Strain identifier
BacDive ID: 155836
Type strain: 
Species: Flavobacterium oncorhynchi
NCBI tax ID(s): 728056 (species)
version 9.3 (current version)
General
@ref: 61960
BacDive-ID: 155836
keywords: genome sequence, Bacteria, aerobe, mesophilic
description: Flavobacterium oncorhynchi CCUG 59446 is an aerobe, mesophilic bacterium that was isolated from Trout,diseased .
NCBI tax id
- NCBI tax id: 728056
- Matching level: species
doi: 10.13145/bacdive155836.20250331.9.3
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/bacteroidota
- domain: Bacteria
- phylum: Bacteroidota
- class: Flavobacteriia
- order: Flavobacteriales
- family: Flavobacteriaceae
- genus: Flavobacterium
- species: Flavobacterium oncorhynchi
- full scientific name: Flavobacterium oncorhynchi Zamora et al. 2012
@ref: 61960
domain: Bacteria
phylum: Bacteroidetes
class: Flavobacteriia
order: Flavobacteriales
family: Flavobacteriaceae
genus: Flavobacterium
species: Flavobacterium oncorhynchi
type strain: yes
Morphology
cell morphology
| @ref | gram stain | confidence | motility |
|---|---|---|---|
| 125439 | negative | 99.9 | |
| 125438 | 94 | no | |
| 125438 | negative | 96.727 |
Culture and growth conditions
culture temp
- @ref: 61960
- growth: positive
- type: growth
- temperature: 30
Physiology and metabolism
oxygen tolerance
| @ref | oxygen tolerance | confidence |
|---|---|---|
| 61960 | aerobe | |
| 125439 | aerobe | 95.2 |
spore formation
- @ref: 125439
- spore formation: no
- confidence: 99.6
Isolation, sampling and environmental information
isolation
- @ref: 61960
- sample type: Trout,diseased (Oncorhynchus mykiss)
- sampling date: 2008-06-01
- geographic location: Madrid
- country: Spain
- origin.country: ESP
- continent: Europe
isolation source categories
| Cat1 | Cat2 |
|---|---|
| #Host | #Fishes |
| #Infection | #Disease |
Sequence information
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Flavobacterium oncorhynchi CCUG 59446 | GCA_002217355 | scaffold | ncbi | 728056 |
| 66792 | Flavobacterium oncorhynchi strain CCUG 59446 | 728056.4 | wgs | patric | 728056 |
| 66792 | Flavobacterium oncorhynchi CCUG 59446 | 2916300131 | draft | img | 728056 |
Genome-based predictions
predictions
| @ref | model | trait | description | prediction | confidence | training_data |
|---|---|---|---|---|---|---|
| 125438 | gram-positive | gram-positive | Positive reaction to Gram-staining | no | 96.727 | no |
| 125438 | anaerobic | anaerobic | Ability to grow under anoxygenic conditions (including facultative anaerobes) | no | 97.89 | yes |
| 125438 | aerobic | aerobic | Ability to grow under oxygenic conditions (including facultative aerobes) | yes | 88.623 | yes |
| 125438 | spore-forming | spore-forming | Ability to form endo- or exospores | no | 88 | no |
| 125438 | thermophile | thermophilic | Ability to grow at temperatures above or equal to 45°C | no | 98.859 | no |
| 125438 | motile2+ | flagellated | Ability to perform flagellated movement | no | 94 | no |
| 125439 | BacteriaNet | spore_formation | Ability to form endo- or exospores | no | 99.6 | |
| 125439 | BacteriaNet | motility | Ability to perform movement | no | 65.5 | |
| 125439 | BacteriaNet | gram_stain | Reaction to gram-staining | negative | 99.9 | |
| 125439 | BacteriaNet | oxygen_tolerance | Oxygenic conditions needed for growth | aerobe | 95.2 |
External links
@ref: 61960
culture collection no.: CCUG 59446, CECT 7678
straininfo link
- @ref: 109205
- straininfo: 379801
literature
| topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
|---|---|---|---|---|---|---|---|---|
| Phylogeny | 22227311 | Flavobacterium oncorhynchi sp. nov., a new species isolated from rainbow trout (Oncorhynchus mykiss). | Zamora L, Fernandez-Garayzabal JF, Svensson-Stadler LA, Palacios MA, Dominguez L, Moore ER, Vela AI | Syst Appl Microbiol | 10.1016/j.syapm.2011.11.007 | 2012 | Animals, Bacterial Typing Techniques, Base Composition, Base Sequence, DNA, Bacterial/analysis/genetics, DNA, Ribosomal/analysis/genetics, Flavobacteriaceae Infections/*microbiology, Flavobacterium/*classification/*genetics/isolation & purification, Molecular Sequence Data, Oncorhynchus mykiss/*microbiology, Phylogeny, RNA, Ribosomal, 16S/analysis/genetics, Sequence Alignment, Sequence Analysis, DNA | Genetics |
| Phylogeny | 23825681 | Flavobacterium plurextorum sp. nov. Isolated from Farmed Rainbow Trout (Oncorhynchus mykiss). | Zamora L, Fernandez-Garayzabal JF, Sanchez-Porro C, Palacios MA, Moore ER, Dominguez L, Ventosa A, Vela AI | PLoS One | 10.1371/journal.pone.0067741 | 2013 | Animals, *Aquaculture, Flavobacterium/classification/genetics/*isolation & purification, Genotype, Oncorhynchus mykiss/*growth & development/*microbiology, Phenotype, Phylogeny | Genetics |
Reference
| @id | authors | title | doi/url | catalogue | journal | pubmed |
|---|---|---|---|---|---|---|
| 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 | |||
| 61960 | Curators of the CCUG | https://www.ccug.se/strain?id=59446 | Culture Collection University of Gothenburg (CCUG) (CCUG 59446) | |||
| 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 | |||
| 66794 | Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg | BRENDA, the ELIXIR core data resource in 2021: new developments and updates | 10.1093/nar/gkaa1025 | Nucleic Acids Res. 49: D498-D508 2020 | 33211880 | |
| 109205 | 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-ID379801.1 | |||
| 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 |