Strain identifier
BacDive ID: 5505
Type strain:
Species: Dokdonia donghaensis
Strain Designation: DSW-1
Strain history: CIP <- 2006, KCTC <- JH Yoon, KRIBB: strain DSW-1
NCBI tax ID(s): 326320 (species)
General
@ref: 6810
BacDive-ID: 5505
DSM-Number: 17200
keywords: genome sequence, 16S sequence, Bacteria, aerobe, mesophilic, Gram-negative, rod-shaped
description: Dokdonia donghaensis DSW-1 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from sea water.
NCBI tax id
- NCBI tax id: 326320
- Matching level: species
strain history
@ref | history |
---|---|
6810 | <- J.-H. Yoon; DSW-1 |
67771 | <- JH Yoon, KRIBB |
118963 | CIP <- 2006, KCTC <- JH Yoon, KRIBB: strain DSW-1 |
doi: 10.13145/bacdive5505.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/bacteroidota
- domain: Bacteria
- phylum: Bacteroidota
- class: Flavobacteriia
- order: Flavobacteriales
- family: Flavobacteriaceae
- genus: Dokdonia
- species: Dokdonia donghaensis
- full scientific name: Dokdonia donghaensis Yoon et al. 2005
@ref: 6810
domain: Bacteria
phylum: Bacteroidetes
class: Flavobacteriia
order: Flavobacteriales
family: Flavobacteriaceae
genus: Dokdonia
species: Dokdonia donghaensis
full scientific name: Dokdonia donghaensis Yoon et al. 2005
strain designation: DSW-1
type strain: yes
Morphology
cell morphology
@ref | gram stain | cell length | cell width | cell shape | motility | confidence |
---|---|---|---|---|---|---|
31565 | negative | 13.25 µm | 0.45 µm | rod-shaped | no | |
67771 | rod-shaped | no | ||||
67771 | negative | |||||
69480 | negative | 99.996 | ||||
118963 | negative | rod-shaped | no |
pigmentation
- @ref: 31565
- production: yes
Culture and growth conditions
culture medium
@ref | name | growth | link | composition |
---|---|---|---|---|
6810 | BACTO MARINE BROTH (DIFCO 2216) (DSMZ Medium 514) | yes | https://mediadive.dsmz.de/medium/514 | Name: BACTO MARINE BROTH (DIFCO 2216) (DSMZ Medium 514) Composition: NaCl 19.45 g/l MgCl2 5.9 g/l Bacto peptone 5.0 g/l Na2SO4 3.24 g/l CaCl2 1.8 g/l Yeast extract 1.0 g/l KCl 0.55 g/l NaHCO3 0.16 g/l Fe(III) citrate 0.1 g/l KBr 0.08 g/l SrCl2 0.034 g/l H3BO3 0.022 g/l Na2HPO4 0.008 g/l Na-silicate 0.004 g/l NaF 0.0024 g/l (NH4)NO3 0.0016 g/l Distilled water |
118963 | CIP Medium 13 | yes | https://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=13 |
culture temp
@ref | growth | type | temperature | range |
---|---|---|---|---|
6810 | positive | growth | 30 | mesophilic |
31565 | positive | growth | 04-35 | |
31565 | positive | optimum | 30 | mesophilic |
67771 | positive | growth | 30 | mesophilic |
culture pH
@ref | ability | type | pH |
---|---|---|---|
31565 | positive | growth | 5.5-8.0 |
31565 | positive | optimum | 7.5 |
Physiology and metabolism
oxygen tolerance
@ref | oxygen tolerance |
---|---|
31565 | aerobe |
67771 | aerobe |
spore formation
@ref | spore formation | confidence |
---|---|---|
31565 | no | |
67771 | no | |
69481 | no | 100 |
69480 | no | 99.999 |
118963 | no |
halophily
@ref | salt | growth | tested relation | concentration |
---|---|---|---|---|
31565 | NaCl | positive | growth | <7 % |
31565 | NaCl | positive | optimum | 2 % |
observation
- @ref: 67771
- observation: quinones: MK-6
metabolite utilization
@ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
---|---|---|---|---|
31565 | 53424 | tween 20 | + | carbon source |
31565 | 53423 | tween 40 | + | carbon source |
31565 | 53426 | tween 80 | + | carbon source |
31565 | 4853 | esculin | + | hydrolysis |
118963 | 17632 | nitrate | - | reduction |
118963 | 16301 | nitrite | - | reduction |
metabolite production
- @ref: 118963
- Chebi-ID: 35581
- metabolite: indole
- production: no
enzymes
@ref | value | activity | ec |
---|---|---|---|
31565 | alkaline phosphatase | + | 3.1.3.1 |
31565 | catalase | + | 1.11.1.6 |
31565 | cytochrome oxidase | + | 1.9.3.1 |
