Strain identifier
BacDive ID: 14284
Type strain: 
Species: Sphingopyxis ummariensis
Strain Designation: UI2
Strain history: <- MTCC <- R. Lal, Univ. Delhi, Dept. Zoology, India
NCBI tax ID(s): 429001 (subspecies)
version 8.1 (current version)
General
@ref: 17635
BacDive-ID: 14284
DSM-Number: 24316
keywords: genome sequence, 16S sequence, Bacteria, aerobe, mesophilic, motile, rod-shaped
description: Sphingopyxis ummariensis UI2 is an aerobe, mesophilic, motile bacterium that was isolated from HCH contaminated soil.
NCBI tax id
- NCBI tax id: 429001
- Matching level: subspecies
strain history
- @ref: 17635
- history: <- MTCC <- R. Lal, Univ. Delhi, Dept. Zoology, India
doi: 10.13145/bacdive14284.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/pseudomonadota
- domain: Bacteria
- phylum: Pseudomonadota
- class: Alphaproteobacteria
- order: Sphingomonadales
- family: Sphingomonadaceae
- genus: Sphingopyxis
- species: Sphingopyxis ummariensis
- full scientific name: Sphingopyxis ummariensis Sharma et al. 2010
synonyms
- @ref: 20215
- synonym: Sphingopyxis terrae subsp. ummariensis
@ref: 17635
domain: Bacteria
phylum: Proteobacteria
class: Alphaproteobacteria
order: Sphingomonadales
family: Sphingomonadaceae
genus: Sphingopyxis
species: Sphingopyxis terrae
full scientific name: Sphingopyxis ummariensis Sharma et al. 2010
strain designation: UI2
type strain: yes
Morphology
cell morphology
| @ref | cell length | cell width | cell shape | motility | gram stain | confidence |
|---|---|---|---|---|---|---|
| 29216 | 1 µm | 0.8 µm | rod-shaped | yes | ||
| 69480 | negative | 99.965 |
pigmentation
- @ref: 29216
- production: yes
Culture and growth conditions
culture temp
- @ref: 29216
- growth: positive
- type: optimum
- temperature: 28
- range: mesophilic
culture pH
- @ref: 29216
- ability: positive
- type: optimum
- pH: 7.5
Physiology and metabolism
oxygen tolerance
- @ref: 29216
- oxygen tolerance: aerobe
spore formation
| @ref | spore formation | confidence |
|---|---|---|
| 69481 | no | 100 |
| 69480 | no | 99.98 |
halophily
- @ref: 29216
- salt: NaCl
- growth: positive
- tested relation: optimum
- concentration: 1 %
metabolite utilization
| @ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
|---|---|---|---|---|
| 29216 | 22599 | arabinose | + | carbon source |
| 29216 | 17057 | cellobiose | + | carbon source |
| 29216 | 28757 | fructose | + | carbon source |
| 29216 | 28260 | galactose | + | carbon source |
| 29216 | 17234 | glucose | + | carbon source |
| 29216 | 17716 | lactose | + | carbon source |
| 29216 | 17306 | maltose | + | carbon source |
| 29216 | 37684 | mannose | + | carbon source |
| 29216 | 33942 | ribose | + | carbon source |
| 29216 | 30911 | sorbitol | + | carbon source |
| 29216 | 27082 | trehalose | + | carbon source |
| 29216 | 18222 | xylose | + | carbon source |
| 29216 | 4853 | esculin | + | hydrolysis |
| 65237 | 17306 | maltose | - | assimilation |
enzymes
| @ref | value | activity | ec |
|---|---|---|---|
| 29216 | catalase | + | 1.11.1.6 |
| 29216 | cytochrome oxidase | + | 1.9.3.1 |
| 65237 | alpha-glucosidase | - | 3.2.1.20 |
Isolation, sampling and environmental information
isolation
- @ref: 17635
- sample type: HCH contaminated soil
- geographic location: Ummari village, Lucknow
- country: India
- origin.country: IND
- continent: Asia
isolation source categories
| Cat1 | Cat2 | Cat3 |
|---|---|---|
| #Engineered | #Contamination | |
| #Environmental | #Terrestrial | #Soil |
taxonmaps
- @ref: 69479
- File name: preview.99_5371.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_20;96_1020;97_1190;98_4004;99_5371&stattab=map
- Last taxonomy: Sphingopyxis
- 16S sequence: EF424391
- Sequence Identity:
- Total samples: 301
- soil counts: 39
- aquatic counts: 172
- animal counts: 73
- plant counts: 17
Safety information
risk assessment
- @ref: 17635
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
- @ref: 17635
