Strain identifier
BacDive ID: 7183
Type strain: 
Species: Methylobacterium iners
Strain Designation: 5317S-33
Strain history: KACC 11765 <-- H.-Y. Weon 5317S-33.
NCBI tax ID(s): 418707 (species)
version 9.3 (current version)
General
@ref: 7832
BacDive-ID: 7183
DSM-Number: 19015
keywords: genome sequence, 16S sequence, Bacteria, aerobe, mesophilic, Gram-negative, motile, rod-shaped
description: Methylobacterium iners 5317S-33 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from air sample.
NCBI tax id
- NCBI tax id: 418707
- Matching level: species
strain history
| @ref | history |
|---|---|
| 7832 | <- S.-W. Kwon, KACC; 5317S-33 |
| 67770 | KACC 11765 <-- H.-Y. Weon 5317S-33. |
doi: 10.13145/bacdive7183.20250331.9.3
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 iners
- full scientific name: Methylobacterium iners Weon et al. 2008
@ref: 7832
domain: Bacteria
phylum: Proteobacteria
class: Alphaproteobacteria
order: Rhizobiales
family: Methylobacteriaceae
genus: Methylobacterium
species: Methylobacterium iners
full scientific name: Methylobacterium iners Weon et al. 2008
strain designation: 5317S-33
type strain: yes
Morphology
cell morphology
| @ref | gram stain | cell length | cell width | cell shape | motility | confidence |
|---|---|---|---|---|---|---|
| 32155 | negative | 2 µm | 1 µm | rod-shaped | yes | |
| 125439 | negative | 95.2 | ||||
| 125438 | negative | 96.815 |
pigmentation
- @ref: 32155
- production: yes
Culture and growth conditions
culture medium
- @ref: 7832
- 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 | growth | type | temperature |
|---|---|---|---|
| 7832 | positive | growth | 30 |
| 32155 | positive | growth | 10-30 |
| 32155 | positive | optimum | 26.5 |
| 67770 | positive | growth | 30 |
culture pH
| @ref | ability | type | pH |
|---|---|---|---|
| 32155 | positive | growth | 06-08 |
| 32155 | positive | optimum | 7 |
Physiology and metabolism
oxygen tolerance
- @ref: 32155
- oxygen tolerance: aerobe
spore formation
- @ref: 125439
- spore formation: no
- confidence: 97.7
halophily
- @ref: 32155
- salt: NaCl
- growth: positive
- tested relation: growth
- concentration: <2 %
metabolite utilization
| @ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
|---|---|---|---|---|
| 32155 | 30089 | acetate | + | carbon source |
| 32155 | 22653 | asparagine | + | carbon source |
| 32155 | 35391 | aspartate | + | carbon source |
| 32155 | 15740 | formate | + | carbon source |
| 32155 | 29987 | glutamate | + | carbon source |
| 32155 | 24996 | lactate | + | carbon source |
| 32155 | 17272 | propionate | + | carbon source |
| 32155 | 51850 | methyl pyruvate | + | carbon source |
| 32155 | 30031 | succinate | + | carbon source |
enzymes
| @ref | value | activity | ec |
|---|---|---|---|
| 32155 | catalase | + | 1.11.1.6 |
| 32155 | cytochrome oxidase | + | 1.9.3.1 |
Isolation, sampling and environmental information
isolation
| @ref | sample type | geographic location | country | origin.country | continent |
|---|---|---|---|---|---|
| 7832 | air sample | Suwon city | Republic of Korea | KOR | Asia |
| 67770 | Air sample in Suwon City | Republic of Korea | KOR | Asia |
isolation source categories
- Cat1: #Environmental
- Cat2: #Air
Safety information
risk assessment
- @ref: 7832
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
- @ref: 7832
- description: Methylobacterium iners strain 5317S-33 16S ribosomal RNA gene, partial sequence
- accession: EF174497
- length: 1353
- database: nuccore
- NCBI tax ID: 418707
Genome sequences
- @ref: 66792
- description: Methylobacterium iners DSM 19015
- accession: GCA_022179305
- assembly level: contig
- database: ncbi
- NCBI tax ID: 418707
GC content
| @ref | GC-content | method |
|---|---|---|
| 7832 | 68.0 | |
| 32155 | 68 | |
| 67770 | 68 | high performance liquid chromatography (HPLC) |
Genome-based predictions
predictions
| @ref | model | trait | description | prediction | confidence | training_data |
|---|---|---|---|---|---|---|
| 125438 | gram-positive | gram-positive | Positive reaction to Gram-staining | no | 96.815 | yes |
| 125438 | anaerobic | anaerobic | Ability to grow under anoxygenic conditions (including facultative anaerobes) | no | 91.787 | no |
