Strain identifier

BacDive ID: 5223

Type strain: Yes

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)

« back to strain detail view
For citation purpose refer to the digital object identifier (doi) of the current version.
Archive
version 9.3 (current version):
version 9.2:
version 9.1:
version 9:
version 8.1:
version 8:
version 7.1:
version 7:
version 6:
version 5:
version 4.1:
version 4:
version 3:
version 2.1:
version 2:
version 1:
version 9.3 (current version)

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 idMatching level
29486species
527005strain

strain history

@refhistory
7565<- CIP <- H. H. Mollaret, Institut Pasteur, Paris <- CDC
67770CIP 82.80 <-- H. H. Mollaret <-- CDC 2396-61.
122299CIP <- 1982, H.H. Mollaret, Inst. Pasteur, Paris, France <- CDC: strain 2396-61

doi: 10.13145/bacdive5223.20250331.9.3

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

@refgram staincell shapemotilityconfidence
122299negativerod-shapedno
125438negative99.5
125439negative97.8

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
7565TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535)yeshttps://mediadive.dsmz.de/medium/535Name: TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535) Composition: Trypticase soy broth 30.0 g/l Agar 15.0 g/l Distilled water
41652MEDIUM 72- for trypto casein soja agaryesDistilled water make up to (1000.000 ml);Trypto casein soy agar (40.000 g)
122299CIP Medium 3yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=3
122299CIP Medium 72yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72

culture temp

@refgrowthtypetemperature
7565positivegrowth30
41652positivegrowth30
46043positivegrowth26
67770positivegrowth30

Physiology and metabolism

oxygen tolerance

  • @ref: 125439
  • oxygen tolerance: aerobe
  • confidence: 90.9

spore formation

@refspore formationconfidence
125438no91.507
125439no98

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
6836830849L-arabinose-fermentation
6836827613amygdalin-fermentation
6836828053melibiose-fermentation
6836817992sucrose-fermentation
6836862345L-rhamnose-fermentation
6836830911sorbitol-fermentation
6836817268myo-inositol-fermentation
6836816899D-mannitol+fermentation
6836817634D-glucose+fermentation
683685291gelatin-hydrolysis
6836827897tryptophan-energy source
6836816199urea-hydrolysis
6836816947citrate-assimilation
6836818257ornithine+degradation
6836825094lysine+degradation

metabolite production

@refChebi-IDmetaboliteproduction
6836815688acetoinyes
6836835581indoleno
6836816136hydrogen sulfideno

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testindole test
6836815688acetoin+
6836835581indole-

enzymes

@refvalueactivityec
68368ornithine decarboxylase+4.1.1.17
68368cytochrome oxidase-1.9.3.1
68368gelatinase-
68368tryptophan deaminase-4.1.99.1
68368urease-3.5.1.5
68368lysine decarboxylase+4.1.1.18
68368beta-galactosidase+3.2.1.23

API 20E

@refONPGADH ArgLDC LysODCCITH2SURETDA TrpINDVPGELGLUMANINOSorRHASACMELAMYARAOX
7565+-++-----+-++--------
7565++++-----+-++--------
7565++++-----+-++--------

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
7565rainbowtrout with red-mouth diseaseIdahoUSAUSANorth America
46043Rainbow trout with red mouth diseaseUSAUSANorth America
67770Rainbow trout with red mouth disease
122299Rainbow trout, red mouth diseaseIdahoUnited States of AmericaUSANorth America

isolation source categories

Cat1Cat2Cat3
#Infection#Disease
#Host#Fishes#Salmonidae
#Host Body-Site#Oral cavity and airways#Mouth

