Strain identifier
BacDive ID: 164066
Type strain: 
Species: Polaribacter pacificus
Strain history: X.-H. Zhang and Y. Wang; Coll. of Mar. Life Sci., Ocean Univ. of China, China; HRA130-1.
NCBI tax ID(s): 1775173 (species)
version 8.1 (current version)
General
@ref: 67770
BacDive-ID: 164066
keywords: genome sequence, 16S sequence, Bacteria, psychrophilic, Gram-negative
description: Polaribacter pacificus JCM 31460 is a psychrophilic, Gram-negative bacterium that was isolated from Deep-sea polymetallic nodule from the Pacific Clarion-Clipperton Fracture Zone.
NCBI tax id
- NCBI tax id: 1775173
- Matching level: species
strain history
- @ref: 67770
- history: X.-H. Zhang and Y. Wang; Coll. of Mar. Life Sci., Ocean Univ. of China, China; HRA130-1.
doi: 10.13145/bacdive164066.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/bacteroidota
- domain: Bacteria
- phylum: Bacteroidota
- class: Flavobacteriia
- order: Flavobacteriales
- family: Flavobacteriaceae
- genus: Polaribacter
- species: Polaribacter pacificus
- full scientific name: Polaribacter pacificus Wu et al. 2017
@ref: 67770
domain: Bacteria
phylum: Bacteroidetes
class: Flavobacteriia
order: Flavobacteriales
family: Flavobacteriaceae
genus: Polaribacter
species: Polaribacter pacificus
full scientific name: Polaribacter pacificus Wu et al. 2017
type strain: yes
Morphology
cell morphology
- @ref: 69480
- gram stain: negative
- confidence: 99.993
Culture and growth conditions
culture temp
- @ref: 67770
- growth: positive
- type: growth
- temperature: 16
- range: psychrophilic
Physiology and metabolism
spore formation
| @ref | spore formation | confidence |
|---|---|---|
| 69480 | no | 99.988 |
| 69481 | no | 100 |
observation
- @ref: 67770
- observation: quinones: MK-6
Isolation, sampling and environmental information
isolation
- @ref: 67770
- sample type: Deep-sea polymetallic nodule from the Pacific Clarion-Clipperton Fracture Zone
taxonmaps
- @ref: 69479
- File name: preview.99_137972.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_214;96_41217;97_68597;98_91893;99_137972&stattab=map
- Last taxonomy: Polaribacter pacificus subclade
- 16S sequence: KU315476
- Sequence Identity:
- Total samples: 640
- soil counts: 25
- aquatic counts: 594
- animal counts: 21
Sequence information
16S sequences
- @ref: 67770
- description: Polaribacter pacificus 16S ribosomal RNA gene, partial sequence
- accession: KU315476
- length: 1486
- database: ena
- NCBI tax ID: 1775173
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Polaribacter pacificus CGMCC 1.15763 | GCA_014643655 | scaffold | ncbi | 1775173 |
| 66792 | Polaribacter pacificus strain CGMCC 1.15763 | 1775173.3 | wgs | patric | 1775173 |
GC content
- @ref: 67770
- GC-content: 35.9
- method: high performance liquid chromatography (HPLC)
Genome-based predictions
predictions
| trait | prediction | confidence | training_data |
|---|---|---|---|
| spore-forming | no | 100 | no |
| flagellated | no | 96.234 | no |
| gram-positive | no | 98.109 | no |
| anaerobic | no | 99.284 | no |
| aerobic | yes | 88.339 | no |
| halophile | no | 81.653 | no |
| spore-forming | no | 96.743 | no |
| glucose-util | yes | 85.76 | no |
| thermophile | no | 97.657 | no |
| motile | no | 87.818 | no |
| glucose-ferment | no | 92.389 | no |
External links
@ref: 67770
culture collection no.: JCM 31460, CGMCC 1.15763, KCTC 52370, MCCC 1K03199
literature
- topic: Phylogeny
- Pubmed-ID: 28829019
- title: Polaribacter pacificus sp. nov., isolated from a deep-sea polymetallic nodule from the Eastern Pacific Ocean.
- authors: Wu Y, Yu M, Zhang Z, Wang Y, Yang X, Wang X, Ren Q, Sun Z, Shi X, Zhang XH
- journal: Int J Syst Evol Microbiol
- DOI: 10.1099/ijsem.0.002082
- year: 2017
- mesh: Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Flavobacteriaceae/*classification/genetics/isolation & purification, Molecular Sequence Data, Nucleic Acid Hybridization, Pacific Ocean, Phospholipids/chemistry, *Phylogeny, Pigmentation, RNA, Ribosomal, 16S/genetics, Seawater/*microbiology, Sequence Analysis, DNA, Vitamin K 2/analogs & derivatives/chemistry
- topic2: Genetics
Reference
| @id | authors | title | doi/url |
|---|---|---|---|
| 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 |
| 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 |
| 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. | MicrobeAtlas 1.0 beta | https://microbeatlas.org/ |
| 69480 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | Predictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) | https://diaspora-project.de/progress.html#genomes |
| 69481 | Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch | Predictions based on the model GenomeNet Sporulation v. 1 | 10.21203/rs.3.rs-2527258/v1 |