- description: Sphingopyxis ummariensis strain UI2 16S ribosomal RNA gene, partial sequence
- accession: EF424391
- length: 1408
- database: ena
- NCBI tax ID: 429001
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Sphingopyxis terrae subsp. ummariensis DSM 24316 | GCA_002374275 | contig | ncbi | 429001 |
| 66792 | Sphingopyxis ummariensis strain DSM 24316 | 429001.4 | wgs | patric | 429001 |
| 66792 | Sphingopyxis terrae subsp. ummariensis UI2 | GCA_900177755 | contig | ncbi | 429001 |
GC content
| @ref | GC-content | method |
|---|---|---|
| 17635 | 65.2 | sequence analysis |
| 29216 | 68 | |
| 65237 | 65 | genome sequence analysis |
Genome-based predictions
predictions
| trait | prediction | confidence | training_data |
|---|---|---|---|
| spore-forming | no | 100 | no |
| gram-positive | no | 97.406 | no |
| anaerobic | no | 99.393 | yes |
| halophile | no | 94.698 | yes |
| spore-forming | no | 94.523 | no |
| glucose-util | yes | 82.795 | yes |
| aerobic | yes | 92.515 | yes |
| flagellated | no | 86.493 | no |
| thermophile | no | 97.661 | yes |
| motile | yes | 70.954 | yes |
| glucose-ferment | no | 94.157 | no |
External links
@ref: 17635
culture collection no.: DSM 24316, CCM 7428, MTCC 8591
literature
| topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
|---|---|---|---|---|---|---|---|---|
| Phylogeny | 19656938 | Sphingopyxis ummariensis sp. nov., isolated from a hexachlorocyclohexane dump site. | Sharma P, Verma M, Bala K, Nigam A, Lal R | Int J Syst Evol Microbiol | 10.1099/ijs.0.008805-0 | 2009 | Bacterial Typing Techniques, DNA, Ribosomal/analysis/genetics, Fatty Acids/analysis, Genes, rRNA, Hexachlorocyclohexane/*metabolism, India, Insecticides/*metabolism, Molecular Sequence Data, Nucleic Acid Hybridization, Phenotype, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Soil Pollutants/*metabolism, Species Specificity, Sphingomonadaceae/*classification/genetics/*isolation & purification/physiology | Metabolism |
| Phylogeny | 23264504 | Sphingopyxis italica sp. nov., isolated from Roman catacombs. | Alias-Villegas C, Jurado V, Laiz L, Saiz-Jimenez C | Int J Syst Evol Microbiol | 10.1099/ijs.0.046573-0 | 2012 | Bacterial Typing Techniques, DNA, Bacterial/genetics, Fatty Acids/analysis, Molecular Sequence Data, Nucleic Acid Hybridization, *Phylogeny, RNA, Ribosomal, 16S/genetics, Rome, Sequence Analysis, DNA, *Soil Microbiology, Sphingomonadaceae/*classification/genetics/isolation & purification, Ubiquinone/analogs & derivatives/analysis | Genetics |
| Phylogeny | 29087277 | Genome-based reclassification of Sphingopyxis ummariensis as a later heterotypic synonym of Sphingopyxis terrae, with the descriptions of Sphingopyxis terrae subsp. terrae subsp. nov. and Sphingopyxis terrae subsp. ummariensis subsp. nov. | Feng GD, Wang DD, Yang SZ, Li HP, Zhu HH | Int J Syst Evol Microbiol | 10.1099/ijsem.0.002465 | 2017 | Bacterial Typing Techniques, DNA, Bacterial/genetics, Nucleic Acid Hybridization, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sphingomonadaceae/*classification | Transcriptome |
Reference
| @id | authors | catalogue | doi/url | title | ID_cross_reference | pubmed | journal |
|---|---|---|---|---|---|---|---|
| 17635 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 24316) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-24316 | ||||
| 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 | ||||
| 29216 | 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 | 25637 | 28776041 | ||
| 65237 | Guang-Da Feng, Dong-Dong Wang, Song-Zhen Yang, Hua-Ping Li, Hong-Hui Zhu | 10.1099/ijsem.0.002465 | Genome-based reclassification of Sphingopyxis ummariensis as a later heterotypic synonym of Sphingopyxis terrae, with the descriptions of Sphingopyxis terrae subsp. terrae subsp. nov. and Sphingopyxis terrae subsp. ummariensis subsp. nov. | 29087277 | IJSEM 67: 5279-5283 2017 | ||
| 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 |