Safety information

risk assessment

@refpathogenicity animalbiosafety levelbiosafety level comment
7565yes1Risk group (German classification)
1222992Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Yersinia ruckeri strain CCUG 14190 16S ribosomal RNA gene, partial sequenceEF1791321461nuccore29486
20218Yersinia ruckeri strain ATCC 29473 16S ribosomal RNA gene, partial sequenceFJ518718410nuccore29486
20218Yersinia ruckeri ATCC 29473 16S ribosomal RNA gene, partial sequenceFJ518778311nuccore527005
20218Yersinia ruckeri (ATCC 29473) partial 16S ribosomal RNA geneX752751485nuccore29486
7565Yersinia ruckeri 16S ribosomal RNA gene, partial sequenceAF3663851461nuccore29486
7565Yersinia ruckeri ATCC 29473 genomic scaffold scaffold1, whole genome shotgun sequenceKN1507473672847nuccore527005
124043Yersinia ruckeri ATCC 29473 16S ribosomal RNA gene, partial sequence.FJ518716410nuccore29486
124043Yersinia ruckeri ATCC 29473 16S ribosomal RNA gene, partial sequence.FJ518717410nuccore29486
124043Yersinia ruckeri ATCC 29473 16S ribosomal RNA gene, partial sequence.FJ518721410nuccore630
124043Yersinia ruckeri ATCC 29473 16S ribosomal RNA gene, partial sequence.FJ518722410nuccore630
124043Yersinia ruckeri ATCC 29473 16S ribosomal RNA gene, partial sequence.FJ518723410nuccore630
124043Yersinia ruckeri ATCC 29473 16S ribosomal RNA gene, partial sequence.FJ518724410nuccore630
124043Yersinia ruckeri ATCC 29473 16S ribosomal RNA gene, partial sequence.FJ518725410nuccore630
124043Yersinia ruckeri ATCC 29473 16S ribosomal RNA gene, partial sequence.FJ518726410nuccore632
124043Yersinia ruckeri ATCC 29473 16S ribosomal RNA gene, partial sequence.FJ518727410nuccore632
124043Yersinia ruckeri ATCC 29473 16S ribosomal RNA gene, partial sequence.FJ518776311nuccore29486
124043Yersinia ruckeri ATCC 29473 16S ribosomal RNA gene, partial sequence.FJ518777311nuccore29486

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Yersinia ruckeri ATCC 29473527005.28wgspatric527005
66792Yersinia ruckeri ATCC 29473527005.3wgspatric527005
66792Yersinia ruckeri CSF007-8229486.12wgspatric29486
66792Yersinia ruckeri strain NCTC1298629486.126wgspatric29486
66792Yersinia ruckeri ATCC 294732609460118draftimg527005
66792Yersinia ruckeri NCTC 129862826154096draftimg29486
66792Yersinia ruckeri ATCC 29473645058791draftimg527005
67770Yersinia ruckeri ATCC 29473GCA_000173755contigncbi527005
67770Yersinia ruckeri ATCC 29473GCA_000754815scaffoldncbi527005
67770Yersinia ruckeri NCTC12986GCA_900460715contigncbi29486

GC content

  • @ref: 67770
  • GC-content: 46.5-48.5
  • method: thermal denaturation, midpoint method (Tm)

Genome-based predictions

predictions

@refmodeltraitdescriptionpredictionconfidencetraining_data
125438gram-positivegram-positivePositive reaction to Gram-stainingno99.5no
125438anaerobicanaerobicAbility to grow under anoxygenic conditions (including facultative anaerobes)no97.336no
125438spore-formingspore-formingAbility to form endo- or exosporesno91.507no
125438aerobicaerobicAbility to grow under oxygenic conditions (including facultative aerobes)no67.59no
125438thermophilethermophilicAbility to grow at temperatures above or equal to 45°Cno98.5yes
125438motile2+flagellatedAbility to perform flagellated movementyes79.237no
125439BacteriaNetspore_formationAbility to form endo- or exosporesno98
125439BacteriaNetmotilityAbility to perform movementyes82.2
125439BacteriaNetgram_stainReaction to gram-stainingnegative97.8
125439BacteriaNetoxygen_toleranceOxygenic conditions needed for growthaerobe90.9

