Strain identifier
BacDive ID: 8205
Type strain: 
Species: Psychrobacter pacificensis
Strain history: CIP <- 2015, DSMZ <- A. Maruyama, AIST <- IFO <- A. Maruyama, Res. Inst. Genome-based BIofactory, Sapporo, Japan: strain NIBH P2K16
NCBI tax ID(s): 112002 (species)
version 8.1 (current version)
General
@ref: 16848
BacDive-ID: 8205
DSM-Number: 23406
keywords: genome sequence, 16S sequence, Bacteria, mesophilic
description: Psychrobacter pacificensis DSM 23406 is a mesophilic bacterium that was isolated from Seawater from a depth of 6000 m.
NCBI tax id
- NCBI tax id: 112002
- Matching level: species
strain history
| @ref | history |
|---|---|
| 16848 | <- NBRC <- A. Maruyama (AIST) <- IFO <- A. Maruyama, Res. Inst. Genome-based Biofactory, Natl. Inst. Advanced Industrial Sci. and Technology (AIST), Sapporo, Japan; NIBH P2K6 |
| 121502 | CIP <- 2015, DSMZ <- A. Maruyama, AIST <- IFO <- A. Maruyama, Res. Inst. Genome-based BIofactory, Sapporo, Japan: strain NIBH P2K16 |
doi: 10.13145/bacdive8205.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/pseudomonadota
- domain: Bacteria
- phylum: Pseudomonadota
- class: Gammaproteobacteria
- order: Pseudomonadales
- family: Moraxellaceae
- genus: Psychrobacter
- species: Psychrobacter pacificensis
- full scientific name: Psychrobacter pacificensis Maruyama et al. 2000
@ref: 16848
domain: Bacteria
phylum: Proteobacteria
class: Gammaproteobacteria
order: Pseudomonadales
family: Moraxellaceae
genus: Psychrobacter
species: Psychrobacter pacificensis
full scientific name: Psychrobacter pacificensis Maruyama et al. 2000
type strain: yes
Morphology
cell morphology
| @ref | motility | confidence | gram stain | cell shape |
|---|---|---|---|---|
| 69480 | no | 96.203 | ||
| 69480 | 99.976 | negative | ||
| 121502 | no | negative | rod-shaped |
Culture and growth conditions
culture medium
| @ref | name | growth | link | composition |
|---|---|---|---|---|
| 16848 | BACTO MARINE BROTH (DIFCO 2216) (DSMZ Medium 514) | yes | https://mediadive.dsmz.de/medium/514 | 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 |
| 36201 | Marine agar (MA) | yes | Distilled water make up to (1000.000 ml);Marine agar (55.100 g) | |
| 121502 | CIP Medium 13 | yes | https://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=13 |
culture temp
| @ref | growth | type | temperature | range |
|---|---|---|---|---|
| 16848 | positive | growth | 28 | mesophilic |
| 36201 | positive | growth | 30 | mesophilic |
Physiology and metabolism
spore formation
| @ref | spore formation | confidence |
|---|---|---|
| 69481 | no | 100 |
| 69480 | no | 99.998 |
Isolation, sampling and environmental information
isolation
| @ref | sample type | country | origin.country | continent |
|---|---|---|---|---|
| 16848 | Seawater from a depth of 6000 m | Japan | JPN | Asia |
| 121502 | Environment, Seawater from a depth of 6000 m | Japan | JPN | Asia |
isolation source categories
| Cat1 | Cat2 | Cat3 |
|---|---|---|
| #Environmental | #Aquatic | #Marine |
| #Environmental | #Terrestrial | #Core sample |
taxonmaps
- @ref: 69479
- File name: preview.99_4865.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_80;96_193;97_2757;98_3642;99_4865&stattab=map
- Last taxonomy: Psychrobacter pacificensis subclade
- 16S sequence: AB681982
- Sequence Identity:
- Total samples: 3122
- soil counts: 90
- aquatic counts: 2631
- animal counts: 395
- plant counts: 6
Safety information
risk assessment
| @ref | biosafety level | biosafety level comment |
|---|---|---|
| 16848 | 1 | Risk group (German classification) |
| 121502 | 1 | Risk group (French classification) |
Sequence information
16S sequences
| @ref | description | accession | length | database | NCBI tax ID |
|---|---|---|---|---|---|
| 20218 | Psychrobacter pacificensis DNA for 16S rRNA, partial sequence, strain:NIBH P2K6(T)(=IFO 16279(T)) | AB016057 | 1526 | ena | 112002 |
| 20218 | Psychrobacter pacificensis gene for 16S rRNA, partial sequence, strain: NBRC 103191 | AB681982 | 1464 | ena | 112002 |
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Psychrobacter pacificensis DSM 23406 | GCA_900101915 | scaffold | ncbi | 112002 |
| 66792 | Psychrobacter pacificensis strain DSM 23406 | 112002.5 | wgs | patric | 112002 |
