Strain identifier
BacDive ID: 130668
Type strain: 
Species: Novosphingobium fluoreni
Strain Designation: HLJ-RS18
Strain history: <- S. Gao, China Agric. Univ., Beijing; HLJ-RS18
NCBI tax ID(s): 1391222 (species)
version 8.1 (current version)
General
@ref: 21704
BacDive-ID: 130668
DSM-Number: 27568
keywords: genome sequence, 16S sequence, Bacteria, mesophilic, Gram-negative
description: Novosphingobium fluoreni HLJ-RS18 is a mesophilic, Gram-negative bacterium that was isolated from rice seeds' surface.
NCBI tax id
- NCBI tax id: 1391222
- Matching level: species
strain history
- @ref: 21704
- history: <- S. Gao, China Agric. Univ., Beijing; HLJ-RS18
doi: 10.13145/bacdive130668.20230509.8.1
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 fluoreni
- full scientific name: Novosphingobium fluoreni Gao et al. 2015
@ref: 21704
domain: Bacteria
phylum: Proteobacteria
class: Alphaproteobacteria
order: Pseudomonadales
family: Erythrobacteraceae
genus: Novosphingobium
species: Novosphingobium fluoreni
full scientific name: Novosphingobium fluoreni Gao et al. 2015
strain designation: HLJ-RS18
type strain: yes
Morphology
cell morphology
- @ref: 69480
- gram stain: negative
- confidence: 99.976
multimedia
- @ref: 21704
- multimedia content: https://www.dsmz.de/microorganisms/photos/DSM_27568.jpg
- intellectual property rights: © Leibniz-Institut DSMZ
Culture and growth conditions
culture medium
- @ref: 21704
- name: LB (Luria-Bertani) MEDIUM (DSMZ Medium 381)
- growth: yes
- link: https://mediadive.dsmz.de/medium/381
- composition: Name: LB (Luria-Bertani) MEDIUM (DSMZ Medium 381) Composition: Agar 20.0 g/l NaCl 10.0 g/l Tryptone 10.0 g/l Yeast extract 5.0 g/l Distilled water
culture temp
- @ref: 21704
- growth: positive
- type: growth
- temperature: 28
- range: mesophilic
Physiology and metabolism
spore formation
| @ref | spore formation | confidence |
|---|---|---|
| 69481 | no | 100 |
| 69480 | no | 99.99 |
Isolation, sampling and environmental information
isolation
- @ref: 21704
- sample type: rice seeds' surface
- geographic location: Heilongjiang Province, Jiansanjiang
- country: China
- origin.country: CHN
- continent: Asia
isolation source categories
| Cat1 | Cat2 | Cat3 |
|---|---|---|
| #Host | #Plants | #Herbaceous plants (Grass,Crops) |
| #Host Body-Site | #Plant | #Fruit (Seed) |
taxonmaps
- @ref: 69479
- File name: preview.99_2160.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_20;96_795;97_1388;98_1686;99_2160&stattab=map
- Last taxonomy: Novosphingobium fluoreni
- 16S sequence: KF460450
- Sequence Identity:
- Total samples: 1098
- soil counts: 151
- aquatic counts: 162
- animal counts: 651
- plant counts: 134
Safety information
risk assessment
- @ref: 21704
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
- @ref: 21704
- description: Novosphingobium fluoreni strain HLJ-RS18 16S ribosomal RNA gene, partial sequence
- accession: KF460450
- length: 1450
- database: ena
- NCBI tax ID: 1391222
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Novosphingobium fluoreni DSM 27568 | GCA_014196615 | scaffold | ncbi | 1391222 |
| 66792 | Novosphingobium fluoreni strain DSM 27568 | 1391222.3 | wgs | patric | 1391222 |
| 66792 | Novosphingobium fluoreni DSM 27568 | 2829922874 | draft | img | 1391222 |
GC content
- @ref: 21704
- GC-content: 62
- method: thermal denaturation, midpoint method (Tm)
Genome-based predictions
predictions
| trait | prediction | confidence | training_data |
|---|---|---|---|
| spore-forming | no | 100 | no |
| flagellated | no | 92.328 | no |
| gram-positive | no | 97.429 | no |
| anaerobic | no | 97.61 | no |
| aerobic | yes | 88.969 | no |
| halophile | no | 97.375 | no |
| spore-forming | no | 93.938 | no |
| glucose-util | yes | 83.041 | no |
| thermophile | no | 99.09 | yes |
| motile | yes | 52.914 | no |
| glucose-ferment | no | 92.896 | no |
External links
@ref: 21704
culture collection no.: DSM 27568, ACCC 19180
straininfo link
- @ref: 89176
- straininfo: 401291
literature
- topic: Phylogeny
- Pubmed-ID: 25667393
- title: Novosphingobium fluoreni sp. nov., isolated from rice seeds.
- authors: Gao S, Zhang Y, Jiang N, Luo L, Li QX, Li J
- journal: Int J Syst Evol Microbiol
- DOI: 10.1099/ijs.0.000111
- year: 2015
- mesh: Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Fatty Acids/chemistry, Molecular Sequence Data, Nucleic Acid Hybridization, Oryza/*microbiology, Phospholipids/chemistry, *Phylogeny, Pigmentation, RNA, Ribosomal, 16S/genetics, Seeds/*microbiology, Sequence Analysis, DNA, Spermidine/chemistry, Sphingomonadaceae/*classification/genetics/isolation & purification, Ubiquinone/chemistry
- topic2: Genetics
Reference
| @id | authors | title | doi/url | catalogue |
|---|---|---|---|---|
| 20215 | Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M. | List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ | 10.1099/ijsem.0.004332 | |
| 21704 | Curators of the DSMZ | https://www.dsmz.de/collection/catalogue/details/culture/DSM-27568 | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 27568) | |
| 66792 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | Automatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) | https://diaspora-project.de/progress.html#genomes | |
| 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. | MicrobeAtlas 1.0 beta | https://microbeatlas.org/ | |
| 69480 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | Predictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) | https://diaspora-project.de/progress.html#genomes | |
| 69481 | Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch | Predictions based on the model GenomeNet Sporulation v. 1 | 10.21203/rs.3.rs-2527258/v1 | |
| 89176 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | StrainInfo: A central database for resolving microbial strain identifiers | 10.60712/SI-ID401291.1 |