Strain identifier
BacDive ID: 14247
Type strain:
Species: Sphingomonas dokdonensis
Strain Designation: DS-4
Strain history: CIP <- 2005, J.H. Yoon, KRIBB, Taejon, South Korea: strain DS-4
NCBI tax ID(s): 344880 (species)
General
@ref: 15517
BacDive-ID: 14247
DSM-Number: 21029
keywords: genome sequence, 16S sequence, Bacteria, aerobe, mesophilic, Gram-negative
description: Sphingomonas dokdonensis DS-4 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from soil.
NCBI tax id
- NCBI tax id: 344880
- Matching level: species
strain history
@ref | history |
---|---|
15517 | <- KCTC <- J.-H. Yoon, Korea Res. Inst. Biosci. & Biotechnol. (KRIBB), Taejon, South Korea; DS-4 |
67771 | <- JH Yoon, KRIBB |
118956 | CIP <- 2005, J.H. Yoon, KRIBB, Taejon, South Korea: strain DS-4 |
doi: 10.13145/bacdive14247.20230509.8.1
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 dokdonensis
- full scientific name: Sphingomonas dokdonensis Yoon et al. 2006
@ref: 15517
domain: Bacteria
phylum: Proteobacteria
class: Alphaproteobacteria
order: Sphingomonadales
family: Sphingomonadaceae
genus: Sphingomonas
species: Sphingomonas dokdonensis
full scientific name: Sphingomonas dokdonensis Yoon et al. 2006
strain designation: DS-4
type strain: yes
Morphology
cell morphology
@ref | gram stain | confidence | cell shape | motility |
---|---|---|---|---|
67771 | negative | |||
69480 | negative | 99.97 | ||
118956 | negative | rod-shaped | yes |
colony morphology
- @ref: 118956
Culture and growth conditions
culture medium
@ref | name | growth | link | composition |
---|---|---|---|---|
15517 | 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 |
38338 | MEDIUM 72- for trypto casein soja agar | yes | Distilled water make up to (1000.000 ml);Trypto casein soy agar (40.000 g) | |
118956 | CIP Medium 72 | yes | https://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72 |
culture temp
@ref | growth | type | temperature | range |
---|---|---|---|---|
15517 | positive | growth | 25 | mesophilic |
38338 | positive | growth | 25 | mesophilic |
67771 | positive | growth | 25 | mesophilic |
Physiology and metabolism
oxygen tolerance
@ref | oxygen tolerance |
---|---|
67771 | aerobe |
118956 | obligate aerobe |
spore formation
- @ref: 69480
- spore formation: no
- confidence: 99.998
metabolite utilization
@ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
---|---|---|---|---|
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 |
118956 | 17632 | nitrate | - | reduction |
118956 | 16301 | nitrite | - | reduction |
metabolite production
@ref | Chebi-ID | metabolite | production |
---|---|---|---|
68369 | 35581 | indole | no |
118956 | 35581 | indole | 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 |
118956 | oxidase | - | |
118956 | alcohol dehydrogenase | - | 1.1.1.1 |
118956 | catalase | + | 1.11.1.6 |
118956 | lysine decarboxylase | - | 4.1.1.18 |
118956 | ornithine decarboxylase | - | 4.1.1.17 |
118956 | urease | - | 3.5.1.5 |
68382 | alkaline phosphatase | + | 3.1.3.1 |
68382 | esterase (C 4) | + | |
68382 | esterase lipase (C 8) | + | |
68382 | lipase (C 14) | - | |
68382 | leucine arylamidase | + | 3.4.11.1 |
68382 | valine arylamidase | + | |
68382 | cystine arylamidase | - | 3.4.11.3 |
68382 | trypsin | + | 3.4.21.4 |
68382 | alpha-chymotrypsin | + | 3.4.21.1 |
68382 | acid phosphatase | + | 3.1.3.2 |
68382 | naphthol-AS-BI-phosphohydrolase | + | |
68382 | alpha-galactosidase | - | 3.2.1.22 |
68382 | beta-galactosidase | - | 3.2.1.23 |
68382 | beta-glucuronidase | - | 3.2.1.31 |
68382 | alpha-glucosidase | - | 3.2.1.20 |
68382 | beta-glucosidase | - | 3.2.1.21 |
68382 | N-acetyl-beta-glucosaminidase | - | 3.2.1.52 |
68382 | alpha-mannosidase | - | 3.2.1.24 |
68382 | alpha-fucosidase | - | 3.2.1.51 |
API zym
