Strain identifier
BacDive ID: 23265
Type strain: 
Species: Novosphingobium barchaimii
Strain Designation: LL02
Strain history: <- R. Lal, Univ. Delhi, Dept. Zoology, India; LL02 <- J. Damborsky, Masaryk Univ., Faculty of Science, Brno, Czech Republic
NCBI tax ID(s): 1420591 (species)
version 9.1 (current version)
General
@ref: 19229
BacDive-ID: 23265
DSM-Number: 25411
keywords: genome sequence, 16S sequence, Bacteria, aerobe, Gram-negative, rod-shaped
description: Novosphingobium barchaimii LL02 is an aerobe, Gram-negative, rod-shaped bacterium that was isolated from hexachlorocyclohexane contaminated soil besides lindane producing plant.
NCBI tax id
- NCBI tax id: 1420591
- Matching level: species
strain history
- @ref: 19229
- history: <- R. Lal, Univ. Delhi, Dept. Zoology, India; LL02 <- J. Damborsky, Masaryk Univ., Faculty of Science, Brno, Czech Republic
doi: 10.13145/bacdive23265.20240916.9.1
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 barchaimii
- full scientific name: Novosphingobium barchaimii Niharika et al. 2013
@ref: 19229
domain: Bacteria
phylum: Proteobacteria
class: Alphaproteobacteria
order: Sphingomonadales
family: Erythrobacteraceae
genus: Novosphingobium
species: Novosphingobium barchaimii
full scientific name: Novosphingobium barchaimii Niharika et al. 2013
strain designation: LL02
type strain: yes
Morphology
cell morphology
| @ref | gram stain | cell length | cell width | cell shape | motility | confidence |
|---|---|---|---|---|---|---|
| 30604 | negative | 1 µm | 1 µm | rod-shaped | no | |
| 69480 | negative | 95.797 |
pigmentation
- @ref: 30604
- production: yes
multimedia
- @ref: 19229
- multimedia content: https://www.dsmz.de/microorganisms/photos/DSM_25411.jpg
- intellectual property rights: © Leibniz-Institut DSMZ
Culture and growth conditions
culture medium
- @ref: 19229
- 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 |
|---|---|---|---|
| 19229 | positive | growth | 28 |
| 30604 | positive | growth | 28-37 |
| 30604 | positive | optimum | 28 |
culture pH
| @ref | ability | type | pH |
|---|---|---|---|
| 30604 | positive | growth | 05-07 |
| 30604 | positive | optimum | 7 |
Physiology and metabolism
oxygen tolerance
- @ref: 30604
- oxygen tolerance: aerobe
halophily
| @ref | salt | growth | tested relation | concentration |
|---|---|---|---|---|
| 30604 | NaCl | positive | growth | 0-3 % |
| 30604 | NaCl | positive | optimum | 1 % |
metabolite utilization
| @ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
|---|---|---|---|---|
| 30604 | 17234 | glucose | + | carbon source |
| 30604 | 26546 | rhamnose | + | carbon source |
| 30604 | 17992 | sucrose | + | carbon source |
| 30604 | 53424 | tween 20 | + | carbon source |
| 30604 | 4853 | esculin | + | hydrolysis |
| 30604 | 17632 | nitrate | + | reduction |
enzymes
| @ref | value | activity | ec |
|---|---|---|---|
| 30604 | gelatinase | + | |
| 30604 | urease | + | 3.5.1.5 |
Isolation, sampling and environmental information
isolation
- @ref: 19229
- 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_1591.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_20;96_795;97_926;98_1256;99_1591&stattab=map
- Last taxonomy: Novosphingobium barchaimii
- 16S sequence: JN695619
- Sequence Identity:
- Total samples: 600
- soil counts: 125
- aquatic counts: 120
- animal counts: 298
- plant counts: 57
Safety information
risk assessment
- @ref: 19229
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
- @ref: 19229
- description: Novosphingobium barchaimii LL02 16S ribosomal RNA gene, partial sequence
- accession: JN695619
- length: 1405
- database: nuccore
- NCBI tax ID: 1114963
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Novosphingobium barchaimii LL02 | GCA_001046635 | scaffold | ncbi | 1114963 |
| 66792 | Novosphingobium barchaimii LL02 | 1114963.3 | wgs | patric | 1114963 |
| 66792 | Novosphingobium barchaimii LL02 | 2654587500 | draft | img | 1114963 |
GC content
| @ref | GC-content | method |
|---|---|---|
| 19229 | 67.72 | fluorimetric |
| 30604 | 67.72 |
Genome-based predictions
predictions
| @ref | trait | model | description | prediction | confidence | training_data |
|---|---|---|---|---|---|---|
| 69480 | gram-positive | gram-positive | Positive reaction to Gram-staining | no | 95.797 | yes |
| 69480 | anaerobic | anaerobic | Ability to grow under anoxygenic conditions (including facultative anaerobes) | no | 95.187 | yes |
| 69480 | aerobic | aerobic | Ability to grow under oxygenic conditions (including facultative aerobes) | yes | 88.969 | no |
| 69480 | spore-forming | spore-forming | Ability to form endo- or exospores | no | 85.153 | no |
| 69480 | thermophilic | thermophile | Ability to grow at temperatures above or equal to 45°C | no | 97.885 | yes |
| 69480 | flagellated | motile2+ | Ability to perform flagellated movement | yes | 60.331 | no |
External links
@ref: 19229
culture collection no.: DSM 25411, CCM 7980
straininfo link
- @ref: 87488
- straininfo: 401713
literature
| topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
|---|---|---|---|---|---|---|---|---|
| Phylogeny | 22544801 | Novosphingobium barchaimii sp. nov., isolated from hexachlorocyclohexane-contaminated soil. | Niharika N, Moskalikova H, Kaur J, Sedlackova M, Hampl A, Damborsky J, Prokop Z, Lal R | Int J Syst Evol Microbiol | 10.1099/ijs.0.039826-0 | 2012 | Bacterial Typing Techniques, Base Composition, 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/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 | 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 |
Reference
| @id | authors | catalogue | doi/url | title | ID_cross_reference | pubmed | journal |
|---|---|---|---|---|---|---|---|
| 19229 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 25411) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-25411 | ||||
| 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 | ||||
| 30604 | 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 | 26935 | 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) | ||||
| 87488 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID401713.1 | StrainInfo: A central database for resolving microbial strain identifiers |