| 125438 | aerobic | aerobic | Ability to grow under oxygenic conditions (including facultative aerobes) | yes | 81.51 | no |
| 125438 | spore-forming | spore-forming | Ability to form endo- or exospores | no | 84.464 | no |
| 125438 | thermophile | thermophilic | Ability to grow at temperatures above or equal to 45°C | no | 96.832 | yes |
| 125438 | motile2+ | flagellated | Ability to perform flagellated movement | yes | 74.086 | no |
| 125439 | BacteriaNet | spore_formation | Ability to form endo- or exospores | no | 97.7 | |
| 125439 | BacteriaNet | motility | Ability to perform movement | yes | 67.8 | |
| 125439 | BacteriaNet | gram_stain | Reaction to gram-staining | negative | 95.2 | |
| 125439 | BacteriaNet | oxygen_tolerance | Oxygenic conditions needed for growth | aerobe | 83.3 |
External links
@ref: 7832
culture collection no.: DSM 19015, KACC 11765, JCM 16407
straininfo link
- @ref: 76636
- straininfo: 323974
literature
| topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
|---|---|---|---|---|---|---|---|---|
| Phylogeny | 18175690 | Methylobacterium iners sp. nov. and Methylobacterium aerolatum sp. nov., isolated from air samples in Korea. | Weon HY, Kim BY, Joa JH, Son JA, Song MH, Kwon SW, Go SJ, Yoon SH | Int J Syst Evol Microbiol | 10.1099/ijs.0.65047-0 | 2008 | *Air Microbiology, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/analysis, Fatty Acids/analysis, Genes, rRNA, Korea, Methylobacterium/*classification/genetics/*isolation & purification/physiology, Molecular Sequence Data, Nucleic Acid Hybridization, Phenotype, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Species Specificity | Genetics |
| Phylogeny | 21378138 | Methylobacterium gossipiicola sp. nov., a pink-pigmented, facultatively methylotrophic bacterium isolated from the cotton phyllosphere. | Madhaiyan M, Poonguzhali S, Senthilkumar M, Lee JS, Lee KC | Int J Syst Evol Microbiol | 10.1099/ijs.0.030148-0 | 2011 | Bacterial Typing Techniques, Base Composition, Carbon/metabolism, Cluster Analysis, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis, Gossypium/*microbiology, India, Locomotion, Methylobacterium/*classification/genetics/*isolation & purification/physiology, Molecular Sequence Data, Nucleic Acid Hybridization, Phylogeny, Pigments, Biological/metabolism, Plant Leaves/*microbiology, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA | Metabolism |
| Phylogeny | 21908681 | Methylobacterium oxalidis sp. nov., isolated from leaves of Oxalis corniculata. | Tani A, Sahin N, Kimbara K | Int J Syst Evol Microbiol | 10.1099/ijs.0.033019-0 | 2011 | Bacterial Typing Techniques, Cluster Analysis, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis, Ferns/*microbiology, Locomotion, Methylobacterium/*classification/genetics/*isolation & purification/physiology, Molecular Sequence Data, Nucleic Acid Hybridization, Phylogeny, Pigments, Biological/metabolism, Plant Leaves/microbiology, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA | Genetics |
Reference
| @id | authors | catalogue | doi/url | title | ID_cross_reference | pubmed |
|---|---|---|---|---|---|---|
| 7832 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 19015) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-19015 | |||
| 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 | |||
| 32155 | Barberan A, Caceres Velazquez H, Jones S, Fierer N. | 10.1128/mSphere.00237-17 | Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information | 28398 | 28776041 | |
| 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/ | ||||
| 76636 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID323974.1 | StrainInfo: A central database for resolving microbial strain identifiers | |||
| 125438 | Julia Koblitz, Lorenz Christian Reimer, Rüdiger Pukall, Jörg Overmann | 10.1101/2024.08.12.607695 | Predicting bacterial phenotypic traits through improved machine learning using high-quality, curated datasets | |||
| 125439 | Philipp Münch, René Mreches, Martin Binder, Hüseyin Anil Gündüz, Xiao-Yin To, Alice McHardy | https://github.com/GenomeNet/deepG | deepG: Deep Learning for Genome Sequence Data. R package version 0.3.1 |