Strain identifier
BacDive ID: 24015
Type strain: 
Species: Dokdonia sp.
Strain Designation: PR095
Strain history: <- T. Riedel, HZI, Braunschweig, Germany; PR095 <- T. Riedel and I. Wagner-Döbler
NCBI tax ID(s): 2024995 (species)
version 8.1 (current version)
General
@ref: 20530
BacDive-ID: 24015
DSM-Number: 26625
keywords: genome sequence, 16S sequence, Bacteria, Gram-negative
description: Dokdonia sp. PR095 is a Gram-negative bacterium that was isolated from surface water of North Sea.
NCBI tax id
- NCBI tax id: 2024995
- Matching level: species
strain history
- @ref: 20530
- history: <- T. Riedel, HZI, Braunschweig, Germany; PR095 <- T. Riedel and I. Wagner-Döbler
doi: 10.13145/bacdive24015.20230509.8.1
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 sp.
- full scientific name: Dokdonia Yoon et al. 2005
synonyms
- @ref: 20215
- synonym: Krokinobacter
@ref: 20530
domain: Bacteria
phylum: Bacteroidetes
class: Flavobacteriia
order: Flavobacteriales
family: Flavobacteriaceae
genus: Dokdonia
species: Dokdonia sp.
full scientific name: Dokdonia sp.
strain designation: PR095
type strain: no
Morphology
cell morphology
- @ref: 69480
- gram stain: negative
- confidence: 99.998
Culture and growth conditions
culture medium
- @ref: 20530
- name: BACTO MARINE BROTH (DIFCO 2216) (DSMZ Medium 514)
- growth: yes
- link: https://mediadive.dsmz.de/medium/514
- composition: 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
culture temp
- @ref: 20530
- growth: positive
- type: growth
- temperature: 10-30
Physiology and metabolism
spore formation
| @ref | spore formation | confidence |
|---|---|---|
| 69481 | no | 100 |
| 69480 | no | 99.999 |
Isolation, sampling and environmental information
isolation
- @ref: 20530
- sample type: surface water of North Sea
- country: Germany
- origin.country: DEU
- continent: Europe
isolation source categories
| Cat1 | Cat2 | Cat3 |
|---|---|---|
| #Environmental | #Aquatic | #Marine |
| #Environmental | #Aquatic | #Surface water |
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: FJ627052
- Sequence Identity:
- Total samples: 11394
- soil counts: 263
- aquatic counts: 10205
- animal counts: 829
- plant counts: 97
Sequence information
16S sequences
- @ref: 20530
- description: Dokdonia sp. PRO95 16S ribosomal RNA gene, partial sequence
- accession: FJ627052
- length: 1432
- database: ena
- NCBI tax ID: 1239415
Genome sequences
- @ref: 66792
- description: Dokdonia sp. PRO95
- accession: 1239415.5
- assembly level: complete
- database: patric
- NCBI tax ID: 1239415
Genome-based predictions
predictions
| trait | prediction | confidence | training_data |
|---|---|---|---|
| spore-forming | no | 100 | no |
| motile | no | 86.307 | no |
| gram-positive | no | 98.29 | no |
| anaerobic | no | 99.502 | no |
| aerobic | yes | 92.53 | no |
| halophile | yes | 57.786 | no |
| spore-forming | no | 94.275 | no |
| thermophile | no | 99.101 | no |
| glucose-util | yes | 86.913 | no |
| flagellated | no | 93.994 | no |
| glucose-ferment | no | 91.855 | no |
External links
@ref: 20530
culture collection no.: DSM 26625
straininfo link
- @ref: 87989
- straininfo: 402400
Reference
| @id | authors | title | doi/url | catalogue |
|---|---|---|---|---|
| 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 | |
| 20530 | Curators of the DSMZ | https://www.dsmz.de/collection/catalogue/details/culture/DSM-26625 | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 26625) | |
| 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 | |
| 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. | MicrobeAtlas 1.0 beta | https://microbeatlas.org/ | |
| 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 | |
| 87989 | 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-ID402400.1 |