| 66792 | Psychrobacter pacificensis DSM 23406 | 2599185216 | draft | img | 112002 |
Genome-based predictions
predictions
| trait | prediction | confidence | training_data |
|---|---|---|---|
| spore-forming | no | 100 | no |
| motile | no | 88.034 | no |
| flagellated | no | 88.354 | no |
| gram-positive | no | 98.15 | no |
| anaerobic | no | 98.629 | no |
| aerobic | yes | 84.368 | no |
| halophile | yes | 84.071 | no |
| spore-forming | no | 96.887 | no |
| glucose-ferment | no | 93.042 | no |
| thermophile | no | 99.254 | yes |
| glucose-util | yes | 50.723 | no |
External links
@ref: 16848
culture collection no.: DSM 23406, NBRC 103191, NIBH P2K6, CIP 110991, NIBH P2K16
straininfo link
- @ref: 77608
- straininfo: 62368
literature
| topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
|---|---|---|---|---|---|---|---|---|
| Phylogeny | 10758895 | Phylogenetic analysis of psychrophilic bacteria isolated from the Japan Trench, including a description of the deep-sea species Psychrobacter pacificensis sp. nov. | Maruyama A, Honda D, Yamamoto H, Kitamura K, Higashihara T | Int J Syst Evol Microbiol | 10.1099/00207713-50-2-835 | 2000 | *Cold Temperature, DNA, Bacterial/genetics, DNA, Ribosomal/genetics, Gammaproteobacteria/*classification/genetics/isolation & purification/physiology, Halomonas/classification/genetics/isolation & purification, Japan, Moraxella/classification/genetics/isolation & purification, Movement, Nucleic Acid Hybridization, Phenotype, *Phylogeny, RNA, Ribosomal, 16S/genetics, Seawater/*microbiology, Sequence Analysis, DNA, Water Microbiology | Enzymology |
| Phylogeny | 19717579 | Psychrobacter aestuarii sp. nov., isolated from a tidal flat sediment. | Baik KS, Park SC, Lim CH, Lee KH, Jeon DY, Kim CM, Seong CN | Int J Syst Evol Microbiol | 10.1099/ijs.0.016782-0 | 2009 | Base Sequence, Fatty Acids/analysis, Geologic Sediments/*microbiology, Molecular Sequence Data, Phylogeny, Psychrobacter/*classification/genetics/isolation & purification/physiology, RNA, Ribosomal, 16S/genetics, Seawater/*microbiology | Genetics |
| Phylogeny | 25678681 | Psychrobacter oceani sp. nov., isolated from marine sediment. | Matsuyama H, Minami H, Sakaki T, Kasahara H, Watanabe A, Onoda T, Hirota K, Yumoto I | Int J Syst Evol Microbiol | 10.1099/ijs.0.000118 | 2015 | Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Geologic Sediments/*microbiology, Molecular Sequence Data, Nucleic Acid Hybridization, Pacific Ocean, *Phylogeny, Psychrobacter/*classification/genetics/isolation & purification, RNA, Ribosomal, 16S/genetics, Seawater/*microbiology, Sequence Analysis, DNA, Ubiquinone/chemistry | Genetics |
| Phylogeny | 27609593 | Psychrobacter pocilloporae sp. nov., isolated from a coral, Pocillopora eydouxi. | Zachariah S, Kumari P, Das SK | Int J Syst Evol Microbiol | 10.1099/ijsem.0.001476 | 2016 | Animals, Anthozoa/*microbiology, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, India, Nucleic Acid Hybridization, Phospholipids/chemistry, *Phylogeny, Psychrobacter/*classification/genetics/isolation & purification, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA | Transcriptome |
Reference
| @id | authors | catalogue | doi/url | title | journal | pubmed |
|---|---|---|---|---|---|---|
| 16848 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 23406) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-23406 | |||
| 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 | |||
| 20218 | Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P. | 10.1016/j.syapm.2013.11.002 | StrainInfo introduces electronic passports for microorganisms. | Syst Appl Microbiol. 37: 42-50 2014 | 24321274 | |
| 36201 | Curators of the CIP | https://brclims.pasteur.fr/brcWeb/souche/detail/1/34598 | ||||
| 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) | |||
| 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 | |||
| 77608 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID62368.1 | StrainInfo: A central database for resolving microbial strain identifiers | |||
| 121502 | Curators of the CIP | Collection of Institut Pasteur (CIP 110991) | https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20110991 |