Strain identifier
BacDive ID: 130799
Type strain: 
Species: Leisingera aquaemixtae
Strain Designation: SSK6-1
Strain history: <- CECT <- J. H. Yoon, Sungkyunkwan Univ., Suwon, Republic of Korea
NCBI tax ID(s): 1396826 (species)
version 9.3 (current version)
General
@ref: 21858
BacDive-ID: 130799
DSM-Number: 29957
keywords: genome sequence, 16S sequence, Bacteria, mesophilic, Gram-negative
description: Leisingera aquaemixtae SSK6-1 is a mesophilic, Gram-negative bacterium that was isolated from water collected from the zone where the ocean and a freshwater spring meet.
NCBI tax id
- NCBI tax id: 1396826
- Matching level: species
strain history
- @ref: 21858
- history: <- CECT <- J. H. Yoon, Sungkyunkwan Univ., Suwon, Republic of Korea
doi: 10.13145/bacdive130799.20250331.9.3
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/pseudomonadota
- domain: Bacteria
- phylum: Pseudomonadota
- class: Alphaproteobacteria
- order: Rhodobacterales
- family: Roseobacteraceae
- genus: Leisingera
- species: Leisingera aquaemixtae
- full scientific name: Leisingera aquaemixtae (Park et al. 2014) Breider et al. 2014
synonyms
- @ref: 20215
- synonym: Phaeobacter aquaemixtae
@ref: 21858
domain: Bacteria
phylum: Proteobacteria
class: Alphaproteobacteria
order: Rhodobacterales
family: Rhodobacteraceae
genus: Leisingera
species: Leisingera aquaemixtae
full scientific name: Leisingera aquaemixtae (Park et al. 2014) Breider et al. 2014
strain designation: SSK6-1
type strain: yes
Morphology
cell morphology
| @ref | gram stain | confidence |
|---|---|---|
| 125438 | negative | 99.5 |
| 125439 | negative | 97.5 |
colony morphology
- @ref: 21858
- incubation period: 2-3 days
Culture and growth conditions
culture medium
- @ref: 21858
- 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: 21858
- growth: positive
- type: growth
- temperature: 30
Physiology and metabolism
oxygen tolerance
- @ref: 125439
- oxygen tolerance: aerobe
- confidence: 92.2
spore formation
| @ref | spore formation | confidence |
|---|---|---|
| 125438 | no | 90.103 |
| 125439 | no | 96.4 |
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 | 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 |
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 |
|---|---|---|---|
| 21858 | catalase | + | 1.11.1.6 |
| 21858 | cytochrome-c oxidase | + | 1.9.3.1 |
| 68369 | urease | - | 3.5.1.5 |
| 68369 | gelatinase | - | |
| 68369 | beta-glucosidase | - | 3.2.1.21 |
| 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 |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 21858 | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - |
Isolation, sampling and environmental information
isolation
- @ref: 21858
- sample type: water collected from the zone where the ocean and a freshwater spring meet
- geographic location: Jeju Island
- country: Republic of Korea
- origin.country: KOR
- continent: Asia
isolation source categories
| Cat1 | Cat2 | Cat3 |
|---|---|---|
| #Environmental | #Aquatic | #Freshwater |
| #Environmental | #Aquatic | #Marine |
| #Environmental | #Aquatic | #Spring |
taxonmaps
- @ref: 69479
- File name: preview.99_7997.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_19;96_355;97_800;98_927;99_7997&stattab=map
- Last taxonomy: Leisingera aquaemixtae
- 16S sequence: KF554505
- Sequence Identity:
- Total samples: 222
- soil counts: 5
- aquatic counts: 207
- animal counts: 10
Safety information
risk assessment
- @ref: 21858
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
- @ref: 21858
- description: Leisingera aquaemixtae strain SSK6-1 16S ribosomal RNA gene, partial sequence
- accession: KF554505
- length: 1386
- database: nuccore
- NCBI tax ID: 1396826
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Leisingera aquaemixtae CECT 8399 | GCA_001458395 | contig | ncbi | 1396826 |
| 66792 | Leisingera aquaemixtae strain CECT 8399 | 1396826.3 | wgs | patric | 1396826 |
