Strain identifier
BacDive ID: 14162
Type strain: 
Species: Novosphingobium mathurense
Strain Designation: SM117
Strain history: <- CCM <- MTCC; SM117 <- R. Lal, Univ. Delhi, Dept. Zoology, India
NCBI tax ID(s): 428990 (species)
version 8.1 (current version)
General
@ref: 16714
BacDive-ID: 14162
DSM-Number: 23374
keywords: genome sequence, 16S sequence, Bacteria, aerobe, mesophilic, Gram-negative, motile, rod-shaped
description: Novosphingobium mathurense SM117 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from oil-contaminated soil.
NCBI tax id
- NCBI tax id: 428990
- Matching level: species
strain history
- @ref: 16714
- history: <- CCM <- MTCC; SM117 <- R. Lal, Univ. Delhi, Dept. Zoology, India
doi: 10.13145/bacdive14162.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/pseudomonadota
- domain: Bacteria
- phylum: Pseudomonadota
- class: Alphaproteobacteria
- order: Sphingomonadales
- family: Erythrobacteraceae
- genus: Novosphingobium
- species: Novosphingobium mathurense
- full scientific name: Novosphingobium mathurense Gupta et al. 2009
@ref: 16714
domain: Bacteria
phylum: Proteobacteria
class: Alphaproteobacteria
order: Sphingomonadales
family: Sphingomonadaceae
genus: Novosphingobium
species: Novosphingobium mathurense
full scientific name: Novosphingobium mathurense Gupta et al. 2009
strain designation: SM117
type strain: yes
Morphology
cell morphology
| @ref | gram stain | cell length | cell width | cell shape | motility | confidence |
|---|---|---|---|---|---|---|
| 32592 | negative | 1.4 µm | 0.8 µm | rod-shaped | yes | |
| 69480 | negative | 99.988 |
pigmentation
- @ref: 32592
- production: no
Culture and growth conditions
culture temp
| @ref | growth | type | temperature | range |
|---|---|---|---|---|
| 32592 | positive | growth | 28-37 | mesophilic |
| 32592 | positive | optimum | 32.5 | mesophilic |
culture pH
- @ref: 32592
- ability: positive
- type: optimum
- pH: 7.2
Physiology and metabolism
oxygen tolerance
- @ref: 32592
- oxygen tolerance: aerobe
spore formation
| @ref | spore formation | confidence |
|---|---|---|
| 32592 | no | |
| 69481 | no | 100 |
| 69480 | no | 99.991 |
metabolite utilization
| @ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
|---|---|---|---|---|
| 32592 | 22599 | arabinose | + | carbon source |
| 32592 | 28757 | fructose | + | carbon source |
| 32592 | 28260 | galactose | + | carbon source |
| 32592 | 17234 | glucose | + | carbon source |
| 32592 | 17716 | lactose | + | carbon source |
| 32592 | 17306 | maltose | + | carbon source |
| 32592 | 37684 | mannose | + | carbon source |
| 32592 | 16634 | raffinose | + | carbon source |
| 32592 | 26546 | rhamnose | + | carbon source |
| 32592 | 27082 | trehalose | + | carbon source |
| 32592 | 53426 | tween 80 | + | carbon source |
| 32592 | 18222 | xylose | + | carbon source |
| 32592 | 4853 | esculin | + | hydrolysis |
Isolation, sampling and environmental information
isolation
- @ref: 16714
- sample type: oil-contaminated soil
- geographic location: Mathura
- country: India
- origin.country: IND
- continent: Asia
isolation source categories
| Cat1 | Cat2 | Cat3 |
|---|---|---|
| #Engineered | #Contamination | #Oil (Fuel) |
| #Environmental | #Terrestrial | #Soil |
taxonmaps
- @ref: 69479
- File name: preview.99_2040.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_20;96_795;97_926;98_1256;99_2040&stattab=map
- Last taxonomy: Novosphingobium
- 16S sequence: EF424403
- Sequence Identity:
- Total samples: 4077
- soil counts: 623
- aquatic counts: 1963
- animal counts: 828
- plant counts: 663
Safety information
risk assessment
- @ref: 16714
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
- @ref: 16714
- description: Novosphingobium mathurense strain SM117 16S ribosomal RNA gene, partial sequence
- accession: EF424403
- length: 1381
- database: ena
- NCBI tax ID: 428990
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Novosphingobium mathurense SM117 | GCA_900168325 | scaffold | ncbi | 428990 |
| 66792 | Novosphingobium mathurense SM117 | 2706795032 | draft | img | 428990 |
Genome-based predictions
predictions
| trait | prediction | confidence | training_data |
|---|---|---|---|
| spore-forming | no | 100 | no |
| motile | yes | 65.219 | yes |
| flagellated | no | 82.638 | no |
| gram-positive | no | 97.647 | yes |
| anaerobic | no | 98.323 | yes |
| aerobic | yes | 88.407 | yes |
| halophile | no | 90.764 | no |
| spore-forming | no | 95.055 | yes |
| thermophile | no | 97.554 | yes |
| glucose-util | yes | 93.844 | yes |
| glucose-ferment | no | 91.098 | no |
External links
@ref: 16714
culture collection no.: DSM 23374, CCM 7473, MTCC 9020
literature
| topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
|---|---|---|---|---|---|---|---|---|
