Strain identifier
BacDive ID: 14257
Type strain:
Species: Sphingomonas insulae
Strain Designation: DS-28
Strain history: CIP <- 2012, JCM <- 2007, J.H. Yoon: strain DS-28
NCBI tax ID(s): 424800 (species)
General
@ref: 15956
BacDive-ID: 14257
DSM-Number: 21792
keywords: genome sequence, 16S sequence, Bacteria, aerobe, mesophilic, Gram-negative, motile, rod-shaped
description: Sphingomonas insulae DS-28 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from soil.
NCBI tax id
- NCBI tax id: 424800
- Matching level: species
strain history
@ref | history |
---|---|
15956 | <- KCTC <- J.-H. Yoon, KRIBB |
67770 | J.-H. Yoon DS-28. |
67771 | <- JH Yoon, KRIBB |
120141 | CIP <- 2012, JCM <- 2007, J.H. Yoon: strain DS-28 |
doi: 10.13145/bacdive14257.20230509.8.1
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 insulae
- full scientific name: Sphingomonas insulae Yoon et al. 2008
@ref: 15956
domain: Bacteria
phylum: Proteobacteria
class: Alphaproteobacteria
order: Sphingomonadales
family: Sphingomonadaceae
genus: Sphingomonas
species: Sphingomonas insulae
full scientific name: Sphingomonas insulae Yoon et al. 2008
strain designation: DS-28
type strain: yes
Morphology
cell morphology
@ref | gram stain | cell length | cell width | cell shape | motility | confidence |
---|---|---|---|---|---|---|
32175 | negative | 3 µm | 0.45 µm | rod-shaped | yes | |
67771 | negative | |||||
69480 | negative | 99.966 | ||||
120141 | negative | rod-shaped | yes |
pigmentation
- @ref: 32175
- production: yes
Culture and growth conditions
culture medium
@ref | name | growth | link | composition |
---|---|---|---|---|
15956 | NUTRIENT AGAR (DSMZ Medium 1) | yes | https://mediadive.dsmz.de/medium/1 | 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 |
36905 | MEDIUM 328- for nutrient agar | yes | Distilled water make up to (1000.000 ml);Agar (15.000 g);Peptone (5.000g);Beef extract (3.000 g) | |
120141 | CIP Medium 328 | yes | https://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=328 |
culture temp
@ref | growth | type | temperature | range |
---|---|---|---|---|
15956 | positive | growth | 28 | mesophilic |
32175 | positive | growth | 04-34 | |
32175 | positive | optimum | 25 | mesophilic |
36905 | positive | growth | 25 | mesophilic |
67770 | positive | growth | 25 | mesophilic |
67771 | positive | growth | 25 | mesophilic |
culture pH
@ref | ability | type | pH | PH range |
---|---|---|---|---|
32175 | positive | growth | 5-8.5 | alkaliphile |
32175 | positive | optimum | 6.5 |
Physiology and metabolism
oxygen tolerance
@ref | oxygen tolerance |
---|---|
32175 | aerobe |
67771 | aerobe |
spore formation
@ref | spore formation | confidence |
---|---|---|
69481 | no | 96 |
69480 | no | 99.988 |
halophily
@ref | salt | growth | tested relation | concentration |
---|---|---|---|---|
32175 | NaCl | positive | growth | 0-2 % |
32175 | NaCl | positive | optimum | 0.25 % |
observation
- @ref: 67770
- observation: quinones: Q-10
metabolite utilization
@ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
---|---|---|---|---|
32175 | 22599 | arabinose | + | carbon source |
32175 | 17057 | cellobiose | + | carbon source |
32175 | 16947 | citrate | + | carbon source |
32175 | 28757 | fructose | + | carbon source |
32175 | 28260 | galactose | + | carbon source |
32175 | 17234 | glucose | + | carbon source |
32175 | 17754 | glycerol | + | carbon source |
32175 | 25115 | malate | + | carbon source |
32175 | 17306 | maltose | + | carbon source |
32175 | 37684 | mannose | + | carbon source |
32175 | 28053 | melibiose | + | carbon source |
32175 | 506227 | N-acetylglucosamine | + | carbon source |
32175 | 16634 | raffinose | + | carbon source |
32175 | 26546 | rhamnose | + | carbon source |
32175 | 17814 | salicin | + | carbon source |
32175 | 17992 | sucrose | + | carbon source |
32175 | 27082 | trehalose | + | carbon source |
32175 | 18222 | xylose | + | carbon source |
32175 | 4853 | esculin | + | hydrolysis |
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 |
---|---|---|---|
32175 | acid phosphatase | + | 3.1.3.2 |
32175 | alkaline phosphatase | + | 3.1.3.1 |
32175 | catalase | + | 1.11.1.6 |
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 |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
15956 | - | - | - | - | - | + | - | + | + | + | + | - | + | - | - | - | - | + | + | - | + |
Isolation, sampling and environmental information
isolation
