Strain identifier
BacDive ID: 132281
Type strain: 
Species: Donghicola tyrosinivorans
Strain Designation: 13-93-B1
Strain history: <- K.-S. Shin, KRIBB <- H.-R. Sung; 13-93-B1
NCBI tax ID(s): 1652492 (species)
version 8.1 (current version)
General
@ref: 24070
BacDive-ID: 132281
DSM-Number: 100212
keywords: genome sequence, 16S sequence, Bacteria, mesophilic, Gram-negative
description: Donghicola tyrosinivorans 13-93-B1 is a mesophilic, Gram-negative bacterium that was isolated from surface seawater.
NCBI tax id
- NCBI tax id: 1652492
- Matching level: species
strain history
- @ref: 24070
- history: <- K.-S. Shin, KRIBB <- H.-R. Sung; 13-93-B1
doi: 10.13145/bacdive132281.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/pseudomonadota
- domain: Bacteria
- phylum: Pseudomonadota
- class: Alphaproteobacteria
- order: Rhodobacterales
- family: Roseobacteraceae
- genus: Donghicola
- species: Donghicola tyrosinivorans
- full scientific name: Donghicola tyrosinivorans Sung et al. 2015
@ref: 24070
domain: Bacteria
phylum: Proteobacteria
class: Alphaproteobacteria
order: Rhodobacterales
family: Rhodobacteraceae
genus: Donghicola
species: Donghicola tyrosinivorans
full scientific name: Donghicola tyrosinivorans Sung et al. 2015
strain designation: 13-93-B1
type strain: yes
Morphology
cell morphology
- @ref: 69480
- gram stain: negative
- confidence: 99.999
Culture and growth conditions
culture medium
- @ref: 24070
- 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: 24070
- growth: positive
- type: growth
- temperature: 30
- range: mesophilic
Physiology and metabolism
spore formation
| @ref | spore formation | confidence |
|---|---|---|
| 69481 | no | 100 |
| 69480 | no | 99.967 |
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 | 16024 | D-mannose | + | 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 | 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 |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 24070 | - | - | - | - | - | + | - | - | + | +/- | + | +/- | - | + | - | - | - | - | - | - |
Isolation, sampling and environmental information
isolation
- @ref: 24070
- sample type: surface seawater
- geographic location: Jeju Island, adjacent to Seogwipo-si
- country: Republic of Korea
- origin.country: KOR
- continent: Asia
isolation source categories
| Cat1 | Cat2 | Cat3 |
|---|---|---|
| #Environmental | #Aquatic | #Marine |
| #Environmental | #Aquatic | #Surface water |
taxonmaps
- @ref: 69479
- File name: preview.99_170530.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_19;96_11109;97_82479;98_111737;99_170530&stattab=map
- Last taxonomy: Donghicola tyrosinivorans subclade
- 16S sequence: KP901250
- Sequence Identity:
- Total samples: 1652
- soil counts: 18
- aquatic counts: 1427
- animal counts: 201
- plant counts: 6
Safety information
risk assessment
- @ref: 24070
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
- @ref: 24070
- description: Donghicola tyrosinivorans strain 13-93-B1 16S ribosomal RNA gene, partial sequence
- accession: KP901250
- length: 1403
- database: ena
- NCBI tax ID: 1652492
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Donghicola tyrosinivorans DSM 100212 | GCA_003003355 | scaffold | ncbi | 1652492 |
| 66792 | Donghicola tyrosinivorans strain DSM 100212 | 1652492.3 | wgs | patric | 1652492 |
| 66792 | Donghicola tyrosinivorans DSM 100212 | 2731639258 | draft | img | 1652492 |
GC content
- @ref: 24070
- GC-content: 60.4
- method: high performance liquid chromatography (HPLC)
Genome-based predictions
predictions
| trait | prediction | confidence | training_data |
|---|---|---|---|
| spore-forming | no | 100 | no |
| flagellated | no | 66.479 | no |
| gram-positive | no | 98.889 | no |
| anaerobic | no | 97.492 | no |
| halophile | yes | 56.199 | no |
| spore-forming | no | 96.752 | no |
| glucose-util | yes | 91.813 | yes |
| aerobic | yes | 85.613 | no |
| thermophile | no | 97.058 | yes |
| motile | yes | 74.462 | no |
| glucose-ferment | no | 89.943 | yes |
External links
@ref: 24070
culture collection no.: DSM 100212, KCTC 42571
straininfo link
- @ref: 90628
- straininfo: 407562
literature
| topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
|---|---|---|---|---|---|---|---|---|
| Phylogeny | 26311168 | Donghicola tyrosinivorans sp. nov., a tyrosine-degrading bacterium isolated from seawater. | Sung HR, Lee JM, Kim M, Yun BR, Shin KS | Int J Syst Evol Microbiol | 10.1099/ijsem.0.000543 | 2015 | Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Nucleic Acid Hybridization, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, Rhodobacteraceae/*classification/genetics/isolation & purification, Seawater/*microbiology, Sequence Analysis, DNA, Tyrosine/metabolism, Ubiquinone/chemistry | Transcriptome |
| Phylogeny | 33263508 | Donghicola mangrovi sp. nov., a member of the family Rhodobacteraceae isolated from mangrove forest in Thailand. | Charoenyingcharoen P, Kim JS, Theeragool G, Lee KC, Yukphan P, Lee JS | Int J Syst Evol Microbiol | 10.1099/ijsem.0.004570 | 2020 | Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Nucleic Acid Hybridization, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Rhodobacteraceae/*classification/isolation & purification, Sequence Analysis, DNA, Thailand, Ubiquinone/analogs & derivatives/chemistry, *Wetlands | 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 | |||
| 24070 | Curators of the DSMZ | https://www.dsmz.de/collection/catalogue/details/culture/DSM-100212 | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 100212) | |||
| 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 | |||||
| 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 | |||
| 90628 | 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-ID407562.1 |