Strain identifier
BacDive ID: 7204
Type strain: 
Species: Microvirga aerophila
Strain Designation: 5420S-12
Strain history: <- S.-W. Kwon, KACC; 5420S-12 <- H.-Y. Weon
NCBI tax ID(s): 670291 (species)
version 8.1 (current version)
General
@ref: 15630
BacDive-ID: 7204
DSM-Number: 21344
keywords: genome sequence, 16S sequence, Bacteria, aerobe, mesophilic, Gram-negative, rod-shaped
description: Microvirga aerophila 5420S-12 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from air.
NCBI tax id
- NCBI tax id: 670291
- Matching level: species
strain history
- @ref: 15630
- history: <- S.-W. Kwon, KACC; 5420S-12 <- H.-Y. Weon
doi: 10.13145/bacdive7204.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/pseudomonadota
- domain: Bacteria
- phylum: Pseudomonadota
- class: Alphaproteobacteria
- order: Hyphomicrobiales
- family: Methylobacteriaceae
- genus: Microvirga
- species: Microvirga aerophila
- full scientific name: Microvirga aerophila Weon et al. 2010
@ref: 15630
domain: Bacteria
phylum: Proteobacteria
class: Alphaproteobacteria
order: Rhizobiales
family: Methylobacteriaceae
genus: Microvirga
species: Microvirga aerophila
full scientific name: Microvirga aerophila Weon et al. 2010
strain designation: 5420S-12
type strain: yes
Morphology
cell morphology
| @ref | gram stain | cell length | cell width | cell shape | motility | confidence |
|---|---|---|---|---|---|---|
| 29689 | negative | 1.6-4.2 µm | 0.8-1.1 µm | rod-shaped | no | |
| 69480 | negative | 99.99 |
pigmentation
- @ref: 29689
- production: yes
Culture and growth conditions
culture medium
- @ref: 15630
- 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 | range |
|---|---|---|---|---|
| 15630 | positive | growth | 28 | mesophilic |
| 29689 | positive | growth | 10-35 | |
| 29689 | positive | optimum | 30 | mesophilic |
culture pH
| @ref | ability | type | pH | PH range |
|---|---|---|---|---|
| 29689 | positive | growth | 07-10 | alkaliphile |
| 29689 | positive | optimum | 07-10 |
Physiology and metabolism
oxygen tolerance
- @ref: 29689
- oxygen tolerance: aerobe
spore formation
| @ref | spore formation | confidence |
|---|---|---|
| 29689 | no | |
| 69481 | no | 100 |
| 69480 | no | 99.971 |
halophily
| @ref | salt | growth | tested relation | concentration |
|---|---|---|---|---|
| 29689 | NaCl | positive | growth | 0-2 % |
| 29689 | NaCl | positive | optimum | 0-2 % |
observation
- @ref: 29689
- observation: aggregates in chains
enzymes
- @ref: 29689
- value: catalase
- activity: +
- ec: 1.11.1.6
Isolation, sampling and environmental information
isolation
- @ref: 15630
- sample type: air
- geographic location: Suwon
- country: Republic of Korea
- origin.country: KOR
- continent: Asia
isolation source categories
- Cat1: #Environmental
- Cat2: #Air
taxonmaps
- @ref: 69479
- File name: preview.99_14163.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_86;96_1174;97_8763;98_10742;99_14163&stattab=map
- Last taxonomy: Microvirga aerophila subclade
- 16S sequence: GQ421848
- Sequence Identity:
- Total samples: 466
- soil counts: 412
- aquatic counts: 20
- animal counts: 21
- plant counts: 13
Safety information
risk assessment
- @ref: 15630
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
| @ref | description | accession | length | database | NCBI tax ID |
|---|---|---|---|---|---|
| 20218 | Microvirga aerophila gene for 16S rRNA, partial sequence, strain: NBRC 106136 | AB682367 | 1412 | ena | 670291 |
| 15630 | Microvirga aerophila strain 5420S-12 16S ribosomal RNA gene, partial sequence | GQ421848 | 1439 | ena | 670291 |
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Microvirga aerophila DSM 21344 | GCA_003332305 | contig | ncbi | 670291 |
| 66792 | Microvirga aerophila NBRC 106136 | GCA_007991675 | contig | ncbi | 670291 |
| 66792 | Microvirga aerophila strain DSM 21344 | 670291.3 | wgs | patric | 670291 |
| 66792 | Microvirga aerophila strain NBRC 106136 | 670291.4 | wgs | patric | 670291 |
| 66792 | Microvirga aerophila DSM 21344 | 2894369371 | draft | img | 670291 |
