Strain identifier
BacDive ID: 5223
Type strain:
Species: Yersinia ruckeri
Strain Designation: 2396-61
Strain history: CIP <- 1982, H.H. Mollaret, Inst. Pasteur, Paris, France <- CDC: strain 2396-61
NCBI tax ID(s): 527005 (strain), 29486 (species)
General
@ref: 7565
BacDive-ID: 5223
DSM-Number: 18506
keywords: genome sequence, 16S sequence, Bacteria, mesophilic, Gram-negative, rod-shaped, animal pathogen
description: Yersinia ruckeri 2396-61 is a mesophilic, Gram-negative, rod-shaped animal pathogen that was isolated from rainbowtrout with red-mouth disease.
NCBI tax id
NCBI tax id | Matching level |
---|---|
527005 | strain |
29486 | species |
strain history
@ref | history |
---|---|
7565 | <- CIP <- H. H. Mollaret, Institut Pasteur, Paris <- CDC |
67770 | CIP 82.80 <-- H. H. Mollaret <-- CDC 2396-61. |
122299 | CIP <- 1982, H.H. Mollaret, Inst. Pasteur, Paris, France <- CDC: strain 2396-61 |
doi: 10.13145/bacdive5223.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/pseudomonadota
- domain: Bacteria
- phylum: Pseudomonadota
- class: Gammaproteobacteria
- order: Enterobacterales
- family: Yersiniaceae
- genus: Yersinia
- species: Yersinia ruckeri
- full scientific name: Yersinia ruckeri Ewing et al. 1978 (Approved Lists 1980)
@ref: 7565
domain: Bacteria
phylum: Proteobacteria
class: Gammaproteobacteria
order: Enterobacteriales, not validated
family: Yersiniaceae
genus: Yersinia
species: Yersinia ruckeri
full scientific name: Yersinia ruckeri Ewing et al. 1978
strain designation: 2396-61
type strain: yes
Morphology
cell morphology
- @ref: 122299
- gram stain: negative
- cell shape: rod-shaped
- motility: no
Culture and growth conditions
culture medium
@ref | name | growth | link | composition |
---|---|---|---|---|
7565 | TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535) | yes | https://mediadive.dsmz.de/medium/535 | Name: TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535) Composition: Trypticase soy broth 30.0 g/l Agar 15.0 g/l Distilled water |
41652 | MEDIUM 72- for trypto casein soja agar | yes | Distilled water make up to (1000.000 ml);Trypto casein soy agar (40.000 g) | |
122299 | CIP Medium 3 | yes | https://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=3 | |
122299 | CIP Medium 72 | yes | https://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72 |
culture temp
@ref | growth | type | temperature | range |
---|---|---|---|---|
7565 | positive | growth | 30 | mesophilic |
41652 | positive | growth | 30 | mesophilic |
46043 | positive | growth | 26 | mesophilic |
67770 | positive | growth | 30 | mesophilic |
Physiology and metabolism
metabolite utilization
@ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
---|---|---|---|---|
68368 | 30849 | L-arabinose | - | fermentation |
68368 | 27613 | amygdalin | - | fermentation |
68368 | 28053 | melibiose | - | fermentation |
68368 | 17992 | sucrose | - | fermentation |
68368 | 62345 | L-rhamnose | - | fermentation |
68368 | 30911 | sorbitol | - | fermentation |
68368 | 17268 | myo-inositol | - | fermentation |
68368 | 16899 | D-mannitol | + | fermentation |
68368 | 17634 | D-glucose | + | fermentation |
68368 | 5291 | gelatin | - | hydrolysis |
68368 | 27897 | tryptophan | - | energy source |
68368 | 16199 | urea | - | hydrolysis |
68368 | 16947 | citrate | - | assimilation |
68368 | 18257 | ornithine | + | degradation |
68368 | 25094 | lysine | + | degradation |
metabolite production
@ref | Chebi-ID | metabolite | production |
---|---|---|---|
68368 | 15688 | acetoin | yes |
68368 | 35581 | indole | no |
68368 | 16136 | hydrogen sulfide | no |
metabolite tests
@ref | Chebi-ID | metabolite | voges-proskauer-test | indole test |
---|---|---|---|---|
68368 | 15688 | acetoin | + | |
68368 | 35581 | indole | - |
enzymes
@ref | value | activity | ec |
---|---|---|---|
68368 | cytochrome oxidase | - | 1.9.3.1 |
68368 | gelatinase | - | |
68368 | tryptophan deaminase | - | 4.1.99.1 |
68368 | urease | - | 3.5.1.5 |
68368 | ornithine decarboxylase | + | 4.1.1.17 |
68368 | lysine decarboxylase | + | 4.1.1.18 |
