Strain identifier
BacDive ID: 23238
Type strain: 
Species: Pelagimonas phthalicica
Strain Designation: KU27E1
Strain history: <- H Iwaki, Kansai Univ., Japan
NCBI tax ID(s): 1037362 (species)
version 8.1 (current version)
General
@ref: 19147
BacDive-ID: 23238
DSM-Number: 26923
keywords: genome sequence, 16S sequence, Bacteria, aerobe, mesophilic, Gram-negative
description: Pelagimonas phthalicica KU27E1 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from seawater.
NCBI tax id
- NCBI tax id: 1037362
- Matching level: species
strain history
| @ref | history |
|---|---|
| 19147 | <- JCM <- H. Iwaki; KU27E1 |
| 67770 | H. Iwaki KU27E1. |
| 67771 | <- H Iwaki, Kansai Univ., Japan |
doi: 10.13145/bacdive23238.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/pseudomonadota
- domain: Bacteria
- phylum: Pseudomonadota
- class: Alphaproteobacteria
- order: Rhodobacterales
- family: Roseobacteraceae
- genus: Pelagimonas
- species: Pelagimonas phthalicica
- full scientific name: Pelagimonas phthalicica (Iwaki et al. 2012) Hördt et al. 2020
synonyms
@ref synonym 20215 Tropicibacter phthalicus 20215 Tropicibacter phthalicicus
@ref: 19147
domain: Bacteria
phylum: Proteobacteria
class: Alphaproteobacteria
order: Rhodobacterales
family: Rhodobacteraceae
genus: Pelagimonas
species: Pelagimonas phthalicica
full scientific name: Pelagimonas phthalicica (Iwaki et al. 2012) Hördt et al. 2020
strain designation: KU27E1
type strain: yes
Morphology
cell morphology
| @ref | gram stain | confidence |
|---|---|---|
| 67771 | negative | |
| 69480 | negative | 99.994 |
colony morphology
- @ref: 19147
- incubation period: 2-3 days
Culture and growth conditions
culture medium
- @ref: 19147
- 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 |
|---|---|---|---|---|
| 19147 | positive | growth | 25 | mesophilic |
| 67770 | positive | growth | 25 | mesophilic |
| 67771 | positive | growth | 25 | mesophilic |
Physiology and metabolism
oxygen tolerance
- @ref: 67771
- oxygen tolerance: aerobe
spore formation
| @ref | spore formation | confidence |
|---|---|---|
| 69481 | no | 100 |
| 69480 | no | 99.987 |
observation
- @ref: 67770
- observation: quinones: Q-10
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 |
|---|---|---|---|
| 19147 | catalase | + | 1.11.1.6 |
| 19147 | cytochrome-c 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 |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 19147 | - | - | - | - | - | + | + | + | - | - | - | - | - | - | - | - | - | - | - | - |
Isolation, sampling and environmental information
isolation
| @ref | sample type | geographic location | country | origin.country | continent |
|---|---|---|---|---|---|
| 19147 | seawater | coastal region of Ishigaki Island | Japan | JPN | Asia |
| 67770 | Seawater obtained from the coastal region of Ishigaki Island | Japan | JPN | Asia | |
| 67771 | From seawater | Ishigaki island, Okinawa | Japan | JPN | Asia |
isolation source categories
- Cat1: #Environmental
- Cat2: #Aquatic
- Cat3: #Marine
Safety information
risk assessment
- @ref: 19147
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
- @ref: 19147
- description: Tropicibacter phthalicicus gene for 16S rRNA, partial sequence
- accession: AB636139
- length: 1422
- database: ena
- NCBI tax ID: 1037362
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Tropicibacter phthalicicus strain DSM 26923 | 1037362.5 | wgs | patric | 1037362 |
| 66792 | Tropicibacter phthalicicus DSM 26923 | 2734482174 | draft | img | 1037362 |
| 67770 | Pelagimonas phthalicica DSM 26923 | GCA_004364805 | contig | ncbi | 1037362 |
GC content
- @ref: 19147
- GC-content: 58.7
- method: high performance liquid chromatography (HPLC)
Genome-based predictions
predictions
| trait | prediction | confidence | training_data |
|---|---|---|---|
| spore-forming | no | 100 | no |
| motile | yes | 61.225 | no |
| flagellated | no | 64.611 | no |
| gram-positive | no | 98.627 | yes |
| anaerobic | no | 97.949 | no |
| aerobic | yes | 86.842 | yes |
| halophile | yes | 58.425 | no |
| spore-forming | no | 95.291 | no |
| thermophile | no | 97.568 | no |
| glucose-util | yes | 67.944 | yes |
| glucose-ferment | no | 89.272 | yes |
External links
@ref: 19147
culture collection no.: DSM 26923, JCM 17793, KCTC 23703
straininfo link
- @ref: 87464
- straininfo: 380604
literature
- topic: Phylogeny
- Pubmed-ID: 22278761
- title: Tropicibacter phthalicus sp. nov., a phthalate-degrading bacterium from seawater.
- authors: Iwaki H, Nishimura A, Hasegawa Y
- journal: Curr Microbiol
- DOI: 10.1007/s00284-012-0085-8
- year: 2012
- mesh: Aerobiosis, Bacterial Typing Techniques, Base Composition, Cluster Analysis, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis, Flagella/physiology, Hydrogen-Ion Concentration, Japan, Locomotion, Molecular Sequence Data, Phthalic Acids/*metabolism, Phylogeny, Quinones/analysis, RNA, Ribosomal, 16S/genetics, Rhodobacteraceae/*classification/genetics/*isolation & purification/physiology, Seawater/*microbiology, Sequence Analysis, DNA, Sodium Chloride/metabolism, Temperature
- topic2: Genetics
Reference
| @id | authors | catalogue | doi/url | title | journal | pubmed |
|---|---|---|---|---|---|---|
| 19147 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 26923) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-26923 | |||
| 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 | |||
| 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 | Nucleic Acids Res. 49: D498-D508 2020 | 33211880 | |
| 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 | |||||
| 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 | |||
| 87464 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID380604.1 | StrainInfo: A central database for resolving microbial strain identifiers |