Strain identifier
BacDive ID: 130505
Type strain: 
Species: Undibacterium seohonense
Strain Designation: SHS5-24
Strain history: <- S.-W. Kwon, KACC <- S.-J. Kim, Agricultural Microbiology Division, National Academy of Agricultural Science, Suwon, Korea
NCBI tax ID(s): 1344950 (species)
version 8.1 (current version)
General
@ref: 22053
BacDive-ID: 130505
DSM-Number: 29980
keywords: genome sequence, 16S sequence, Bacteria, mesophilic, Gram-negative
description: Undibacterium seohonense SHS5-24 is a mesophilic, Gram-negative bacterium that was isolated from freshwater.
NCBI tax id
- NCBI tax id: 1344950
- Matching level: species
strain history
- @ref: 22053
- history: <- S.-W. Kwon, KACC <- S.-J. Kim, Agricultural Microbiology Division, National Academy of Agricultural Science, Suwon, Korea
doi: 10.13145/bacdive130505.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/pseudomonadota
- domain: Bacteria
- phylum: Pseudomonadota
- class: Betaproteobacteria
- order: Burkholderiales
- family: Oxalobacteraceae
- genus: Undibacterium
- species: Undibacterium seohonense
- full scientific name: Undibacterium seohonense Kim et al. 2014
@ref: 22053
domain: Bacteria
phylum: Proteobacteria
class: Betaproteobacteria
order: Burkholderiales
family: Oxalobacteraceae
genus: Undibacterium
species: Undibacterium seohonense
full scientific name: Undibacterium seohonense Kim et al. 2014
strain designation: SHS5-24
type strain: yes
Morphology
cell morphology
- @ref: 69480
- gram stain: negative
- confidence: 99.99
Culture and growth conditions
culture medium
- @ref: 22053
- 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: 22053
- growth: positive
- type: growth
- temperature: 28
- range: mesophilic
Physiology and metabolism
spore formation
| @ref | spore formation | confidence |
|---|---|---|
| 69481 | no | 100 |
| 69480 | no | 99.997 |
Isolation, sampling and environmental information
isolation
- @ref: 22053
- sample type: freshwater
- geographic location: Suwon city, Seoho Lake
- country: Republic of Korea
- origin.country: KOR
- continent: Asia
isolation source categories
- Cat1: #Environmental
- Cat2: #Aquatic
- Cat3: #Freshwater
taxonmaps
- @ref: 69479
- File name: preview.99_37529.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_12;96_6220;97_18411;98_22926;99_37529&stattab=map
- Last taxonomy: Undibacterium
- 16S sequence: KC735151
- Sequence Identity:
- Total samples: 308
- soil counts: 58
- aquatic counts: 215
- animal counts: 24
- plant counts: 11
Safety information
risk assessment
- @ref: 22053
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
- @ref: 22053
- description: Undibacterium seohonense strain SHS5-24 16S ribosomal RNA gene, partial sequence
- accession: KC735151
- length: 1425
- database: ena
- NCBI tax ID: 1344950
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Undibacterium seohonense KACC 16656 | GCA_014284305 | scaffold | ncbi | 1344950 |
| 66792 | Undibacterium seohonense strain KACC 16656 | 1344950.3 | wgs | patric | 1344950 |
| 66792 | Undibacterium seohonense KACC 16656 | 2914845077 | draft | img | 1344950 |
Genome-based predictions
predictions
| trait | prediction | confidence | training_data |
|---|---|---|---|
| spore-forming | no | 100 | no |
| flagellated | yes | 70.473 | no |
| gram-positive | no | 98.539 | no |
| anaerobic | no | 98.145 | no |
| aerobic | yes | 89.692 | no |
| halophile | no | 97.973 | no |
| spore-forming | no | 93.77 | no |
| thermophile | no | 99.082 | yes |
| glucose-util | yes | 68.904 | no |
| motile | yes | 80.92 | no |
| glucose-ferment | no | 91.266 | no |
External links
@ref: 22053
culture collection no.: DSM 29980, KACC 16656, NBRC 108929
straininfo link
- @ref: 89028
- straininfo: 400458
literature
| topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
|---|---|---|---|---|---|---|---|---|
| Phylogeny | 24048872 | Undibacterium jejuense sp. nov. and Undibacterium seohonense sp. nov., isolated from soil and freshwater, respectively. | Kim SJ, Moon JY, Weon HY, Hong SB, Seok SJ, Kwon SW | Int J Syst Evol Microbiol | 10.1099/ijs.0.056846-0 | 2013 | Bacterial Typing Techniques, DNA, Bacterial/genetics, Fatty Acids/chemistry, Lakes/*microbiology, Molecular Sequence Data, Nucleic Acid Hybridization, Oxalobacteraceae/*classification/genetics/isolation & purification, *Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, Sequence Analysis, DNA, *Soil Microbiology, Ubiquinone/chemistry | Genetics |
| Phylogeny | 24363293 | Undibacterium macrobrachii sp. nov., isolated from a freshwater shrimp culture pond. | Sheu SY, Lin YS, Chen JC, Chen WM | Int J Syst Evol Microbiol | 10.1099/ijs.0.057661-0 | 2013 | Animals, Aquaculture, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Decapoda, Fatty Acids/chemistry, Hydroxybutyrates/chemistry, Molecular Sequence Data, Oxalobacteraceae/*classification/genetics/isolation & purification, *Phylogeny, Polyamines/chemistry, Polyesters/chemistry, Ponds/*microbiology, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Taiwan, Ubiquinone/chemistry | Genetics |
| Phylogeny | 26303040 | Undibacterium aquatile sp. nov., isolated from a waterfall. | Du J, Akter S, Won K, Singh H, Shik Yin C, Kook M, Yi TH | Int J Syst Evol Microbiol | 10.1099/ijsem.0.000545 | 2015 | Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Nucleic Acid Hybridization, Oxalobacteraceae/*classification/genetics/isolation & purification, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, Sequence Analysis, DNA, Ubiquinone/chemistry, *Water Microbiology | Transcriptome |
| Phylogeny | 29058644 | Undibacterium amnicola sp. nov., isolated from a freshwater stream. | Chen WM, Hsieh TY, Young CC, Sheu SY | Int J Syst Evol Microbiol | 10.1099/ijsem.0.002422 | 2017 | Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Nucleic Acid Hybridization, Oxalobacteraceae/*classification/genetics/isolation & purification, *Phylogeny, Pigmentation, Putrescine/analogs & derivatives/chemistry, RNA, Ribosomal, 16S/genetics, Rivers/*microbiology, Sequence Analysis, DNA, Taiwan, Ubiquinone/chemistry | Transcriptome |
Reference
| @id | authors | title | doi/url | catalogue |
|---|---|---|---|---|
| 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 | |
| 22053 | Curators of the DSMZ | https://www.dsmz.de/collection/catalogue/details/culture/DSM-29980 | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 29980) | |
| 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 | |
| 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 | |
| 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 | |
| 89028 | 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-ID400458.1 |