Strain identifier
BacDive ID: 130665
Type strain:
Species: Novosphingobium kunmingense
Strain Designation: 18-11HK
Strain history: <- F. Xie, Henan Key Laboratory of Microbial Eng., Zhengzhou, China; 18-11HK
NCBI tax ID(s): 1211806 (species)
General
@ref: 21701
BacDive-ID: 130665
DSM-Number: 25975
keywords: genome sequence, 16S sequence, Bacteria, mesophilic, Gram-negative
description: Novosphingobium kunmingense 18-11HK is a mesophilic, Gram-negative bacterium that was isolated from phosphate rock powder from a phosphate-mining field.
NCBI tax id
- NCBI tax id: 1211806
- Matching level: species
strain history
- @ref: 21701
- history: <- F. Xie, Henan Key Laboratory of Microbial Eng., Zhengzhou, China; 18-11HK
doi: 10.13145/bacdive130665.20230509.8.1
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 kunmingense
- full scientific name: Novosphingobium kunmingense Xie et al. 2014
@ref: 21701
domain: Bacteria
phylum: Proteobacteria
class: Alphaproteobacteria
order: Pseudomonadales
family: Erythrobacteraceae
genus: Novosphingobium
species: Novosphingobium kunmingense
full scientific name: Novosphingobium kunmingense Xie et al. 2014
strain designation: 18-11HK
type strain: yes
Morphology
cell morphology
- @ref: 69480
- gram stain: negative
- confidence: 99.946
multimedia
- @ref: 21701
- multimedia content: https://www.dsmz.de/microorganisms/photos/DSM_25975.jpg
- intellectual property rights: © Leibniz-Institut DSMZ
Culture and growth conditions
culture medium
- @ref: 21701
- name: NUTRIENT AGAR (DSMZ Medium 1)
- growth: yes
- link: https://mediadive.dsmz.de/medium/1
- composition: Name: NUTRIENT AGAR (DSMZ Medium 1) Composition: Agar 15.0 g/l Peptone 5.0 g/l Meat extract 3.0 g/l Distilled water
culture temp
- @ref: 21701
- growth: positive
- type: growth
- temperature: 28
- range: mesophilic
Physiology and metabolism
spore formation
@ref | spore formation | confidence |
---|---|---|
69481 | no | 100 |
69480 | no | 99.992 |
metabolite utilization
@ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
---|---|---|---|---|
68369 | 25115 | malate | - | assimilation |
68369 | 17128 | adipate | - | assimilation |
68369 | 27689 | decanoate | - | assimilation |
68369 | 24265 | gluconate | - | assimilation |
68369 | 17306 | maltose | - | assimilation |
68369 | 59640 | N-acetylglucosamine | - | assimilation |
68369 | 16899 | D-mannitol | - | assimilation |
68369 | 16024 | D-mannose | - | assimilation |
68369 | 30849 | L-arabinose | - | assimilation |
68369 | 17634 | D-glucose | - | assimilation |
68369 | 5291 | gelatin | - | hydrolysis |
68369 | 4853 | esculin | + | hydrolysis |
68369 | 16199 | urea | - | hydrolysis |
68369 | 29016 | arginine | - | hydrolysis |
68369 | 17634 | D-glucose | - | fermentation |
68369 | 27897 | tryptophan | - | energy source |
68369 | 17632 | nitrate | - | reduction |
metabolite production
- @ref: 68369
- Chebi-ID: 35581
- metabolite: indole
- production: no
metabolite tests
- @ref: 68369
- Chebi-ID: 35581
- metabolite: indole
- indole test: -
enzymes
@ref | value | activity | ec |
---|---|---|---|
68369 | cytochrome oxidase | + | 1.9.3.1 |
68369 | gelatinase | - | |
68369 | beta-glucosidase | + | 3.2.1.21 |
68369 | urease | - | 3.5.1.5 |
68369 | arginine dihydrolase | - | 3.5.3.6 |
API 20NE
@ref | NO3 | TRP | GLU_ Ferm | ADH Arg | URE | ESC | GEL | PNPG | GLU_ Assim | ARA | MNE | MAN | NAG | MAL | GNT | CAP | ADI | MLT | CIT | PAC | OX |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
21701 | - | - | - | - | - | + | - | - | - | - | - | - | - | - | - | - | - | - | - | - | + |
Isolation, sampling and environmental information
isolation
- @ref: 21701
- sample type: phosphate rock powder from a phosphate-mining field
- geographic location: Yunnan Province, suburb of Kunming
- country: China
- origin.country: CHN
- continent: Asia
isolation source categories
Cat1 | Cat2 | Cat3 |
---|---|---|
#Engineered | #Other | #Mine |
#Environmental | #Terrestrial | #Geologic |
Safety information
risk assessment
- @ref: 21701
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
- @ref: 21701
- description: Novosphingobium kunmingense strain 18-11HK 16S ribosomal RNA gene, partial sequence
- accession: JQ246446
- length: 1453
- database: ena
- NCBI tax ID: 1211806
Genome sequences
@ref | description | accession | assembly level | database | NCBI tax ID |
---|---|---|---|---|---|
66792 | Novosphingobium kunmingense CGMCC 1.12274 | GCA_002813245 | contig | ncbi | 1211806 |
66792 | Novosphingobium kunmingense strain CGMCC 1.12274 | 1211806.3 | wgs | patric | 1211806 |
66792 | Novosphingobium kunmingense CGMCC 1.12274 | 2718217687 | draft | img | 1211806 |
GC content
- @ref: 21701
- GC-content: 65.3
- method: thermal denaturation, midpoint method (Tm)
Genome-based predictions
predictions
trait | prediction | confidence | training_data |
---|---|---|---|
spore-forming | no | 100 | no |
motile | no | 94.025 | no |
gram-positive | no | 96.897 | no |
anaerobic | no | 99.218 | no |
aerobic | yes | 93.874 | no |
halophile | no | 95.459 | no |
spore-forming | no | 94.745 | no |
thermophile | no | 95.574 | no |
glucose-util | yes | 74.654 | yes |
flagellated | no | 97.955 | no |
glucose-ferment | no | 91.362 | yes |
External links
@ref: 21701
culture collection no.: DSM 25975, CGMCC 1.12274
straininfo link
- @ref: 89173
- straininfo: 398635
literature
topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
---|---|---|---|---|---|---|---|---|
Phylogeny | 24737793 | Novosphingobium kunmingense sp. nov., isolated from a phosphate mine. | Xie F, Quan S, Liu D, He W, Wang Y, Ma H, Chen G, Chao Y, Qian S | Int J Syst Evol Microbiol | 10.1099/ijs.0.057273-0 | 2014 | Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Fatty Acids/chemistry, *Mining, Molecular Sequence Data, Nucleic Acid Hybridization, Phosphates/*chemistry, *Phylogeny, Pigmentation, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, 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 |
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 | |||
21701 | Curators of the DSMZ | https://www.dsmz.de/collection/catalogue/details/culture/DSM-25975 | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 25975) | |||
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 | |
68369 | Automatically annotated from API 20NE | |||||
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 | |||
89173 | 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-ID398635.1 |