Strain identifier
BacDive ID: 24563
Type strain: 
Species: Sphingomonas guangdongensis
Strain Designation: 9NM-8
Strain history: <- G.-D. Feng, Guangdong Inst. Microbiology, Guangdong Academy Sci., China; 9NM-8
NCBI tax ID(s): 1141890 (species)
version 8.1 (current version)
General
@ref: 20820
BacDive-ID: 24563
DSM-Number: 27570
keywords: genome sequence, 16S sequence, Bacteria, mesophilic, Gram-negative
description: Sphingomonas guangdongensis 9NM-8 is a mesophilic, Gram-negative bacterium that was isolated from abandoned lead-zinc ore.
NCBI tax id
- NCBI tax id: 1141890
- Matching level: species
strain history
- @ref: 20820
- history: <- G.-D. Feng, Guangdong Inst. Microbiology, Guangdong Academy Sci., China; 9NM-8
doi: 10.13145/bacdive24563.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/pseudomonadota
- domain: Bacteria
- phylum: Pseudomonadota
- class: Alphaproteobacteria
- order: Sphingomonadales
- family: Sphingomonadaceae
- genus: Sphingomonas
- species: Sphingomonas guangdongensis
- full scientific name: Sphingomonas guangdongensis Feng et al. 2014
@ref: 20820
domain: Bacteria
phylum: Proteobacteria
class: Alphaproteobacteria
order: Pseudomonadales
family: Sphingomonadaceae
genus: Sphingomonas
species: Sphingomonas guangdongensis
full scientific name: Sphingomonas guangdongensis Feng et al. 2014
strain designation: 9NM-8
type strain: yes
Morphology
cell morphology
- @ref: 69480
- gram stain: negative
- confidence: 99.975
multimedia
- @ref: 20820
- multimedia content: https://www.dsmz.de/microorganisms/photos/DSM_27570.jpg
- intellectual property rights: © Leibniz-Institut DSMZ
Culture and growth conditions
culture medium
- @ref: 20820
- name: R2A MEDIUM (DSMZ Medium 830)
- growth: yes
- link: https://mediadive.dsmz.de/medium/830
- composition: Name: R2A MEDIUM (DSMZ Medium 830) Composition: Agar 15.0 g/l Casamino acids 0.5 g/l Starch 0.5 g/l Glucose 0.5 g/l Proteose peptone 0.5 g/l Yeast extract 0.5 g/l K2HPO4 0.3 g/l Na-pyruvate 0.3 g/l MgSO4 x 7 H2O 0.05 g/l Distilled water
culture temp
- @ref: 20820
- growth: positive
- type: growth
- temperature: 28
- range: mesophilic
Physiology and metabolism
spore formation
| @ref | spore formation | confidence |
|---|---|---|
| 69481 | no | 98 |
| 69480 | no | 99.977 |
Isolation, sampling and environmental information
isolation
- @ref: 20820
- sample type: abandoned lead-zinc ore
- geographic location: Guangdong Province, Meizhou, mining area in Mei county
- country: China
- origin.country: CHN
- continent: Asia
- latitude: 24.3622
- longitude: 116.276
isolation source categories
| Cat1 | Cat2 | Cat3 |
|---|---|---|
| #Engineered | #Other | #Mine |
| #Environmental | #Terrestrial |
Safety information
risk assessment
- @ref: 20820
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
- @ref: 20820
- description: Sphingomonas guangdongensis strain 9NM-8 16S ribosomal RNA gene, partial sequence
- accession: JQ608326
- length: 1436
- database: ena
- NCBI tax ID: 1141890
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Sphingomonas guangdongensis CGMCC 1.12672 | GCA_900199185 | contig | ncbi | 1141890 |
| 66792 | Sphingomonas guangdongensis strain CGMCC 1.12672 | 1141890.3 | wgs | patric | 1141890 |
| 66792 | Sphingomonas guangdongensis CGMCC 1.12672 | 2718218511 | draft | img | 1141890 |
GC content
- @ref: 20820
- GC-content: 69.6
- method: high performance liquid chromatography (HPLC)
Genome-based predictions
predictions
| trait | prediction | confidence | training_data |
|---|---|---|---|
| spore-forming | no | 98 | no |
| motile | yes | 74.87 | no |
| flagellated | no | 87.619 | no |
| gram-positive | no | 96.905 | no |
| anaerobic | no | 99.294 | no |
| aerobic | yes | 94.829 | no |
| halophile | no | 95.504 | no |
| spore-forming | no | 95.65 | no |
| thermophile | no | 97.471 | yes |
| glucose-util | yes | 82.678 | no |
| glucose-ferment | no | 90.995 | no |
External links
@ref: 20820
culture collection no.: DSM 27570, CGMCC 1.12672, GIMCC 1.653
straininfo link
- @ref: 88417
- straininfo: 400610
literature
- topic: Phylogeny
- Pubmed-ID: 24523446
- title: Description of a Gram-negative bacterium, Sphingomonas guangdongensis sp. nov.
- authors: Feng GD, Yang SZ, Wang YH, Zhang XX, Zhao GZ, Deng MR, Zhu HH
- journal: Int J Syst Evol Microbiol
- DOI: 10.1099/ijs.0.056853-0
- year: 2014
- mesh: Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Fatty Acids/chemistry, Glycolipids/chemistry, Mining, Molecular Sequence Data, Phospholipids/chemistry, *Phylogeny, Pigmentation, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Spermidine/analogs & derivatives/chemistry, Sphingomonas/*classification/genetics/isolation & purification, Ubiquinone/chemistry
- topic2: Genetics
Reference
| @id | authors | title | doi/url | catalogue | journal | pubmed |
|---|---|---|---|---|---|---|
| 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 | |||
| 20820 | Curators of the DSMZ | https://www.dsmz.de/collection/catalogue/details/culture/DSM-27570 | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 27570) | |||
| 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 | |||
| 66794 | Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg | BRENDA, the ELIXIR core data resource in 2021: new developments and updates | 10.1093/nar/gkaa1025 | Nucleic Acids Res. 49: D498-D508 2020 | 33211880 | |
| 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 | |||
| 88417 | 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-ID400610.1 |