Strain identifier
BacDive ID: 23225
Type strain:
Species: Yoonia tamlensis
Strain Designation: SSW-35
Strain history: <- SD Lee, Cheju Univ.
NCBI tax ID(s): 390270 (species)
General
@ref: 19133
BacDive-ID: 23225
DSM-Number: 26879
keywords: genome sequence, 16S sequence, Bacteria, aerobe, mesophilic, Gram-negative, motile, rod-shaped
description: Yoonia tamlensis SSW-35 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from seawater.
NCBI tax id
- NCBI tax id: 390270
- Matching level: species
strain history
@ref | history |
---|---|
19133 | <- JCM <- S. D. Lee; SSW-35 |
67770 | S. D. Lee SSW-35. |
67771 | <- SD Lee, Cheju Univ. |
doi: 10.13145/bacdive23225.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/pseudomonadota
- domain: Bacteria
- phylum: Pseudomonadota
- class: Alphaproteobacteria
- order: Rhodobacterales
- family: Roseobacteraceae
- genus: Yoonia
- species: Yoonia tamlensis
- full scientific name: Yoonia tamlensis (Lee 2012) Wirth and Whitman 2018
synonyms
- @ref: 20215
- synonym: Loktanella tamlensis
@ref: 19133
domain: Bacteria
phylum: Proteobacteria
class: Alphaproteobacteria
order: Rhodobacterales
family: Rhodobacteraceae
genus: Yoonia
species: Yoonia tamlensis
full scientific name: Yoonia tamlensis (Lee 2012) Wirth and Whitman 2018
strain designation: SSW-35
type strain: yes
Morphology
cell morphology
@ref | gram stain | cell length | cell width | cell shape | motility | confidence |
---|---|---|---|---|---|---|
30106 | negative | 1.1-1.7 µm | 0.7 µm | rod-shaped | yes | |
67771 | negative | |||||
69480 | negative | 99.993 |
colony morphology
- @ref: 19133
- incubation period: 2-3 days
pigmentation
- @ref: 30106
- production: no
Culture and growth conditions
culture medium
- @ref: 19133
- 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 | growth | type | temperature | range |
---|---|---|---|---|
19133 | positive | growth | 30 | mesophilic |
30106 | positive | growth | 4-30 | |
30106 | positive | optimum | 25-30 | mesophilic |
67770 | positive | growth | 30 | mesophilic |
67771 | positive | growth | 30 | mesophilic |
culture pH
@ref | ability | type | pH | PH range |
---|---|---|---|---|
30106 | positive | growth | 07-10 | alkaliphile |
30106 | positive | optimum | 07-08 |
Physiology and metabolism
oxygen tolerance
@ref | oxygen tolerance |
---|---|
30106 | aerobe |
67771 | aerobe |
spore formation
@ref | spore formation | confidence |
---|---|---|
30106 | no | |
69481 | no | 100 |
69480 | no | 99.999 |
halophily
- @ref: 30106
- salt: NaCl
- growth: positive
- tested relation: growth
- concentration: 1-6 %
observation
- @ref: 67770
- observation: quinones: Q-10
metabolite utilization
@ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
---|---|---|---|---|
30106 | 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 | 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 | Chebi-ID | metabolite | production |
---|---|---|---|
30106 | 16136 | hydrogen sulfide | yes |
68369 | 35581 | indole | no |
metabolite tests
- @ref: 68369
- Chebi-ID: 35581
- metabolite: indole
- indole test: -
enzymes
@ref | value | activity | ec |
---|---|---|---|
19133 | catalase | + | 1.11.1.6 |
19133 | cytochrome-c oxidase | + | 1.9.3.1 |
30106 | acid phosphatase | + | 3.1.3.2 |
30106 | alkaline phosphatase | + | 3.1.3.1 |
30106 | catalase | + | 1.11.1.6 |
30106 | 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 |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
19133 | - | - | - | - | - | + | + | + | +/- | - | - | + | + | + | - | - | - | + | - | - |
Isolation, sampling and environmental information
isolation
@ref | sample type | geographic location | country | origin.country | continent |
---|---|---|---|---|---|
19133 | seawater | Jeju, Samyang Beach | Republic of Korea | KOR | Asia |
67770 | Seawater collected from Samyang Beach in Jeju | Republic of Korea | KOR | Asia | |
67771 | From seawater in the coast of Jeju Island | Republic of Korea | KOR | Asia |
isolation source categories
- Cat1: #Environmental
- Cat2: #Aquatic
- Cat3: #Marine
taxonmaps
- @ref: 69479
- File name: preview.99_79986.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_19;96_683;97_4510;98_5790;99_79986&stattab=map
- Last taxonomy: Yoonia tamlensis
- 16S sequence: DQ533556
- Sequence Identity:
- Total samples: 1213