68368 | beta-galactosidase | + | 3.2.1.23 |
API 20E
@ref | ONPG | ADH Arg | LDC Lys | ODC | CIT | H2S | URE | TDA Trp | IND | VP | GEL | GLU | MAN | INO | Sor | RHA | SAC | MEL | AMY | ARA | OX |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
7565 | + | - | + | + | - | - | - | - | - | + | - | + | + | - | - | - | - | - | - | - | - |
7565 | + | + | + | + | - | - | - | - | - | + | - | + | + | - | - | - | - | - | - | - | - |
7565 | + | + | + | + | - | - | - | - | - | + | - | + | + | - | - | - | - | - | - | - | - |
Isolation, sampling and environmental information
isolation
@ref | sample type | geographic location | country | origin.country | continent |
---|---|---|---|---|---|
7565 | rainbowtrout with red-mouth disease | Idaho | USA | USA | North America |
46043 | Rainbow trout with red mouth disease | USA | USA | North America | |
67770 | Rainbow trout with red mouth disease | ||||
122299 | Rainbow trout, red mouth disease | Idaho | United States of America | USA | North America |
isolation source categories
Cat1 | Cat2 | Cat3 |
---|---|---|
#Infection | #Disease | |
#Host | #Fishes | #Salmonidae |
#Host Body-Site | #Oral cavity and airways | #Mouth |
Safety information
risk assessment
@ref | pathogenicity animal | biosafety level | biosafety level comment |
---|---|---|---|
7565 | yes | 1 | Risk group (German classification) |
122299 | 2 | Risk group (French classification) |
Sequence information
16S sequences
@ref | description | accession | length | database | NCBI tax ID |
---|---|---|---|---|---|
20218 | Yersinia ruckeri strain CCUG 14190 16S ribosomal RNA gene, partial sequence | EF179132 | 1461 | ena | 29486 |
20218 | Yersinia ruckeri strain ATCC 29473 16S ribosomal RNA gene, partial sequence | FJ518718 | 410 | ena | 29486 |
20218 | Yersinia ruckeri ATCC 29473 16S ribosomal RNA gene, partial sequence | FJ518778 | 311 | ena | 527005 |
20218 | Yersinia ruckeri (ATCC 29473) partial 16S ribosomal RNA gene | X75275 | 1485 | ena | 29486 |
7565 | Yersinia ruckeri 16S ribosomal RNA gene, partial sequence | AF366385 | 1461 | ena | 29486 |
7565 | Yersinia ruckeri ATCC 29473 genomic scaffold scaffold1, whole genome shotgun sequence | KN150747 | 3672847 | ena | 527005 |
Genome sequences
@ref | description | accession | assembly level | database | NCBI tax ID |
---|---|---|---|---|---|
66792 | Yersinia ruckeri ATCC 29473 | 527005.28 | wgs | patric | 527005 |
66792 | Yersinia ruckeri ATCC 29473 | 527005.3 | wgs | patric | 527005 |
66792 | Yersinia ruckeri CSF007-82 | 29486.12 | wgs | patric | 29486 |
66792 | Yersinia ruckeri strain NCTC12986 | 29486.126 | wgs | patric | 29486 |
66792 | Yersinia ruckeri ATCC 29473 | 2609460118 | draft | img | 527005 |
66792 | Yersinia ruckeri NCTC 12986 | 2826154096 | draft | img | 29486 |
66792 | Yersinia ruckeri ATCC 29473 | 645058791 | draft | img | 527005 |
67770 | Yersinia ruckeri ATCC 29473 | GCA_000173755 | contig | ncbi | 527005 |
67770 | Yersinia ruckeri ATCC 29473 | GCA_000754815 | scaffold | ncbi | 527005 |
67770 | Yersinia ruckeri NCTC12986 | GCA_900460715 | contig | ncbi | 29486 |
GC content
- @ref: 67770
- GC-content: 46.5-48.5
- method: thermal denaturation, midpoint method (Tm)
Genome-based predictions
predictions
trait | prediction | confidence | training_data |
---|---|---|---|
gram-positive | no | 98.403 | no |
anaerobic | no | 97.827 | no |
halophile | no | 93.338 | no |
spore-forming | no | 94.169 | no |
glucose-util | yes | 92.669 | no |
thermophile | no | 97.806 | yes |
motile | yes | 87.799 | no |
aerobic | yes | 90.007 | no |
flagellated | yes | 53.479 | no |
glucose-ferment | yes | 93.227 | yes |
External links
@ref: 7565
culture collection no.: DSM 18506, ATCC 29473, CCM 6093, CCUG 14190, CIP 82.80, JCM 2429, NCIMB 2194, NCTC 12986, CECT 4319, JCM 15110, CDC 2396-61
straininfo link
- @ref: 74715
- straininfo: 39549
literature
topic | Pubmed-ID | title | authors | journal | year | mesh | topic2 | DOI |
---|---|---|---|---|---|---|---|---|