| 66792 | Leisingera aquaemixtae CECT 8399 | 2713896966 | draft | img | 1396826 |
GC content
- @ref: 21858
- GC-content: 64.6
- method: high performance liquid chromatography (HPLC)
Genome-based predictions
predictions
| @ref | model | trait | description | prediction | confidence | training_data |
|---|---|---|---|---|---|---|
| 125438 | gram-positive | gram-positive | Positive reaction to Gram-staining | no | 99.5 | no |
| 125438 | anaerobic | anaerobic | Ability to grow under anoxygenic conditions (including facultative anaerobes) | no | 94.415 | no |
| 125438 | spore-forming | spore-forming | Ability to form endo- or exospores | no | 90.103 | no |
| 125438 | aerobic | aerobic | Ability to grow under oxygenic conditions (including facultative aerobes) | yes | 81.268 | no |
| 125438 | thermophile | thermophilic | Ability to grow at temperatures above or equal to 45°C | no | 96.5 | yes |
| 125438 | motile2+ | flagellated | Ability to perform flagellated movement | yes | 69.8 | no |
| 125439 | BacteriaNet | spore_formation | Ability to form endo- or exospores | no | 96.4 | |
| 125439 | BacteriaNet | motility | Ability to perform movement | yes | 76.1 | |
| 125439 | BacteriaNet | gram_stain | Reaction to gram-staining | negative | 97.5 | |
| 125439 | BacteriaNet | oxygen_tolerance | Oxygenic conditions needed for growth | aerobe | 92.2 |
External links
@ref: 21858
culture collection no.: DSM 29957, CECT 8399, KCTC 32538
straininfo link
- @ref: 89288
- straininfo: 393361
literature
| topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
|---|---|---|---|---|---|---|---|---|
| Phylogeny | 24449788 | Phaeobacter aquaemixtae sp. nov., isolated from the junction between the ocean and a freshwater spring. | Park S, Park DS, Bae KS, Yoon JH | Int J Syst Evol Microbiol | 10.1099/ijs.0.057646-0 | 2014 | Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Fresh Water/*microbiology, Molecular Sequence Data, Nucleic Acid Hybridization, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, Rhodobacteraceae/*classification/genetics/isolation & purification, Seawater/*microbiology, Ubiquinone/chemistry, *Water Microbiology | Genetics |
| Phylogeny | 25180090 | Cribrihabitans neustonicus sp. nov., isolated from coastal surface seawater, and emended description of the genus Cribrihabitans Chen et al. 2014. | Hameed A, Shahina M, Lin SY, Lai WA, Liu YC, Hsu YH, Young CC | Int J Syst Evol Microbiol | 10.1099/ijs.0.066142-0 | 2014 | Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Molecular Sequence Data, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Rhodobacteraceae/*classification/genetics/isolation & purification, Seawater/*microbiology, Sequence Analysis, DNA, Taiwan, Ubiquinone/chemistry | Genetics |
| 26981415 | Draft genome of Leisingera aquaemixtae CECT 8399(T), a member of the Roseobacter clade isolated from a junction of fresh and ocean water in Jeju Island, South Korea. | Rodrigo-Torres L, Pujalte MJ, Arahal DR | Genom Data | 10.1016/j.gdata.2016.01.010 | 2016 |
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 | |
| 21858 | Curators of the DSMZ | https://www.dsmz.de/collection/catalogue/details/culture/DSM-29957 | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 29957) | |
| 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 | |
| 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/ | |
| 89288 | 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-ID393361.1 | |
| 125438 | Julia Koblitz, Lorenz Christian Reimer, Rüdiger Pukall, Jörg Overmann | Predicting bacterial phenotypic traits through improved machine learning using high-quality, curated datasets | 10.1101/2024.08.12.607695 | |
| 125439 | Philipp Münch, René Mreches, Martin Binder, Hüseyin Anil Gündüz, Xiao-Yin To, Alice McHardy | deepG: Deep Learning for Genome Sequence Data. R package version 0.3.1 | https://github.com/GenomeNet/deepG |