tungsten, Ubiquinone/analogs & derivatives/chemistry | Transcriptome |
Reference
@id | authors | title | doi/url | 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 | ||
32286 | 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 | 28526 | 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 | ||
67770 | Curators of the JCM | https://jcm.brc.riken.jp/en/ | |||
67771 | Curators of the KCTC | https://kctc.kribb.re.kr/En/Kctc | |||
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. | MicrobeAtlas 1.0 beta | https://microbeatlas.org/ | ||
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 | ||
91874 | 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-ID323252.1 |