@ref | Control | Alkaline phosphatase | Esterase | Esterase Lipase | Lipase | Leucine arylamidase | Valine arylamidase | Cystine arylamidase | Trypsin | alpha- Chymotrypsin | Acid phosphatase | Naphthol-AS-BI-phosphohydrolase | alpha- Galactosidase | beta- Galactosidase | beta- Glucuronidase | alpha- Glucosidase | beta- Glucosidase | N-acetyl-beta- glucosaminidase | alpha- Mannosidase | alpha- Fucosidase |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
118956 | - | + | + | + | - | + | + | - | + | + | + | + | - | - | - | - | - | - | - | - |
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 |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
15517 | - | - | - | - | - | + | + | - | + | - | + | - | - | - | - | - | + | +/- | - | - | - |
Isolation, sampling and environmental information
isolation
@ref | sample type | geographic location | country | origin.country | continent | isolation date |
---|---|---|---|---|---|---|
15517 | soil | Island Dokdo | Republic of Korea | KOR | Asia | |
67771 | From soil | Dokdo | Republic of Korea | KOR | Asia | |
118956 | Environment, Soil | Dokdo Island | Republic of Korea | KOR | Asia | 2004 |
isolation source categories
- Cat1: #Environmental
- Cat2: #Terrestrial
- Cat3: #Soil
Safety information
risk assessment
@ref | biosafety level | biosafety level comment |
---|---|---|
15517 | 1 | Risk group (German classification) |
118956 | 1 | Risk group (French classification) |
Sequence information
16S sequences
- @ref: 15517
- description: Sphingomonas dokdonensis strain DS-4 16S ribosomal RNA gene, partial sequence
- accession: DQ178975
- length: 1441
- database: ena
- NCBI tax ID: 344880
Genome sequences
@ref | description | accession | assembly level | database | NCBI tax ID |
---|---|---|---|---|---|
66792 | Sphingomonas dokdonensis DSM 21029 | GCA_002197685 | contig | ncbi | 344880 |
66792 | Sphingomonas dokdonensis strain DSM 21029 | 344880.4 | wgs | patric | 344880 |
66792 | Sphingomonas dokdonensis DSM 21029 | 2906672925 | draft | img | 344880 |
Genome-based predictions
predictions
trait | prediction | confidence | training_data |
---|---|---|---|
spore-forming | no | 83 | no |
gram-positive | no | 97.453 | yes |
anaerobic | no | 99.218 | yes |
halophile | no | 92.535 | no |
spore-forming | no | 96.201 | no |
glucose-util | yes | 84.241 | yes |
motile | yes | 68.278 | no |
flagellated | no | 90.502 | no |
thermophile | no | 98.808 | yes |
aerobic | yes | 93.949 | yes |
glucose-ferment | no | 92.023 | no |
External links
@ref: 15517
culture collection no.: DSM 21029, CIP 108841, KCTC 12541
straininfo link
- @ref: 83406
- straininfo: 297316
literature
topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
---|---|---|---|---|---|---|---|---|
Phylogeny | 16957115 | Sphingomonas dokdonensis sp. nov., isolated from soil. | Yoon JH, Lee MH, Kang SJ, Lee SY, Oh TK | Int J Syst Evol Microbiol | 10.1099/ijs.0.64114-0 | 2006 | Bacterial Typing Techniques, DNA, Bacterial/analysis, DNA, Ribosomal/analysis, Fatty Acids/*metabolism, Korea, Molecular Sequence Data, RNA, Ribosomal, 16S/*analysis, *Soil Microbiology, Sphingomonas/classification/genetics/*isolation & purification/metabolism | Metabolism |
Phylogeny | 17267979 | Sphingomonas molluscorum sp. nov., a novel marine isolate with antimicrobial activity. | Romanenko LA, Uchino M, Frolova GM, Tanaka N, Kalinovskaya NI, Latyshev N, Mikhailov VV | Int J Syst Evol Microbiol | 10.1099/ijs.0.64441-0 | 2007 | Aerobiosis, Animals, *Antibiosis, Arcidae/*microbiology, Bacterial Typing Techniques, Carbohydrate Metabolism, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis/chemistry, Genes, rRNA, Glycosphingolipids/analysis/chemistry, Gram-Positive Bacteria/drug effects, Japan, Molecular Sequence Data, Movement, Nucleic Acid Hybridization, Phylogeny, Pigments, Biological/biosynthesis, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sequence Homology, Nucleic Acid, Sphingomonas/*classification/cytology/*isolation & purification/physiology | Genetics |