Enzymology | 24693657 | Fatty acid composition of Yersinia ruckeri isolates from aquaculture ponds in northwestern Germany. | Huang Y, Ryll M, Walker C, Jung A, Runge M, Steinhagen D | Berl Munch Tierarztl Wochenschr | 2014 | Animals, Aquaculture, Fatty Acids/*analysis/chemistry/isolation & purification, Fish Diseases/*microbiology, Germany, Oncorhynchus mykiss/*microbiology, Ponds/microbiology, Yersinia Infections/*microbiology/*veterinary, Yersinia ruckeri/*chemistry | Phylogeny | |
Genetics | 28317294 | Comparative genome analysis reveals important genetic differences among serotype O1 and serotype O2 strains of Y. ruckeri and provides insights into host adaptation and virulence. | Cascales D, Guijarro JA, Garcia-Torrico AI, Mendez J | Microbiologyopen | 2017 | Adaptation, Biological, Animals, Catfishes/*microbiology, *Genetic Variation, *Genome, Bacterial, Salmon/*microbiology, *Serogroup, Virulence, Yersinia ruckeri/*classification/*genetics/isolation & purification/pathogenicity | Phylogeny | 10.1002/mbo3.460 |
29523132 | Invasion and replication of Yersinia ruckeri in fish cell cultures. | Menanteau-Ledouble S, Lawrence ML, El-Matbouli M | BMC Vet Res | 2018 | Animals, Cells, Cultured, Fish Diseases/*microbiology, Kidney/cytology/microbiology, Salmon/microbiology, Yersinia/*growth & development/pathogenicity, Yersinia Infections/microbiology/*veterinary | 10.1186/s12917-018-1408-1 | ||
Phylogeny | 30460204 | pYR4 From a Norwegian Isolate of Yersinia ruckeri Is a Putative Virulence Plasmid Encoding Both a Type IV Pilus and a Type IV Secretion System. | Wrobel A, Ottoni C, Leo JC, Linke D | Front Cell Infect Microbiol | 2018 | Animals, Base Composition, Fimbriae, Bacterial/*genetics, Fish Diseases/*microbiology, Molecular Sequence Annotation, Norway, Plasmids/*analysis/classification, Salmon, Sequence Analysis, DNA, Type IV Secretion Systems/*genetics, Yersinia Infections/microbiology/*veterinary, Yersinia ruckeri/*genetics/*isolation & purification | Transcriptome | 10.3389/fcimb.2018.00373 |
34687878 | Effect of autochthonous lactobacilli on immunologically important molecules of rainbow trout after bacterial infection studied on intestinal primoculture. | Cingelova Maruscakova I, Schusterova P, Popelka P, Gancarcikova S, Csank T, Feckaninova A, Ratvaj M, Mudronova D | Fish Shellfish Immunol | 2021 | *Aeromonas salmonicida, Animals, *Bacterial Infections, Cytokines, *Fish Diseases, Lactobacillus, *Oncorhynchus mykiss, *Yersinia Infections/veterinary, Yersinia ruckeri | 10.1016/j.fsi.2021.10.021 | ||
Genetics | 34871418 | Deeplasmid: deep learning accurately separates plasmids from bacterial chromosomes. | Andreopoulos WB, Geller AM, Lucke M, Balewski J, Clum A, Ivanova NN, Levy A | Nucleic Acids Res | 2022 | Animals, Chromosomes, Bacterial/genetics, *Deep Learning, *Genome, Bacterial, *Plasmids/genetics, Reproducibility of Results, Sequence Analysis, DNA | Transcriptome | 10.1093/nar/gkab1115 |
Reference
@id | authors | catalogue | doi/url | title | journal | pubmed |
---|---|---|---|---|---|---|
7565 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 18506) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-18506 | |||
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 | |
41652 | Curators of the CIP | https://brclims.pasteur.fr/brcWeb/souche/detail/1/11354 | ||||
46043 | Curators of the CCUG | Culture Collection University of Gothenburg (CCUG) (CCUG 14190) | https://www.ccug.se/strain?id=14190 | |||
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) | |||
66794 | Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg | 10.1093/nar/gkaa1025 | BRENDA, the ELIXIR core data resource in 2021: new developments and updates | Nucleic Acids Res. 49: D498-D508 2020 | 33211880 | |
67770 | Curators of the JCM | https://jcm.brc.riken.jp/en/ | ||||
68368 | Automatically annotated from API 20E | |||||
74715 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID39549.1 | StrainInfo: A central database for resolving microbial strain identifiers | |||
122299 | Curators of the CIP | Collection of Institut Pasteur (CIP 82.80) | https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%2082.80 |