@ref | sample type | geographic location | country | origin.country | continent |
---|---|---|---|---|---|
15956 | soil | Dokdo | Republic of Korea | KOR | Asia |
67770 | Soil | ||||
67771 | From soil | Dokdo | Republic of Korea | KOR | Asia |
120141 | Environment, Soil |
isolation source categories
- Cat1: #Environmental
- Cat2: #Terrestrial
- Cat3: #Soil
Safety information
risk assessment
@ref | biosafety level | biosafety level comment |
---|---|---|
15956 | 1 | Risk group (German classification) |
120141 | 1 | Risk group (French classification) |
Sequence information
16S sequences
- @ref: 15956
- description: Sphingomonas insulae strain DS-28 16S ribosomal RNA gene, partial sequence
- accession: EF363714
- length: 1447
- database: ena
- NCBI tax ID: 424800
Genome sequences
@ref | description | accession | assembly level | database | NCBI tax ID |
---|---|---|---|---|---|
66792 | Sphingomonas insulae KCTC 12872 | GCA_010450875 | complete | ncbi | 424800 |
66792 | Sphingomonas insulae strain DSM 21792 | 424800.4 | wgs | patric | 424800 |
66792 | Sphingomonas insulae strain KCTC 12872 | 424800.3 | complete | patric | 424800 |
66792 | Sphingomonas insulae DSM 21792 | 2828333980 | draft | img | 424800 |
67770 | Sphingomonas insulae DSM 21792 | GCA_011762035 | scaffold | ncbi | 424800 |
GC content
@ref | GC-content | method |
---|---|---|
32175 | 67 | |
67770 | 67 | high performance liquid chromatography (HPLC) |
Genome-based predictions
predictions
trait | prediction | confidence | training_data |
---|---|---|---|
spore-forming | no | 96 | no |
motile | yes | 81.383 | yes |
flagellated | no | 85.68 | no |
gram-positive | no | 97.091 | yes |
anaerobic | no | 99.347 | yes |
aerobic | yes | 94.717 | no |
halophile | no | 93.46 | yes |
spore-forming | no | 94.755 | no |
glucose-util | yes | 92.509 | no |
thermophile | no | 99.028 | yes |
glucose-ferment | no | 91.332 | no |
External links
@ref: 15956
culture collection no.: DSM 21792, JCM 14603, KCTC 12872, CIP 110394
straininfo link
- @ref: 83416
- straininfo: 323998
literature
topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
---|---|---|---|---|---|---|---|---|
Phylogeny | 18175714 | Sphingomonas insulae sp. nov., isolated from soil. | Yoon JH, Kang SJ, Lee SY, Oh TK | Int J Syst Evol Microbiol | 10.1099/ijs.0.65075-0 | 2008 | Bacterial Typing Techniques, Base Composition, DNA, Bacterial/analysis, Genes, rRNA, Korea, Molecular Sequence Data, Nucleic Acid Hybridization, Phenotype, Phylogeny, RNA, Ribosomal, 16S, Sequence Analysis, DNA, *Soil Microbiology, Species Specificity, Sphingomonas/*classification/genetics/*isolation & purification | Genetics |
Phylogeny | 22328613 | Sphingomonas cynarae sp. nov., a proteobacterium that produces an unusual type of sphingan. | Tala A, Lenucci M, Gaballo A, Durante M, Tredici SM, Debowles DA, Pizzolante G, Marcuccio C, Carata E, Piro G, Carpita NC, Mita G, Alifano P | Int J Syst Evol Microbiol | 10.1099/ijs.0.032060-0 | 2012 | Bacterial Typing Techniques, Base Composition, Cynara/*microbiology, DNA, Bacterial/genetics, Fatty Acids/analysis, Molecular Sequence Data, Nucleic Acid Hybridization, *Phylogeny, Polyamines/analysis, Polysaccharides, Bacterial/*biosynthesis, RNA, Ribosomal, 16S/genetics, Sphingomonas/*classification/genetics/isolation & purification, Ubiquinone/analysis | Genetics |
Reference
@id | authors | catalogue | doi/url | title | ID_cross_reference | pubmed |
---|---|---|---|---|---|---|
15956 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 21792) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-21792 | |||
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 | |||
32175 | 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 | 28417 | 28776041 | |
36905 | Curators of the CIP | https://brclims.pasteur.fr/brcWeb/souche/detail/1/8249 | ||||
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) | |||
67770 | Curators of the JCM | https://jcm.brc.riken.jp/en/ | ||||
67771 | Curators of the KCTC | https://kctc.kribb.re.kr/En/Kctc | ||||
68369 | Automatically annotated from API 20NE | |||||
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 | |||
83416 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID323998.1 | StrainInfo: A central database for resolving microbial strain identifiers | |||
120141 | Curators of the CIP | Collection of Institut Pasteur (CIP 110394) | https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20110394 |