GC content
| @ref | GC-content | method |
|---|---|---|
| 15630 | 62.2 | high performance liquid chromatography (HPLC) |
| 29689 | 62.2 |
Genome-based predictions
predictions
| trait | prediction | confidence | training_data |
|---|---|---|---|
| spore-forming | no | 100 | no |
| gram-positive | no | 97.814 | no |
| anaerobic | no | 97.995 | yes |
| halophile | no | 90.697 | no |
| spore-forming | no | 96.185 | yes |
| glucose-util | yes | 83.805 | no |
| flagellated | no | 96.61 | yes |
| thermophile | no | 96.345 | no |
| motile | no | 88.687 | yes |
| aerobic | yes | 87.034 | yes |
| glucose-ferment | no | 90.077 | no |
External links
@ref: 15630
culture collection no.: DSM 21344, KACC 12743, NBRC 106136
straininfo link
- @ref: 76657
- straininfo: 405794
literature
| topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
|---|---|---|---|---|---|---|---|---|
| Phylogeny | 20023055 | Description of Microvirga aerophila sp. nov. and Microvirga aerilata sp. nov., isolated from air, reclassification of Balneimonas flocculans Takeda et al. 2004 as Microvirga flocculans comb. nov. and emended description of the genus Microvirga. | Weon HY, Kwon SW, Son JA, Jo EH, Kim SJ, Kim YS, Kim BY, Ka JO | Int J Syst Evol Microbiol | 10.1099/ijs.0.018770-0 | 2009 | *Air Microbiology, Base Composition, Bradyrhizobiaceae/*classification/genetics/*isolation & purification/metabolism, DNA, Bacterial/genetics, Fatty Acids/metabolism, Methylobacteriaceae/*classification/genetics/*isolation & purification/metabolism, Molecular Sequence Data, Phylogeny, RNA, Ribosomal, 16S/genetics | Metabolism |
| Phylogeny | 30062519 | Microvirga rosea sp. nov.: a nanoparticle producing bacterium isolated from soil of rose garden. | Huq MA | Arch Microbiol | 10.1007/s00203-018-1558-3 | 2018 | Base Composition, DNA, Bacterial/chemistry, Fatty Acids/analysis, Gardens, *Metal Nanoparticles, Methylobacteriaceae/*classification/genetics/isolation & purification/*metabolism, Phylogeny, Quinones/analysis, RNA, Ribosomal, 16S/genetics, Rosa, Silver/metabolism, *Soil Microbiology | Metabolism |
| Phylogeny | 30672730 | Microvirga flavescens sp. nov., a novel bacterium isolated from forest soil and emended description of the genus Microvirga. | Zhang XJ, Zhang J, Yao Q, Feng GD, Zhu HH | Int J Syst Evol Microbiol | 10.1099/ijsem.0.003189 | 2019 | Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Fatty Acids/chemistry, *Forests, Methylobacteriaceae/*classification/isolation & purification, Nucleic Acid Hybridization, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Ubiquinone/chemistry | Transcriptome |
| Phylogeny | 34697697 | Description and genome analysis of Microvirga antarctica sp. nov., a novel pink-pigmented psychrotolerant bacterium isolated from Antarctic soil. | Zhu L, Ping W, Zhang S, Chen Y, Zhang Y, Zhang J | Antonie Van Leeuwenhoek | 10.1007/s10482-021-01674-9 | 2021 | Antarctic Regions, Bacterial Typing Techniques, DNA, Bacterial/genetics, Fatty Acids/analysis, Methylobacteriaceae, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil, *Soil Microbiology, Ubiquinone | Transcriptome |
Reference
| @id | authors | catalogue | doi/url | title | journal | pubmed | ID_cross_reference |
|---|---|---|---|---|---|---|---|
| 15630 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 21344) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-21344 | ||||
| 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 | ||
| 29689 | 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 | 28776041 | 26074 | ||
| 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) | ||||
| 66794 | Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg | 10.1093/nar/gkaa1025 | BRENDA, the ELIXIR core data resource in 2021: new developments and updates | Nucleic Acids Res. 49: D498-D508 2020 | 33211880 | ||
| 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 | ||||
| 76657 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID405794.1 | StrainInfo: A central database for resolving microbial strain identifiers |