Strain identifier
BacDive ID: 162615
Type strain: 
Species: Pseudooceanicola flagellatus
Strain history: Y.-Y. Huo DY470.
NCBI tax ID(s): 1387277 (species)
version 9.3 (current version)
General
@ref: 67770
BacDive-ID: 162615
keywords: genome sequence, 16S sequence, Bacteria, mesophilic, Gram-negative
description: Pseudooceanicola flagellatus JCM 19803 is a mesophilic, Gram-negative bacterium that was isolated from Seawater collected from the Pacific Ocean.
NCBI tax id
- NCBI tax id: 1387277
- Matching level: species
strain history
- @ref: 67770
- history: Y.-Y. Huo DY470.
doi: 10.13145/bacdive162615.20250331.9.3
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/pseudomonadota
- domain: Bacteria
- phylum: Pseudomonadota
- class: Alphaproteobacteria
- order: Rhodobacterales
- family: Roseobacteraceae
- genus: Pseudooceanicola
- species: Pseudooceanicola flagellatus
- full scientific name: Pseudooceanicola flagellatus (Huo et al. 2014) Huang et al. 2018
synonyms
@ref synonym 20215 Oceanicola flagellatus 20215 Primorskyibacter flagellatus 20215 Pseudooceanicola flagellatus
@ref: 67770
domain: Bacteria
phylum: Proteobacteria
class: Alphaproteobacteria
order: Rhodobacterales
family: Rhodobacteraceae
genus: Pseudooceanicola
species: Pseudooceanicola flagellatus
full scientific name: Pseudooceanicola flagellatus (Huo et al.) Lai et al.
type strain: yes
Morphology
cell morphology
| @ref | gram stain | confidence |
|---|---|---|
| 125438 | negative | 98.833 |
| 125439 | negative | 95 |
Culture and growth conditions
culture temp
- @ref: 67770
- growth: positive
- type: growth
- temperature: 30
Physiology and metabolism
observation
- @ref: 67770
- observation: quinones: Q-10
Isolation, sampling and environmental information
isolation
- @ref: 67770
- sample type: Seawater collected from the Pacific Ocean
taxonmaps
- @ref: 69479
- File name: preview.99_67099.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_19;96_1952;97_5713;98_47305;99_67099&stattab=map
- Last taxonomy: Pseudooceanicola flagellatus subclade
- 16S sequence: KF434118
- Sequence Identity:
- Total samples: 65
- aquatic counts: 65
Sequence information
16S sequences
- @ref: 67770
- description: Primorskyibacter flagellatus strain DY470 16S ribosomal RNA gene, partial sequence
- accession: KF434118
- length: 1381
- database: nuccore
- NCBI tax ID: 1387277
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Primorskyibacter flagellatus CGMCC 1.12664 | GCA_014638275 | scaffold | ncbi | 1387277 |
| 66792 | Pseudooceanicola flagellatus strain CGMCC 1.12664 | 1387277.6 | wgs | patric | 1387277 |
GC content
- @ref: 67770
- GC-content: 61.8
- 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 | 98.833 | no |
| 125438 | anaerobic | anaerobic | Ability to grow under anoxygenic conditions (including facultative anaerobes) | no | 96.881 | no |
| 125438 | aerobic | aerobic | Ability to grow under oxygenic conditions (including facultative aerobes) | yes | 85.656 | no |
| 125438 | spore-forming | spore-forming | Ability to form endo- or exospores | no | 89.66 | no |
| 125438 | thermophile | thermophilic | Ability to grow at temperatures above or equal to 45°C | no | 97.5 | no |
| 125438 | motile2+ | flagellated | Ability to perform flagellated movement | yes | 58.991 | no |
| 125439 | BacteriaNet | spore_formation | Ability to form endo- or exospores | no | 85.3 | |
| 125439 | BacteriaNet | motility | Ability to perform movement | yes | 66.7 | |
| 125439 | BacteriaNet | gram_stain | Reaction to gram-staining | negative | 95 | |
| 125439 | BacteriaNet | oxygen_tolerance | Oxygenic conditions needed for growth | aerobe | 77.1 |
External links
@ref: 67770
culture collection no.: JCM 19803, CGMCC 1.12664, LMG 27871
straininfo link
- @ref: 113506
- straininfo: 390710
literature
| topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
|---|---|---|---|---|---|---|---|---|
| Phylogeny | 24899659 | Oceanicola antarcticus sp. nov. and Oceanicola flagellatus sp. nov., moderately halophilic bacteria isolated from seawater. | Huo YY, Li ZY, You H, Wang CS, Post AF, Oren A, Xu XW | Int J Syst Evol Microbiol | 10.1099/ijs.0.062588-0 | 2014 | Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Molecular Sequence Data, Nucleic Acid Hybridization, Pacific Ocean, *Phylogeny, RNA, Ribosomal, 16S/genetics, Rhodobacteraceae/*classification/genetics/isolation & purification, Seawater/*microbiology, Sequence Analysis, DNA | Genetics |
| Phylogeny | 25663028 | Pseudooceanicola atlanticus gen. nov. sp. nov., isolated from surface seawater of the Atlantic Ocean and reclassification of Oceanicola batsensis, Oceanicola marinus, Oceanicola nitratireducens, Oceanicola nanhaiensis, Oceanicola antarcticus and Oceanicola flagellatus, as Pseudooceanicola batsensis comb. nov., Pseudooceanicola marinus comb. nov., Pseudooceanicola nitratireducens comb. nov., Pseudooceanicola nanhaiensis comb. nov., Pseudooceanicola antarcticus comb. nov., and Pseudooceanicola flagellatus comb. nov. | Lai Q, Li G, Liu X, Du Y, Sun F, Shao Z | Antonie Van Leeuwenhoek | 10.1007/s10482-015-0398-2 | 2015 | Atlantic Ocean, Base Composition, Cluster Analysis, Cytosol/chemistry, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis, Molecular Sequence Data, Nucleic Acid Hybridization, Phospholipids/analysis, Phylogeny, Quinones/analysis, RNA, Ribosomal, 16S/genetics, Rhodobacteraceae/*classification/genetics/*isolation & purification/physiology, Seawater/*microbiology, Sequence Analysis, DNA, Sodium Chloride/metabolism, Temperature | Genetics |
| Phylogeny | 29219804 | Pseudooceanicola lipolyticus sp. nov., a marine alphaproteobacterium, reclassification of Oceanicola flagellatus as Pseudooceanicola flagellatus comb. nov. and emended description of the genus Pseudooceanicola. | Huang MM, Guo LL, Wu YH, Lai QL, Shao ZZ, Wang CS, Wu M, Xu XW | Int J Syst Evol Microbiol | 10.1099/ijsem.0.002521 | 2017 | Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Nucleic Acid Hybridization, Philippines, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Rhodobacteraceae/*classification/genetics/isolation & purification, Seawater/*microbiology, Sequence Analysis, DNA, Ubiquinone/chemistry, *Water Microbiology | Transcriptome |
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/ |
| 113506 | 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-ID390710.1 |
| 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 |