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

topicPubmed-IDtitleauthorsjournalyearmeshtopic2DOI
Enzymology24693657Fatty acid composition of Yersinia ruckeri isolates from aquaculture ponds in northwestern Germany.Huang Y, Ryll M, Walker C, Jung A, Runge M, Steinhagen DBerl Munch Tierarztl Wochenschr2014Animals, Aquaculture, Fatty Acids/*analysis/chemistry/isolation & purification, Fish Diseases/*microbiology, Germany, Oncorhynchus mykiss/*microbiology, Ponds/microbiology, Yersinia Infections/*microbiology/*veterinary, Yersinia ruckeri/*chemistryPhylogeny
Genetics28317294Comparative 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 JMicrobiologyopen2017Adaptation, Biological, Animals, Catfishes/*microbiology, *Genetic Variation, *Genome, Bacterial, Salmon/*microbiology, *Serogroup, Virulence, Yersinia ruckeri/*classification/*genetics/isolation & purification/pathogenicityPhylogeny10.1002/mbo3.460
29523132Invasion and replication of Yersinia ruckeri in fish cell cultures.Menanteau-Ledouble S, Lawrence ML, El-Matbouli MBMC Vet Res2018Animals, Cells, Cultured, Fish Diseases/*microbiology, Kidney/cytology/microbiology, Salmon/microbiology, Yersinia/*growth & development/pathogenicity, Yersinia Infections/microbiology/*veterinary10.1186/s12917-018-1408-1
Phylogeny30460204pYR4 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 DFront Cell Infect Microbiol2018Animals, 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 & purificationTranscriptome10.3389/fcimb.2018.00373
34687878Effect 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 DFish Shellfish Immunol2021*Aeromonas salmonicida, Animals, *Bacterial Infections, Cytokines, *Fish Diseases, Lactobacillus, *Oncorhynchus mykiss, *Yersinia Infections/veterinary, Yersinia ruckeri10.1016/j.fsi.2021.10.021
Genetics34871418Deeplasmid: deep learning accurately separates plasmids from bacterial chromosomes.Andreopoulos WB, Geller AM, Lucke M, Balewski J, Clum A, Ivanova NN, Levy ANucleic Acids Res2022Animals, Chromosomes, Bacterial/genetics, *Deep Learning, *Genome, Bacterial, *Plasmids/genetics, Reproducibility of Results, Sequence Analysis, DNATranscriptome10.1093/nar/gkab1115

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
7565Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 18506)https://www.dsmz.de/collection/catalogue/details/culture/DSM-18506
20215Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M.10.1099/ijsem.0.004332List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ
20218Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P.10.1016/j.syapm.2013.11.002StrainInfo introduces electronic passports for microorganisms.Syst Appl Microbiol. 37: 42-50 201424321274
41652Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/11354
46043Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 14190)https://www.ccug.se/strain?id=14190
66792Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmannhttps://diaspora-project.de/progress.html#genomesAutomatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)
66794Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg10.1093/nar/gkaa1025BRENDA, the ELIXIR core data resource in 2021: new developments and updatesNucleic Acids Res. 49: D498-D508 202033211880
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
68368Automatically annotated from API 20E
74715Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID39549.1StrainInfo: A central database for resolving microbial strain identifiers
122299Curators of the CIPCollection of Institut Pasteur (CIP 82.80)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%2082.80
124043Isabel Schober, Julia KoblitzData extracted from sequence databases, automatically matched based on designation and taxonomy
125438Julia Koblitz, Lorenz Christian Reimer, Rüdiger Pukall, Jörg Overmann10.1101/2024.08.12.607695Predicting bacterial phenotypic traits through improved machine learning using high-quality, curated datasets
125439Philipp Münch, René Mreches, Martin Binder, Hüseyin Anil Gündüz, Xiao-Yin To, Alice McHardyhttps://github.com/GenomeNet/deepGdeepG: Deep Learning for Genome Sequence Data. R package version 0.3.1