Strain identifier
BacDive ID: 6235
Type strain: 
Species: Pseudidiomarina taiwanensis
Strain Designation: PIT1
Strain history: W. Y. Shieh PIT1.
NCBI tax ID(s): 337250 (species)
version 8.1 (current version)
General
@ref: 8112
BacDive-ID: 6235
DSM-Number: 19709
keywords: genome sequence, 16S sequence, Bacteria, aerobe, mesophilic, Gram-negative, rod-shaped
description: Pseudidiomarina taiwanensis PIT1 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from shallow coastal water.
NCBI tax id
- NCBI tax id: 337250
- Matching level: species
strain history
| @ref | history |
|---|---|
| 8112 | <- BCRC <- W. Y. Shieh, Natl. Taiwan Univ., Inst. Oceanography, Taipei; PIT1 |
| 67770 | W. Y. Shieh PIT1. |
doi: 10.13145/bacdive6235.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/pseudomonadota
- domain: Bacteria
- phylum: Pseudomonadota
- class: Gammaproteobacteria
- order: Alteromonadales
- family: Idiomarinaceae
- genus: Pseudidiomarina
- species: Pseudidiomarina taiwanensis
- full scientific name: Pseudidiomarina taiwanensis Jean et al. 2006
synonyms
- @ref: 20215
- synonym: Idiomarina taiwanensis
@ref: 8112
domain: Bacteria
phylum: Proteobacteria
class: Gammaproteobacteria
order: Alteromonadales
family: Idiomarinaceae
genus: Pseudidiomarina
species: Pseudidiomarina taiwanensis
full scientific name: Pseudidiomarina taiwanensis Jean et al. 2006 emend. Liu et al. 2018
strain designation: PIT1
type strain: yes
Morphology
cell morphology
- @ref: 31684
- gram stain: negative
- cell length: 0.8-2.4 µm
- cell width: 0.6-0.8 µm
- cell shape: rod-shaped
- motility: no
pigmentation
- @ref: 31684
- production: yes
Culture and growth conditions
culture medium
- @ref: 8112
- 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 |
|---|---|---|---|---|
| 8112 | positive | growth | 28 | mesophilic |
| 31684 | positive | growth | 15-42 | |
| 31684 | positive | optimum | 30-35 | mesophilic |
| 67770 | positive | growth | 30 | mesophilic |
culture pH
| @ref | ability | type | pH |
|---|---|---|---|
| 31684 | positive | growth | 8 |
| 31684 | positive | optimum | 8 |
Physiology and metabolism
oxygen tolerance
- @ref: 31684
- oxygen tolerance: aerobe
spore formation
- @ref: 31684
- spore formation: no
halophily
| @ref | salt | growth | tested relation | concentration |
|---|---|---|---|---|
| 31684 | NaCl | positive | growth | 0.5-11 % |
| 31684 | NaCl | positive | optimum | 01-04 % |
observation
- @ref: 31684
- observation: aggregates in chains
metabolite utilization
| @ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
|---|---|---|---|---|
| 31684 | 16449 | alanine | + | carbon source |
| 31684 | 29987 | glutamate | + | carbon source |
| 31684 | 28087 | glycogen | + | carbon source |
| 31684 | 26271 | proline | + | carbon source |
| 31684 | 17822 | serine | + | carbon source |
| 31684 | 30031 | succinate | + | carbon source |
| 31684 | 17632 | nitrate | + | reduction |
enzymes
| @ref | value | activity | ec |
|---|---|---|---|
| 31684 | catalase | + | 1.11.1.6 |
| 31684 | gelatinase | + | |
| 31684 | cytochrome oxidase | + | 1.9.3.1 |
Isolation, sampling and environmental information
isolation
| @ref | sample type | geographic location | country | origin.country | continent |
|---|---|---|---|---|---|
| 8112 | shallow coastal water | An-Ping Harbour | Taiwan | TWN | Asia |
| 67770 | Seawater at the shallow coastal region of An-Ping Harbour | Tainan | Taiwan | TWN | Asia |
isolation source categories
| Cat1 | Cat2 | Cat3 |
|---|---|---|
| #Environmental | #Aquatic | #Marine |
| #Environmental | #Terrestrial | #Coast |
taxonmaps
- @ref: 69479
- File name: preview.99_28027.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_197;96_13864;97_16885;98_20975;99_28027&stattab=map
- Last taxonomy: Pseudidiomarina taiwanensis subclade
- 16S sequence: DQ118948
- Sequence Identity:
- Total samples: 308
- soil counts: 13
- aquatic counts: 247
- animal counts: 47
- plant counts: 1
Safety information
risk assessment
- @ref: 8112
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
- @ref: 8112
- description: Pseudidiomarina taiwanensis strain PIT1 16S ribosomal RNA gene, partial sequence
- accession: DQ118948
- length: 1465
- database: ena
- NCBI tax ID: 337250
Genome sequences
- @ref: 67770
- description: Pseudidiomarina taiwanensis PIT1
- accession: GCA_003987435
- assembly level: contig
- database: ncbi
- NCBI tax ID: 337250
GC content
| @ref | GC-content | method |
|---|---|---|
| 8112 | 49.3 | |
| 67770 | 49.47 | genome sequence analysis |
| 67770 | 49.3 | high performance liquid chromatography (HPLC) |
Genome-based predictions
predictions
| trait | prediction | confidence | training_data |
|---|---|---|---|
| motile | no | 79.511 | no |
| flagellated | no | 97.756 | yes |
| gram-positive | no | 98.732 | yes |
| anaerobic | no | 98.967 | yes |
| aerobic | yes | 92.018 | yes |
| halophile | yes | 60.293 | no |
| spore-forming | no | 97.446 | no |
| thermophile | no | 97.133 | yes |
| glucose-util | yes | 80.523 | no |
| glucose-ferment | no | 78.439 | no |
External links
@ref: 8112
culture collection no.: DSM 19709, BCRC 17465, JCM 13360
straininfo link
- @ref: 75714
- straininfo: 290991
literature
- topic: Phylogeny
- Pubmed-ID: 16585713
- title: Pseudidiomarina taiwanensis gen. nov., sp. nov., a marine bacterium isolated from shallow coastal water of An-Ping Harbour, Taiwan, and emended description of the family Idiomarinaceae.
- authors: Jean WD, Shieh WY, Chiu HH
- journal: Int J Syst Evol Microbiol
- DOI: 10.1099/ijs.0.64048-0
- year: 2006
- mesh: Aerobiosis, Fatty Acids/metabolism, Gammaproteobacteria/*classification/genetics/growth & development/*isolation & purification, Molecular Sequence Data, Phylogeny, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/analysis/genetics, Seawater/*microbiology, Taiwan, Water Microbiology
- topic2: Genetics
Reference
| @id | authors | catalogue | doi/url | title | ID_cross_reference | pubmed | journal |
|---|---|---|---|---|---|---|---|
| 8112 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 19709) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-19709 | ||||
| 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 | ||||
| 31684 | 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 | 27961 | 28776041 | ||
| 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/ | |||||
| 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 | ||||
| 75714 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID290991.1 | StrainInfo: A central database for resolving microbial strain identifiers |