| Phylogeny | 19126741 | Novosphingobium panipatense sp. nov. and Novosphingobium mathurense sp. nov., from oil-contaminated soil. | Gupta SK, Lal D, Lal R | Int J Syst Evol Microbiol | 10.1099/ijs.0.65743-0 | 2009 | Bacterial Typing Techniques, DNA, Bacterial/analysis, DNA, Ribosomal/analysis, Fatty Acids/analysis, Genes, rRNA, Nucleic Acid Hybridization, *Oils, Phenotype, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, *Soil Pollutants, Species Specificity, Sphingomonadaceae/*classification/genetics/*isolation & purification/metabolism | Phenotype |
| Phylogeny | 23104365 | Novosphingobium lindaniclasticum sp. nov., a hexachlorocyclohexane (HCH)-degrading bacterium isolated from an HCH dumpsite. | Saxena A, Anand S, Dua A, Sangwan N, Khan F, Lal R | Int J Syst Evol Microbiol | 10.1099/ijs.0.045443-0 | 2012 | Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/analysis, *Hexachlorocyclohexane, India, Molecular Sequence Data, Nucleic Acid Hybridization, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, *Soil Pollutants, Spermidine/analysis, Sphingomonadaceae/*classification/genetics/isolation & purification, Ubiquinone/analogs & derivatives/analysis | Genetics |
| Phylogeny | 25985829 | Novosphingobium gossypii sp. nov., isolated from Gossypium hirsutum. | Kampfer P, Martin K, McInroy JA, Glaeser SP | Int J Syst Evol Microbiol | 10.1099/ijs.0.000339 | 2015 | Alabama, Bacterial Typing Techniques, DNA, Bacterial/genetics, Fatty Acids/chemistry, Gossypium/*microbiology, Molecular Sequence Data, Nucleic Acid Hybridization, Phospholipids, *Phylogeny, Pigmentation, Plant Stems/microbiology, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Spermidine/chemistry, Sphingomonadaceae/*classification/genetics/isolation & purification, Ubiquinone/chemistry | Genetics |
| Phylogeny | 27199143 | Novosphingobium naphthae sp. nov., from oil-contaminated soil. | Chaudhary DK, Kim J | Int J Syst Evol Microbiol | 10.1099/ijsem.0.001164 | 2016 | Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Nucleic Acid Hybridization, *Petroleum Pollution, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, Sequence Analysis, DNA, *Soil Microbiology, Soil Pollutants, Spermidine/chemistry, Sphingomonadaceae/*classification/genetics/isolation & purification, Ubiquinone/chemistry | Transcriptome |
| Phylogeny | 27664092 | Novosphingobium profundi sp. nov. isolated from a deep-sea seamount. | Zhang DC, Liu YX, Huang HJ | Antonie Van Leeuwenhoek | 10.1007/s10482-016-0769-3 | 2016 | Animals, Anthozoa/*microbiology, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/metabolism, Fatty Acids/chemistry/metabolism, Pacific Ocean, Phylogeny, RNA, Ribosomal, 16S/genetics, Seawater/*microbiology, Sphingomonadaceae/classification/genetics/*isolation & purification/metabolism | Metabolism |
| Phylogeny | 28741990 | Novosphingobium fontis sp. nov., isolated from a spring. | Sheu SY, Liu LP, Young CC, Chen WM | Int J Syst Evol Microbiol | 10.1099/ijsem.0.001973 | 2017 | Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Hydroxybutyrates/metabolism, Natural Springs/*microbiology, Nucleic Acid Hybridization, Phospholipids/chemistry, *Phylogeny, Polyesters/metabolism, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Spermidine/chemistry, Sphingomonadaceae/*classification/genetics/isolation & purification, Taiwan, Ubiquinone/chemistry | Metabolism |
| Phylogeny | 28866996 | Novosphingobium ipomoeae sp. nov., isolated from a water convolvulus field. | Chen WM, Huang CW, Chen JC, Chen ZH, Sheu SY | Int J Syst Evol Microbiol | 10.1099/ijsem.0.002174 | 2017 | Bacterial Typing Techniques, Base Composition, Convolvulus/*microbiology, DNA, Bacterial/genetics, Fatty Acids/chemistry, Nucleic Acid Hybridization, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Spermidine/chemistry, Sphingomonadaceae/*classification/genetics/isolation & purification, Taiwan, Ubiquinone/chemistry | Transcriptome |
| Phylogeny | 33034548 | Novosphingobium aquimarinum sp. nov., isolated from seawater. | Le VV, Ko SR, Lee SA, Jin L, Ahn CY, Oh HM | Int J Syst Evol Microbiol | 10.1099/ijsem.0.004493 | 2020 | Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, Seawater/*microbiology, Sequence Analysis, DNA, Sphingomonadaceae/*classification/isolation & purification, Ubiquinone/analogs & derivatives/chemistry | Transcriptome |
| Phylogeny | 34328829 | Novosphingobium aureum sp. nov., a marine bacterium isolated from salt flat sediment. | Yoo Y, Kim D, Lee H, Khim JS, Kim B, Yang D, Pathiraja D, Choi IG, Kim JJ | Int J Syst Evol Microbiol | 10.1099/ijsem.0.004930 | 2021 | Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, *Fatty Acids/chemistry, Phospholipids, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Sodium Chloride, Sphingomonadaceae, Ubiquinone | Transcriptome |
Reference
| @id | authors | catalogue | doi/url | title | ID_cross_reference | pubmed |
|---|---|---|---|---|---|---|
| 16714 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 23374) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-23374 | |||
| 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 | |||
| 32592 | 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 | 28805 | 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) | |||
| 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 |