Strain identifier
BacDive ID: 23274
Type strain: 
Species: Sphingobium baderi
Strain Designation: LL03
Strain history: <- R. Lal, Univ. Delhi, Dept. Zoology, India; LL03 <- J. Damborsky, Loschmidt Laboratories and Research Centre for Toxic Compounds; Masaryk University
NCBI tax ID(s): 1332080 (species)
version 8.1 (current version)
General
@ref: 19263
BacDive-ID: 23274
DSM-Number: 25433
keywords: genome sequence, 16S sequence, Bacteria, aerobe, mesophilic, Gram-negative, rod-shaped
description: Sphingobium baderi LL03 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from hexachlorocyclohexane-contaminated soil besides lindane producing plant.
NCBI tax id
- NCBI tax id: 1332080
- Matching level: species
strain history
- @ref: 19263
- history: <- R. Lal, Univ. Delhi, Dept. Zoology, India; LL03 <- J. Damborsky, Loschmidt Laboratories and Research Centre for Toxic Compounds; Masaryk University
doi: 10.13145/bacdive23274.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/pseudomonadota
- domain: Bacteria
- phylum: Pseudomonadota
- class: Alphaproteobacteria
- order: Sphingomonadales
- family: Sphingomonadaceae
- genus: Sphingobium
- species: Sphingobium baderi
- full scientific name: Sphingobium baderi Kaur et al. 2013
@ref: 19263
domain: Bacteria
phylum: Proteobacteria
class: Alphaproteobacteria
order: Sphingomonadales
family: Sphingomonadaceae
genus: Sphingobium
species: Sphingobium baderi
full scientific name: Sphingobium baderi Kaur et al. 2013
strain designation: LL03
type strain: yes
Morphology
cell morphology
- @ref: 30605
- gram stain: negative
- cell shape: rod-shaped
- motility: no
pigmentation
- @ref: 30605
- production: yes
Culture and growth conditions
culture medium
- @ref: 19263
- name: TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535)
- growth: yes
- link: https://mediadive.dsmz.de/medium/535
- composition: Name: TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535) Composition: Trypticase soy broth 30.0 g/l Agar 15.0 g/l Distilled water
culture temp
| @ref | growth | type | temperature | range |
|---|---|---|---|---|
| 19263 | positive | growth | 28 | mesophilic |
| 30605 | positive | optimum | 28 | mesophilic |
culture pH
| @ref | ability | type | pH |
|---|---|---|---|
| 30605 | positive | growth | 06-08 |
| 30605 | positive | optimum | 7 |
Physiology and metabolism
oxygen tolerance
- @ref: 30605
- oxygen tolerance: aerobe
halophily
| @ref | salt | growth | tested relation | concentration |
|---|---|---|---|---|
| 30605 | NaCl | positive | growth | 02-03 % |
| 30605 | NaCl | positive | optimum | 2.5 % |
metabolite utilization
| @ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
|---|---|---|---|---|
| 30605 | 17234 | glucose | + | carbon source |
| 30605 | 17306 | maltose | + | carbon source |
| 30605 | 37684 | mannose | + | carbon source |
| 30605 | 4853 | esculin | + | hydrolysis |
| 30605 | 17632 | nitrate | + | reduction |
enzymes
| @ref | value | activity | ec |
|---|---|---|---|
| 30605 | catalase | + | 1.11.1.6 |
| 30605 | cytochrome oxidase | + | 1.9.3.1 |
Isolation, sampling and environmental information
isolation
- @ref: 19263
- sample type: hexachlorocyclohexane-contaminated soil besides lindane producing plant
- country: Czech Republic
- origin.country: CZE
- continent: Europe
isolation source categories
| Cat1 | Cat2 | Cat3 |
|---|---|---|
| #Engineered | #Contamination | |
| #Engineered | #Industrial | #Plant (Factory) |
| #Environmental | #Terrestrial | #Soil |
taxonmaps
- @ref: 69479
- File name: preview.99_3591.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_20;96_774;97_2064;98_2751;99_3591&stattab=map
- Last taxonomy: Sphingobium baderi
- 16S sequence: JN695620
- Sequence Identity:
- Total samples: 817
- soil counts: 193
- aquatic counts: 283
- animal counts: 88
- plant counts: 253
Safety information
risk assessment
- @ref: 19263
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
- @ref: 19263
- description: Sphingobium baderi LL03 16S ribosomal RNA gene, partial sequence
- accession: JN695620
- length: 1462
- database: ena
- NCBI tax ID: 1114964
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Sphingobium baderi LL03 | GCA_001046655 | scaffold | ncbi | 1114964 |
| 66792 | Sphingobium baderi LL03 | GCA_000445145 | contig | ncbi | 1114964 |
| 66792 | Sphingobium baderi LL03 | 1114964.3 | wgs | patric | 1114964 |
| 66792 | Sphingobium baderi LL03 | 1114964.8 | wgs | patric | 1114964 |
| 66792 | Sphingobium baderi LL03 | 2579778767 | draft | img | 1114964 |
GC content
| @ref | GC-content | method |
|---|---|---|
| 19263 | 67.0 | fluorimetric |
| 30605 | 67 |
Genome-based predictions
predictions
| trait | prediction | confidence | training_data |
|---|---|---|---|
| motile | yes | 51.647 | yes |
| flagellated | no | 87.185 | yes |
| gram-positive | no | 96.53 | yes |
| anaerobic | no | 98.513 | yes |
| aerobic | yes | 89.61 | yes |
| halophile | no | 94.383 | no |
| spore-forming | no | 94.066 | no |
| thermophile | no | 96.297 | no |
| glucose-util | yes | 72.461 | no |
| glucose-ferment | no | 93.506 | no |
External links
@ref: 19263
culture collection no.: DSM 25433, CCM 7981
straininfo link
- @ref: 87496
- straininfo: 401448
literature
- topic: Phylogeny
- Pubmed-ID: 22544800
- title: Sphingobium baderi sp. nov., isolated from a hexachlorocyclohexane dump site.
- authors: Kaur J, Moskalikova H, Niharika N, Sedlackova M, Hampl A, Damborsky J, Prokop Z, Lal R
- journal: Int J Syst Evol Microbiol
- DOI: 10.1099/ijs.0.039834-0
- year: 2012
- mesh: Bacterial Typing Techniques, Base Composition, Biodegradation, Environmental, Czech Republic, DNA, Bacterial/genetics, Fatty Acids/analysis, *Hexachlorocyclohexane, Molecular Sequence Data, Nucleic Acid Hybridization, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Soil Pollutants, Spermidine/analysis, Sphingomonadaceae/*classification/genetics/metabolism, Ubiquinone/analogs & derivatives/analysis
- topic2: Genetics
Reference
| @id | authors | catalogue | doi/url | title | ID_cross_reference | pubmed | journal |
|---|---|---|---|---|---|---|---|
| 19263 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 25433) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-25433 | ||||
| 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 | ||||
| 30605 | 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 | 26936 | 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) | ||||
| 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 | 33211880 | Nucleic Acids Res. 49: D498-D508 2020 | ||
| 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 | ||||
| 87496 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID401448.1 | StrainInfo: A central database for resolving microbial strain identifiers |