Strain identifier
BacDive ID: 14271
Type strain: 
Species: Allosphingosinicella indica
Strain Designation: Dd16
Strain history: <- R. Lal, Univ. Delhi, Dept. Zoology, India; Dd16
NCBI tax ID(s): 941907 (species)
version 8.1 (current version)
General
@ref: 18036
BacDive-ID: 14271
DSM-Number: 25434
keywords: genome sequence, 16S sequence, Bacteria, aerobe, Gram-negative, rod-shaped
description: Allosphingosinicella indica Dd16 is an aerobe, Gram-negative, rod-shaped bacterium that was isolated from HCH-contaminated dump site.
NCBI tax id
- NCBI tax id: 941907
- Matching level: species
strain history
- @ref: 18036
- history: <- R. Lal, Univ. Delhi, Dept. Zoology, India; Dd16
doi: 10.13145/bacdive14271.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/pseudomonadota
- domain: Bacteria
- phylum: Pseudomonadota
- class: Alphaproteobacteria
- order: Sphingomonadales
- family: Sphingomonadaceae
- genus: Allosphingosinicella
- species: Allosphingosinicella indica
- full scientific name: Allosphingosinicella indica (Niharika et al. 2012) Hördt et al. 2020
synonyms
- @ref: 20215
- synonym: Sphingomonas indica
@ref: 18036
domain: Bacteria
phylum: Proteobacteria
class: Alphaproteobacteria
order: Sphingomonadales
family: Sphingomonadaceae
genus: Sphingomonas
species: Sphingomonas indica
full scientific name: Sphingomonas indica Niharika et al. 2012
strain designation: Dd16
type strain: yes
Morphology
cell morphology
| @ref | gram stain | cell length | cell width | cell shape | motility | confidence |
|---|---|---|---|---|---|---|
| 30344 | negative | 2.6 µm | 0.9 µm | rod-shaped | no | |
| 69480 | negative | 99.994 |
pigmentation
- @ref: 30344
- production: yes
multimedia
- @ref: 18036
- multimedia content: https://www.dsmz.de/microorganisms/photos/DSM_25434.jpg
- intellectual property rights: © Leibniz-Institut DSMZ
Culture and growth conditions
culture temp
| @ref | growth | type | temperature | range |
|---|---|---|---|---|
| 30344 | positive | growth | 04-28 | |
| 30344 | positive | optimum | 28 | mesophilic |
culture pH
| @ref | ability | type | pH |
|---|---|---|---|
| 30344 | positive | growth | 06-07 |
| 30344 | positive | optimum | 7 |
Physiology and metabolism
oxygen tolerance
- @ref: 30344
- oxygen tolerance: aerobe
spore formation
| @ref | spore formation | confidence |
|---|---|---|
| 30344 | no | |
| 69481 | no | 100 |
| 69480 | no | 99.941 |
halophily
| @ref | salt | growth | tested relation | concentration |
|---|---|---|---|---|
| 30344 | NaCl | positive | growth | 0-2 % |
| 30344 | NaCl | positive | optimum | 1 % |
metabolite utilization
| @ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
|---|---|---|---|---|
| 30344 | 22599 | arabinose | + | carbon source |
| 30344 | 28757 | fructose | + | carbon source |
| 30344 | 28260 | galactose | + | carbon source |
| 30344 | 29864 | mannitol | + | carbon source |
| 30344 | 16634 | raffinose | + | carbon source |
| 30344 | 30911 | sorbitol | + | carbon source |
| 30344 | 17992 | sucrose | + | carbon source |
| 30344 | 27082 | trehalose | + | carbon source |
enzymes
| @ref | value | activity | ec |
|---|---|---|---|
| 30344 | catalase | + | 1.11.1.6 |
| 30344 | cytochrome oxidase | + | 1.9.3.1 |
Isolation, sampling and environmental information
isolation
- @ref: 18036
- sample type: HCH-contaminated dump site
- geographic location: Uttar Pradesh, Lucknow, Ummari village (27° 00' N, 81° 09' E)
- country: India
- origin.country: IND
- continent: Asia
- latitude: 27
- longitude: 81.15
isolation source categories
| Cat1 | Cat2 |
|---|---|
| #Engineered | #Built environment |
| #Engineered | #Contamination |
taxonmaps
- @ref: 69479
- File name: preview.99_7642.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_20;96_3558;97_4370;98_5594;99_7642&stattab=map
- Last taxonomy: Allosphingosinicella indica subclade
- 16S sequence: HQ449390
- Sequence Identity:
- Total samples: 98
- soil counts: 65
- aquatic counts: 10
- animal counts: 7
- plant counts: 16
Safety information
risk assessment
- @ref: 18036
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
- @ref: 18036
- description: Sphingomonas indica strain Dd16 16S ribosomal RNA gene, partial sequence
- accession: HQ449390
- length: 1449
- database: ena
- NCBI tax ID: 941907
Genome sequences
- @ref: 66792
- description: Allosphingosinicella indica Dd16
- accession: GCA_900177405
- assembly level: chromosome
- database: ncbi
- NCBI tax ID: 941907
GC content
| @ref | GC-content | method |
|---|---|---|
| 18036 | 65.8 | fluorimetric |
| 30344 | 65.8 |
Genome-based predictions
predictions
| trait | prediction | confidence | training_data |
|---|---|---|---|
| spore-forming | no | 100 | no |
| motile | yes | 82.329 | no |
| flagellated | no | 91.663 | yes |
| gram-positive | no | 96.756 | yes |
| anaerobic | no | 99.04 | yes |
| aerobic | yes | 92.741 | yes |
| halophile | no | 85.684 | no |
| spore-forming | no | 94.535 | yes |
| thermophile | no | 94.451 | yes |
| glucose-util | yes | 71.542 | no |
| glucose-ferment | no | 92.216 | no |
External links
@ref: 18036
culture collection no.: DSM 25434, CCM 7882, MTCC 10862
Reference
| @id | authors | catalogue | doi/url | title | ID_cross_reference | pubmed | journal |
|---|---|---|---|---|---|---|---|
| 18036 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 25434) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-25434 | ||||
| 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 | ||||
| 30344 | 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 | 26685 | 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 | ||||
| 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 |