- soil counts: 40
- aquatic counts: 1102
- animal counts: 18
- plant counts: 53
Safety information
risk assessment
- @ref: 19133
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
- @ref: 19133
- description: Loktanella tamlensis strain SSW-35 16S ribosomal RNA gene, partial sequence
- accession: DQ533556
- length: 1352
- database: ena
- NCBI tax ID: 390270
Genome sequences
@ref | description | accession | assembly level | database | NCBI tax ID |
---|---|---|---|---|---|
66792 | Yoonia tamlensis strain DSM 26879 | 390270.6 | wgs | patric | 390270 |
66792 | Yoonia tamlensis DSM 26879 | 2619619642 | draft | img | 390270 |
67770 | Yoonia tamlensis DSM 26879 | GCA_900115105 | scaffold | ncbi | 390270 |
GC content
@ref | GC-content | method |
---|---|---|
19133 | 55.0 | high performance liquid chromatography (HPLC) |
30106 | 55 | |
67770 | 55 | high performance liquid chromatography (HPLC) |
Genome-based predictions
predictions
trait | prediction | confidence | training_data |
---|---|---|---|
spore-forming | no | 100 | no |
gram-positive | no | 97.945 | no |
anaerobic | no | 98.944 | yes |
halophile | yes | 71.64 | no |
spore-forming | no | 96.338 | no |
glucose-util | yes | 80.909 | no |
aerobic | yes | 92.926 | no |
flagellated | no | 79.82 | no |
motile | yes | 51.422 | no |
thermophile | no | 98.198 | yes |
glucose-ferment | no | 89.759 | no |
External links
@ref: 19133
culture collection no.: DSM 26879, JCM 14020, KCTC 12722
straininfo link
- @ref: 87451
- straininfo: 401340
literature
topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
---|---|---|---|---|---|---|---|---|
Phylogeny | 21515703 | Loktanella tamlensis sp. nov., isolated from seawater. | Lee SD | Int J Syst Evol Microbiol | 10.1099/ijs.0.029462-0 | 2011 | Aerobiosis, Bacterial Typing Techniques, Base Composition, Cluster Analysis, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis, Hydrogen-Ion Concentration, Locomotion, Molecular Sequence Data, Nucleic Acid Hybridization, Phospholipids/analysis, Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, Rhodobacteraceae/*classification/genetics/*isolation & purification/physiology, Seawater/*microbiology, Sequence Analysis, DNA, Temperature, Ubiquinone/analysis | Genetics |
Phylogeny | 23749279 | Loktanella sediminilitoris sp. nov., isolated from tidal flat sediment. | Park S, Jung YT, Yoon JH | Int J Syst Evol Microbiol | 10.1099/ijs.0.049841-0 | 2013 | Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Geologic Sediments/*microbiology, Molecular Sequence Data, Nucleic Acid Hybridization, *Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, Rhodobacteraceae/*classification/genetics/isolation & purification, Seawater/microbiology, Ubiquinone/analogs & derivatives/chemistry | Genetics |
Phylogeny | 24744019 | Loktanella maritima sp. nov. isolated from shallow marine sediments. | Tanaka N, Romanenko LA, Kurilenko VV, Svetashev VI, Kalinovskaya NI, Mikhailov VV | Int J Syst Evol Microbiol | 10.1099/ijs.0.061747-0 | 2014 | DNA, Bacterial/genetics, Fatty Acids/chemistry, Geologic Sediments/*microbiology, Japan, Molecular Sequence Data, Nucleic Acid Hybridization, Oceans and Seas, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Rhodobacteraceae/*classification/genetics/isolation & purification, Seawater/*microbiology, Ubiquinone/chemistry | Genetics |
Reference
@id | authors | catalogue | doi/url | title | ID_cross_reference | pubmed | journal |
---|---|---|---|---|---|---|---|
19133 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 26879) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-26879 | ||||
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 | ||||
30106 | 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 | 26462 | 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) | ||||
66794 | Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg | 10.1093/nar/gkaa1025 | BRENDA, the ELIXIR core data resource in 2021: new developments and updates | 33211880 | Nucleic Acids Res. 49: D498-D508 2020 | ||
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 | ||||||
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 | ||||
87451 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID401340.1 | StrainInfo: A central database for resolving microbial strain identifiers |