Phylogeny | 19329595 | Sphingomonas sanxanigenens sp. nov., isolated from soil. | Huang HD, Wang W, Ma T, Li GQ, Liang FL, Liu RL | Int J Syst Evol Microbiol | 10.1099/ijs.0.000257-0 | 2009 | Bacterial Typing Techniques, Base Composition, Cluster Analysis, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis, Molecular Sequence Data, Phospholipids/analysis, Phylogeny, Polyamines/analysis, Quinones/analysis, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sequence Homology, Nucleic Acid, *Soil Microbiology, Sphingomonas/chemistry/*classification/genetics/*isolation & purification | Genetics |
Phylogeny | 19406815 | Sphingomonas japonica sp. nov., isolated from the marine crustacean Paralithodes camtschatica. | Romanenko LA, Tanaka N, Frolova GM, Mikhailov VV | Int J Syst Evol Microbiol | 10.1099/ijs.0.003285-0 | 2009 | Animals, Anomura/*microbiology, Bacterial Typing Techniques, DNA, Bacterial/analysis, DNA, Ribosomal/analysis, Fatty Acids/analysis, Genes, rRNA, Genotype, Molecular Sequence Data, Phenotype, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Species Specificity, Sphingomonas/*classification/genetics/isolation & purification/physiology | Genetics |
Phylogeny | 28792375 | Sphingomonas olei sp. nov., with the ability to degrade aliphatic hydrocarbons, isolated from oil-contaminated soil. | Chaudhary DK, Kim J | Int J Syst Evol Microbiol | 10.1099/ijsem.0.002010 | 2017 | Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Hydrocarbons/metabolism, Nepal, Nucleic Acid Hybridization, *Petroleum Pollution, Phospholipids/chemistry, *Phylogeny, Pigmentation, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Soil Pollutants, Sphingomonas/*classification/genetics/isolation & purification, Ubiquinone/chemistry | Transcriptome |
Phylogeny | 28853689 | Sphingomonas silvisoli sp. nov., isolated from forest soil. | Ko Y, Hwang WM, Kim M, Kang K, Ahn TY | Int J Syst Evol Microbiol | 10.1099/ijsem.0.002001 | 2017 | Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, *Forests, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, Sequence Analysis, DNA, *Soil Microbiology, Spermidine/analogs & derivatives/chemistry, Sphingomonas/*classification/genetics/isolation & purification, Ubiquinone/chemistry | Transcriptome |
Genetics | 28860249 | Draft Genome Sequences of Sphingomonas mucosissima DSM 17494 and Sphingomonas dokdonensis DSM 21029. | Poehlein A, Wubbeler JH, Daniel R, Steinbuchel A | Genome Announc | 10.1128/genomeA.00889-17 | 2017 | ||
Phylogeny | 31310195 | Sphingomonas flavalba sp. nov., isolated from a procymidone-contaminated soil. | Zhou XY, Zhang L, Su XJ, Hang P, Hu B, Jiang JD | Int J Syst Evol Microbiol | 10.1099/ijsem.0.003581 | 2019 | Bacterial Typing Techniques, Base Composition, *Bridged Bicyclo Compounds, China, DNA, Bacterial/genetics, Fatty Acids/chemistry, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, *Soil Pollutants, Spermidine/analogs & derivatives/chemistry, Sphingomonas/*classification/isolation & purification, Ubiquinone/chemistry | Transcriptome |
Reference
@id | authors | catalogue | doi/url | title |
---|---|---|---|---|
15517 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 21029) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-21029 | |
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 | |
38338 | Curators of the CIP | https://brclims.pasteur.fr/brcWeb/souche/detail/1/6515 | ||
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) | |
67771 | Curators of the KCTC | https://kctc.kribb.re.kr/En/Kctc | ||
68369 | Automatically annotated from API 20NE | |||
68382 | Automatically annotated from API zym | |||
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) | |
83406 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID297316.1 | StrainInfo: A central database for resolving microbial strain identifiers | |
118956 | Curators of the CIP | Collection of Institut Pasteur (CIP 108841) | https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20108841 |