Strain identifier
BacDive ID: 11375
Type strain: 
Species: Undibacterium oligocarboniphilum
Strain Designation: EM 1
Strain history: <- W. Eder, Roche Diagnostics
NCBI tax ID(s): 666702 (species)
version 8.1 (current version)
General
@ref: 15942
BacDive-ID: 11375
DSM-Number: 21777
keywords: genome sequence, 16S sequence, Bacteria, aerobe, mesophilic, Gram-negative, motile
description: Undibacterium oligocarboniphilum EM 1 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from purified water system.
NCBI tax id
- NCBI tax id: 666702
- Matching level: species
strain history
- @ref: 15942
- history: <- W. Eder, Roche Diagnostics
doi: 10.13145/bacdive11375.20230509.8.1
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 oligocarboniphilum
- full scientific name: Undibacterium oligocarboniphilum Eder et al. 2011
@ref: 15942
domain: Bacteria
phylum: Proteobacteria
class: Betaproteobacteria
order: Burkholderiales
family: Oxalobacteraceae
genus: Undibacterium
species: Undibacterium oligocarboniphilum
full scientific name: Undibacterium oligocarboniphilum Eder et al. 2011
strain designation: EM 1
type strain: yes
Morphology
cell morphology
| @ref | gram stain | cell length | cell width | motility | confidence |
|---|---|---|---|---|---|
| 29681 | negative | 1.75 µm | 0.5 µm | yes | |
| 69480 | yes | 98.232 | |||
| 69480 | negative | 99.995 |
colony morphology
- @ref: 61264
- incubation period: 1 day
multimedia
- @ref: 15942
- multimedia content: https://www.dsmz.de/microorganisms/photos/DSM_21777.jpg
- intellectual property rights: © Leibniz-Institut DSMZ
Culture and growth conditions
culture medium
- @ref: 15942
- 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 |
|---|---|---|---|---|
| 15942 | positive | growth | 28 | mesophilic |
| 29681 | positive | growth | 10-35 | |
| 61264 | positive | growth | 30-37 | mesophilic |
Physiology and metabolism
oxygen tolerance
| @ref | oxygen tolerance |
|---|---|
| 29681 | aerobe |
| 61264 | aerobe |
spore formation
| @ref | spore formation | confidence |
|---|---|---|
| 29681 | no | |
| 69481 | no | 100 |
| 69480 | no | 99.999 |
metabolite utilization
| @ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
|---|---|---|---|---|
| 29681 | 24265 | gluconate | + | carbon source |
| 29681 | 17234 | glucose | + | carbon source |
| 29681 | 17306 | maltose | + | carbon source |
| 29681 | 33942 | ribose | + | carbon source |
| 29681 | 17992 | sucrose | + | carbon source |
| 29681 | 17632 | nitrate | + | reduction |
enzymes
| @ref | value | activity | ec |
|---|---|---|---|
| 29681 | catalase | + | 1.11.1.6 |
| 29681 | cytochrome oxidase | + | 1.9.3.1 |
Isolation, sampling and environmental information
isolation
| @ref | sample type | geographic location | country | origin.country | continent | sampling date |
|---|---|---|---|---|---|---|
| 15942 | purified water system | Penzberg | Germany | DEU | Europe | |
| 61264 | Water,purified system | Germany | DEU | Europe | 2008 |
isolation source categories
- Cat1: #Environmental
- Cat2: #Aquatic
taxonmaps
- @ref: 69479
- File name: preview.99_35450.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_12;96_3927;97_4831;98_6190;99_35450&stattab=map
- Last taxonomy: Undibacterium oligocarboniphilum subclade
- 16S sequence: GQ379228
- Sequence Identity:
- Total samples: 4676
- soil counts: 755
- aquatic counts: 1473
- animal counts: 1998
- plant counts: 450
Safety information
risk assessment
- @ref: 15942
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
- @ref: 15942
- description: Undibacterium oligocarboniphilum strain EM 1 16S ribosomal RNA gene, partial sequence
- accession: GQ379228
- length: 1527
- database: ena
- NCBI tax ID: 666702
Genome sequences
- @ref: 66792
- description: Undibacterium oligocarboniphilum EM 1
- accession: GCA_013377855
- assembly level: scaffold
- database: ncbi
- NCBI tax ID: 666702
GC content
| @ref | GC-content | method |
|---|---|---|
| 15942 | 52.4 | high performance liquid chromatography (HPLC) |
| 29681 | 52.4 |
Genome-based predictions
predictions
| trait | prediction | confidence | training_data |
|---|---|---|---|
| spore-forming | no | 100 | no |
| motile | yes | 86.677 | no |
| flagellated | yes | 82.188 | no |
| gram-positive | no | 98.777 | yes |
| anaerobic | no | 98.781 | yes |
| aerobic | yes | 87.984 | yes |
| halophile | no | 97.171 | no |
| spore-forming | no | 93.949 | no |
| glucose-util | no | 59.569 | no |
| thermophile | no | 95.558 | yes |
| glucose-ferment | no | 90.514 | no |
External links
@ref: 15942
culture collection no.: DSM 21777, CCUG 57265
straininfo link
- @ref: 80605
- straininfo: 399684
literature
| topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
|---|---|---|---|---|---|---|---|---|
| Phylogeny | 20305060 | Description of Undibacterium oligocarboniphilum sp. nov., isolated from purified water, and Undibacterium pigrum strain CCUG 49012 as the type strain of Undibacterium parvum sp. nov., and emended descriptions of the genus Undibacterium and the species Undibacterium pigrum. | Eder W, Wanner G, Ludwig W, Busse HJ, Ziemke-Kageler F, Lang E | Int J Syst Evol Microbiol | 10.1099/ijs.0.018648-0 | 2010 | Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/analysis, Genotype, Glycerophospholipids/analysis, Molecular Sequence Data, Oxalobacteraceae/*classification/genetics/isolation & purification/ultrastructure, Phenotype, *Phylogeny, Polyamines/analysis, Quinones/analysis, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Water Microbiology, Water Purification | Genetics |
| Phylogeny | 25033822 | Undibacterium squillarum sp. nov., isolated from a freshwater shrimp culture pond. | Sheu SY, Lin YS, Chen JC, Kwon SW, Chen WM | Int J Syst Evol Microbiol | 10.1099/ijs.0.065185-0 | 2014 | Animals, Aquaculture, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Decapoda, Fatty Acids/chemistry, Molecular Sequence Data, Oxalobacteraceae/*classification/genetics/isolation & purification, *Phylogeny, Pigmentation, Ponds/*microbiology, Putrescine/analogs & derivatives/chemistry, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Taiwan, Vitamin K 2/analogs & derivatives/chemistry | Genetics |
Reference
| @id | authors | catalogue | doi/url | title | ID_cross_reference | pubmed |
|---|---|---|---|---|---|---|
| 15942 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 21777) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-21777 | |||
| 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 | |||
| 29681 | 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 | 26066 | 28776041 | |
| 61264 | Curators of the CCUG | Culture Collection University of Gothenburg (CCUG) (CCUG 57265) | https://www.ccug.se/strain?id=57265 | |||
| 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) | |||
| 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 | |||
| 80605 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID399684.1 | StrainInfo: A central database for resolving microbial strain identifiers |