68382 | alpha-fucosidase | - | 3.2.1.51 |
68382 | alpha-mannosidase | - | 3.2.1.24 |
68382 | N-acetyl-beta-glucosaminidase | + | 3.2.1.52 |
68382 | beta-glucosidase | - | 3.2.1.21 |
68382 | alpha-glucosidase | + | 3.2.1.20 |
68382 | beta-glucuronidase | - | 3.2.1.31 |
68382 | beta-galactosidase | - | 3.2.1.23 |
68382 | alpha-galactosidase | - | 3.2.1.22 |
68382 | naphthol-AS-BI-phosphohydrolase | + | |
68382 | acid phosphatase | + | 3.1.3.2 |
68382 | alpha-chymotrypsin | - | 3.4.21.1 |
68382 | trypsin | - | 3.4.21.4 |
68382 | cystine arylamidase | - | 3.4.11.3 |
68382 | valine arylamidase | + | |
68382 | leucine arylamidase | + | 3.4.11.1 |
68382 | lipase (C 14) | - | |
68382 | esterase lipase (C 8) | + | |
68382 | esterase (C 4) | + | |
68382 | alkaline phosphatase | + | 3.1.3.1 |
118963 | oxidase | + | |
118963 | catalase | + | 1.11.1.6 |
118963 | urease | - | 3.5.1.5 |
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 |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
118963 | - | + | + | + | - | + | + | - | - | - | + | + | - | - | - | + | - | + | - | - |
Isolation, sampling and environmental information
isolation
@ref | sample type | geographic location | country | origin.country | continent |
---|---|---|---|---|---|
6810 | sea water | Dokdo | Republic of Korea | KOR | Asia |
67771 | From seawater | Dokdo | Republic of Korea | KOR | Asia |
118963 | Environment, Sea water | Dokdo Island | Republic of Korea | KOR | Asia |
isolation source categories
- Cat1: #Environmental
- Cat2: #Aquatic
- Cat3: #Marine
taxonmaps
- @ref: 69479
- File name: preview.99_2807.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_52;96_277;97_306;98_2176;99_2807&stattab=map
- Last taxonomy: Dokdonia
- 16S sequence: DQ003276
- Sequence Identity:
- Total samples: 11394
- soil counts: 263
- aquatic counts: 10205
- animal counts: 829
- plant counts: 97
Safety information
risk assessment
@ref | biosafety level | biosafety level comment |
---|---|---|
6810 | 1 | Risk group (German classification) |
118963 | 1 | Risk group (French classification) |
Sequence information
16S sequences
- @ref: 6810
- description: Dokdonia donghaensis strain DSW-1 16S ribosomal RNA gene, partial sequence
- accession: DQ003276
- length: 1479
- database: ena
- NCBI tax ID: 326320
Genome sequences
@ref | description | accession | assembly level | database | NCBI tax ID |
---|---|---|---|---|---|
66792 | Dokdonia donghaensis DSW-1 | GCA_001653755 | complete | ncbi | 1300343 |
66792 | Dokdonia donghaensis DSW-1 | GCA_000769435 | scaffold | ncbi | 1300343 |
66792 | Dokdonia donghaensis DSW-1 | 1300343.5 | complete | patric | 1300343 |
66792 | Dokdonia donghaensis DSW-1 | 1300343.3 | wgs | patric | 1300343 |
66792 | Dokdonia donghaensis DSW-1 | 2627853639 | draft | img | 1300343 |
GC content
@ref | GC-content |
---|---|
6810 | 38 |
67771 | 38.0 |
Genome-based predictions
predictions
trait | prediction | confidence | training_data |
---|---|---|---|
spore-forming | no | 100 | no |
flagellated | no | 94.877 | yes |
gram-positive | no | 98.191 | yes |
anaerobic | no | 99.472 | no |
aerobic | yes | 92.505 | yes |
halophile | yes | 60.176 | yes |
spore-forming | no | 95.079 | yes |
glucose-util | yes | 85.906 | no |
motile | no | 88.888 | no |
thermophile | no | 99.147 | yes |
glucose-ferment | no | 90.201 | no |
External links
@ref: 6810
culture collection no.: DSM 17200, KCTC 12391, CIP 109306
straininfo link
- @ref: 74990
- straininfo: 361675
literature
topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
---|---|---|---|---|---|---|---|---|
