Strain identifier
BacDive ID: 133490
Type strain: 
Species: Microvirga guangxiensis
Strain Designation: 25B
Strain history: J. Zhang 25B.
NCBI tax ID(s): 549386 (species)
version 8.1 (current version)
General
@ref: 29178
BacDive-ID: 133490
keywords: genome sequence, 16S sequence, Bacteria, aerobe, Gram-negative, rod-shaped
description: Microvirga guangxiensis 25B is an aerobe, Gram-negative, rod-shaped bacterium that was isolated from soil.
NCBI tax id
- NCBI tax id: 549386
- Matching level: species
strain history
- @ref: 67770
- history: J. Zhang 25B.
doi: 10.13145/bacdive133490.20230509.8.1
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 guangxiensis
- full scientific name: Microvirga guangxiensis Zhang et al. 2009
@ref: 29178
domain: Bacteria
phylum: Proteobacteria
class: Alphaproteobacteria
order: Hyphomicrobiales
family: Methylobacteriaceae
genus: Microvirga
species: Microvirga guangxiensis
strain designation: 25B
type strain: yes
Morphology
cell morphology
| @ref | gram stain | cell length | cell width | cell shape | motility | confidence |
|---|---|---|---|---|---|---|
| 29178 | negative | 1.7 µm | 0.7 µm | rod-shaped | no | |
| 69480 | yes | 96.173 | ||||
| 69480 | negative | 99.998 |
pigmentation
- @ref: 29178
- production: yes
Culture and growth conditions
culture temp
| @ref | growth | type | temperature | range |
|---|---|---|---|---|
| 29178 | positive | growth | 16-42 | |
| 29178 | positive | optimum | 37 | mesophilic |
| 67770 | positive | growth | 37 | mesophilic |
culture pH
| @ref | ability | type | pH | PH range |
|---|---|---|---|---|
| 29178 | positive | growth | 5.0-9.5 | alkaliphile |
| 29178 | positive | optimum | 7 |
Physiology and metabolism
oxygen tolerance
- @ref: 29178
- oxygen tolerance: aerobe
spore formation
| @ref | spore formation | confidence |
|---|---|---|
| 29178 | no | |
| 69481 | no | 100 |
| 69480 | no | 99.995 |
halophily
- @ref: 29178
- salt: NaCl
- growth: positive
- tested relation: growth
- concentration: 0-2 %
observation
- @ref: 67770
- observation: quinones: Q-10
metabolite utilization
| @ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
|---|---|---|---|---|
| 29178 | 30089 | acetate | + | carbon source |
| 29178 | 22599 | arabinose | + | carbon source |
| 29178 | 18403 | L-arabitol | + | carbon source |
| 29178 | 24148 | galactonate | + | carbon source |
| 29178 | 17234 | glucose | + | carbon source |
| 29178 | 25115 | malate | + | carbon source |
| 29178 | 15792 | malonate | + | carbon source |
| 29178 | 17306 | maltose | + | carbon source |
| 29178 | 29864 | mannitol | + | carbon source |
| 29178 | 28053 | melibiose | + | carbon source |
| 29178 | 30911 | sorbitol | + | carbon source |
| 29178 | 18222 | xylose | + | carbon source |
| 29178 | 17632 | nitrate | + | reduction |
enzymes
| @ref | value | activity | ec |
|---|---|---|---|
| 29178 | catalase | + | 1.11.1.6 |
| 29178 | cytochrome oxidase | + | 1.9.3.1 |
| 29178 | urease | + | 3.5.1.5 |
Isolation, sampling and environmental information
isolation
| @ref | sample type | country | origin.country | continent |
|---|---|---|---|---|
| 29178 | soil | |||
| 67770 | Rice field soil in Guangxi Province | China | CHN | Asia |
isolation source categories
- Cat1: #Environmental
- Cat2: #Terrestrial
- Cat3: #Soil
Sequence information
16S sequences
- @ref: 29178
- description: Microvirga guangxiensis strain 25B 16S ribosomal RNA gene, partial sequence
- accession: EU727176
- length: 1397
- database: nuccore
- NCBI tax ID: 549386
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Microvirga guangxiensis strain CGMCC 1.7666 | 549386.3 | wgs | patric | 549386 |
| 66792 | Microvirga guangxiensis CGMCC 1.7666 | 2596583582 | draft | img | 549386 |
| 67770 | Microvirga guangxiensis CGMCC 1.7666 | GCA_900102135 | scaffold | ncbi | 549386 |
GC content
- @ref: 67770
- GC-content: 64.3
- method: thermal denaturation, midpoint method (Tm)
Genome-based predictions
predictions
| trait | prediction | confidence | training_data |
|---|---|---|---|
| spore-forming | no | 100 | no |
| gram-positive | no | 98.212 | no |
| anaerobic | no | 97.116 | yes |
| halophile | no | 91 | no |
| spore-forming | no | 95.112 | yes |
| glucose-util | yes | 91.185 | no |
| thermophile | no | 78.98 | no |
| aerobic | yes | 84.384 | no |
| motile | yes | 61.667 | yes |
| flagellated | no | 78.594 | yes |
| glucose-ferment | no | 91.636 | no |
External links
@ref: 29178
culture collection no.: CGMCC 1.7666, JCM 15710
literature
| topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
|---|---|---|---|---|---|---|---|---|
| Phylogeny | 19567564 | Microvirga guangxiensis sp. nov., a novel alphaproteobacterium from soil, and emended description of the genus Microvirga. | Zhang J, Song F, Xin YH, Zhang J, Fang C | Int J Syst Evol Microbiol | 10.1099/ijs.0.007997-0 | 2009 | Aerobiosis, Bacterial Typing Techniques, China, Cluster Analysis, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis, Hydrogen-Ion Concentration, Locomotion, Methylobacteriaceae/*classification/genetics/*isolation & purification/physiology, Molecular Sequence Data, Nucleic Acid Hybridization, Oryza, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Temperature | Genetics |
| Phylogeny | 35750895 | Microvirga terricola sp. nov. and Microvirga solisilvae sp. nov, isolated from forest soil. | Zhang X, Feng GD, Zhen X, Zhang Y, Deng X, Zhu H, Yao Q | Arch Microbiol | 10.1007/s00203-022-02963-1 | 2022 | Bacterial Typing Techniques, Base Composition, *Bradyrhizobiaceae/genetics, DNA, Bacterial/genetics, Fatty Acids/analysis, Forests, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil, Soil Microbiology | Transcriptome |
Reference
| @id | authors | title | doi/url | 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 | |||
| 29178 | 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 | 25602 | 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 | |
| 67770 | Curators of the JCM | https://jcm.brc.riken.jp/en/ | ||||
| 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 |