Strain identifier
BacDive ID: 5753
Type strain: 
Species: Francisella halioticida
Strain Designation: Shimane-1
Strain history: <- O. Brevik, Univ. Bergen, Norway; Shimane-1 <- T. Kamaishi, National Research Institute of Aquaculture, Japan
NCBI tax ID(s): 549298 (species)
version 8.1 (current version)
General
@ref: 17356
BacDive-ID: 5753
DSM-Number: 23729
keywords: genome sequence, 16S sequence, Bacteria, psychrophilic, animal pathogen
description: Francisella halioticida Shimane-1 is a psychrophilic animal pathogen that was isolated from haemolymph of a diseased cultured abalone .
NCBI tax id
- NCBI tax id: 549298
- Matching level: species
strain history
- @ref: 17356
- history: <- O. Brevik, Univ. Bergen, Norway; Shimane-1 <- T. Kamaishi, National Research Institute of Aquaculture, Japan
doi: 10.13145/bacdive5753.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/pseudomonadota
- domain: Bacteria
- phylum: Pseudomonadota
- class: Gammaproteobacteria
- order: Beggiatoales
- family: Francisellaceae
- genus: Francisella
- species: Francisella halioticida
- full scientific name: Francisella halioticida Brevik et al. 2012
@ref: 17356
domain: Bacteria
phylum: Proteobacteria
class: Gammaproteobacteria
order: Thiotrichales
family: Francisellaceae
genus: Francisella
species: Francisella halioticida
full scientific name: Francisella halioticida Brevik et al. 2012
strain designation: Shimane-1
type strain: yes
Morphology
cell morphology
| @ref | motility | confidence | gram stain |
|---|---|---|---|
| 69480 | no | 94.435 | |
| 69480 | 99.952 | negative |
colony morphology
- @ref: 17356
- incubation period: 3-7 days
Culture and growth conditions
culture medium
- @ref: 17356
- name: FRANCISELLA HALIOTICIDA MEDIUM (DSMZ Medium 429d)
- growth: yes
- link: https://mediadive.dsmz.de/medium/429d
- composition: Name: FRANCISELLA HALIOTICIDA MEDIUM (DSMZ Medium 429d) Composition: Columbia agar base 700.0 g/l Horse blood 40.0 g/l Sheep blood 40.0 g/l Glucose 10.0 g/l Agar 2.0 g/l Cysteine 1.0 g/l FeCl3 0.3244 g/l
culture temp
- @ref: 17356
- growth: positive
- type: growth
- temperature: 20
- range: psychrophilic
Physiology and metabolism
spore formation
- @ref: 69480
- spore formation: no
- confidence: 99.999
Isolation, sampling and environmental information
isolation
- @ref: 17356
- sample type: haemolymph of a diseased cultured abalone (Haliotis gigantea)
- host species: Haliotis gigantea
- geographic location: Shimane Prefecture
- country: Japan
- origin.country: JPN
- continent: Asia
isolation source categories
| Cat1 | Cat2 | Cat3 |
|---|---|---|
| #Engineered | #Food production | #Aquaculture |
| #Host | #Invertebrates (Other) | #Mollusca |
| #Host Body Product | #Fluids |
Safety information
risk assessment
- @ref: 17356
- pathogenicity animal: yes
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
| @ref | description | accession | length | database | NCBI tax ID |
|---|---|---|---|---|---|
| 20218 | Francisella halioticida strain Shimane-1 16S ribosomal RNA gene, partial sequence | JF290376 | 1421 | ena | 549298 |
| 17356 | Francisella halioticida gene for 16S rRNA, partial sequence | AB449247 | 1456 | ena | 549298 |
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Francisella halioticida DSM 23729 | GCA_002211785 | complete | ncbi | 549298 |
| 66792 | Francisella halioticida strain DSM 23729 | 549298.4 | complete | patric | 549298 |
| 66792 | Francisella halioticida DSM 23729 | 2773857878 | complete | img | 549298 |
GC content
- @ref: 17356
- GC-content: 31.4
- method: sequence analysis
Genome-based predictions
predictions
| trait | prediction | confidence | training_data |
|---|---|---|---|
| spore-forming | no | 79 | no |
| flagellated | no | 97.203 | no |
| gram-positive | no | 96.591 | no |
| anaerobic | no | 96.241 | no |
| aerobic | no | 64.561 | no |
| halophile | no | 72.677 | no |
| spore-forming | no | 96.218 | no |
| glucose-util | yes | 76.825 | no |
| thermophile | no | 93.809 | no |
| motile | no | 93.478 | no |
| glucose-ferment | no | 73.316 | no |
External links
@ref: 17356
culture collection no.: DSM 23729, LMG 26062
straininfo link
- @ref: 75232
- straininfo: 398675
literature
| topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
|---|---|---|---|---|---|---|---|---|
| Phylogeny | 21883728 | Francisella halioticida sp. nov., a pathogen of farmed giant abalone (Haliotis gigantea) in Japan. | Brevik OJ, Ottem KF, Kamaishi T, Watanabe K, Nylund A | J Appl Microbiol | 10.1111/j.1365-2672.2011.05133.x | 2011 | Animals, Base Composition, DNA, Bacterial/genetics, Francisella/*classification/genetics/isolation & purification, Gastropoda/*microbiology, Japan, Nucleic Acid Hybridization, Phenotype, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA | Phenotype |
| Genetics | 32912905 | Complete Genome Sequence of Francisella halioticida Type Strain DSM 23729 (FSC1005). | Uneklint I, Ohrman C, Karlsson L, Bystrom M, Hagglund E, Forsman M, Sjodin A | Microbiol Resour Announc | 10.1128/MRA.00541-20 | 2020 |
Reference
| @id | authors | catalogue | doi/url | title | journal | pubmed |
|---|---|---|---|---|---|---|
| 17356 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 23729) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-23729 | |||
| 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 | |
| 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) | |||
| 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) | |||
| 75232 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID398675.1 | StrainInfo: A central database for resolving microbial strain identifiers |