Phylogeny | 16280490 | Dokdonia donghaensis gen. nov., sp. nov., isolated from sea water. | Yoon JH, Kang SJ, Lee CH, Oh TK | Int J Syst Evol Microbiol | 10.1099/ijs.0.63817-0 | 2005 | DNA, Bacterial/chemistry/isolation & purification, DNA, Ribosomal/chemistry/isolation & purification, Flavobacteriaceae/classification/cytology/*isolation & purification/physiology, Molecular Sequence Data, RNA, Ribosomal, 16S/analysis/genetics, Seawater/*microbiology, Sodium Chloride/pharmacology | Enzymology |
Phylogeny | 21984677 | Reclassification of the three species of the genus Krokinobacter into the genus Dokdonia as Dokdonia genika comb. nov., Dokdonia diaphoros comb. nov. and Dokdonia eikasta comb. nov., and emended description of the genus Dokdonia Yoon et al. 2005. | Yoon JH, Kang SJ, Park S, Oh TK | Int J Syst Evol Microbiol | 10.1099/ijs.0.035253-0 | 2011 | Bacterial Typing Techniques, DNA, Bacterial/genetics, Fatty Acids/analysis, Flavobacteriaceae/*classification/genetics, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Vitamin K 2/analogs & derivatives/analysis | Transcriptome |
Metabolism | 26574687 | Proteorhodopsin light-enhanced growth linked to vitamin-B1 acquisition in marine Flavobacteria. | Gomez-Consarnau L, Gonzalez JM, Riedel T, Jaenicke S, Wagner-Dobler I, Sanudo-Wilhelmy SA, Fuhrman JA | ISME J | 10.1038/ismej.2015.196 | 2015 | Flavobacteriaceae/*genetics/*metabolism, Gene Expression Regulation, Bacterial, Light, Phylogeny, Rhodopsins, Microbial/metabolism, Seawater/microbiology, Thiamine/*metabolism, Vitamins/metabolism | Phylogeny |
Genetics | 27491981 | Complete Genome Sequence of the Proteorhodopsin-Containing Marine Flavobacterium Dokdonia donghaensis DSW-1T, Isolated from Seawater off Dokdo in the East Sea (Sea of Korea). | Kim K, Kwon SK, Yoon JH, Kim JF | Genome Announc | 10.1128/genomeA.00804-16 | 2016 | Phylogeny | |
Phylogeny | 29570445 | Dokdonia aurantiaca sp. nov., isolated from seaweed Zostera marina. | Choi S, Kang JW, Kim MS, Yoon JH, Seong CN | Int J Syst Evol Microbiol | 10.1099/ijsem.0.002730 | 2018 | Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Flavobacteriaceae/*classification/genetics/isolation & purification, Nucleic Acid Hybridization, Phosphatidylethanolamines/chemistry, *Phylogeny, Pigmentation, RNA, Ribosomal, 16S/genetics, Republic of Korea, Seaweed/*microbiology, Sequence Analysis, DNA, Vitamin K 2/analogs & derivatives/chemistry, Zosteraceae/*microbiology | Transcriptome |
Phylogeny | 32228747 | Dokdonia sinensis sp. nov., a flavobacterium isolated from surface seawater. | Zhou LY, Meng X, Zhong YL, Li GY, Du ZJ, Mu DS | Int J Syst Evol Microbiol | 10.1099/ijsem.0.003949 | 2020 | Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Fatty Acids/chemistry, Flavobacteriaceae/classification, Flavobacterium/*classification/isolation & purification, Nucleic Acid Hybridization, Phosphatidylethanolamines/chemistry, *Phylogeny, Pigmentation, RNA, Ribosomal, 16S/genetics, Seawater/*microbiology, Sequence Analysis, DNA, Vitamin K 2/analogs & derivatives/chemistry, Water Microbiology | Transcriptome |
Reference
@id | authors | catalogue | doi/url | title | ID_cross_reference | pubmed |
---|---|---|---|---|---|---|
6810 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 17200) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-17200 | |||
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 | |||
31565 | 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 | 27855 | 28776041 | |
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 | ||||
68382 | Automatically annotated from API zym | |||||
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. | https://microbeatlas.org/ | MicrobeAtlas 1.0 beta | |||
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 | |||
74990 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID361675.1 | StrainInfo: A central database for resolving microbial strain identifiers | |||
118963 | Curators of the CIP | Collection of Institut Pasteur (CIP 109306) | https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20109306 |