Strain identifier

BacDive ID: 5226

Type strain: Yes

Species: Yersinia bercovieri

Strain history: CIP <- 1989, H.H. Mollaret, Inst. Pasteur, Paris, France: strain CNY 7506

NCBI tax ID(s): 349968 (strain), 634 (species)

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General

@ref: 7579

BacDive-ID: 5226

DSM-Number: 18528

keywords: genome sequence, 16S sequence, Bacteria, aerobe, mesophilic, motile

description: Yersinia bercovieri DSM 18528 is an aerobe, mesophilic, motile bacterium that was isolated from human stool.

NCBI tax id

NCBI tax idMatching level
349968strain
634species

strain history

@refhistory
7579<- CIP <- H. H. Mollaret, Inst. Pasteur, Paris; CNY 7506
329361989, H.H. Mollaret, Inst. Pasteur, Paris, France: strain CNY 7506
116787CIP <- 1989, H.H. Mollaret, Inst. Pasteur, Paris, France: strain CNY 7506

doi: 10.13145/bacdive5226.20230509.8.1

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 bercovieri
  • full scientific name: Yersinia bercovieri Wauters et al. 1988

@ref: 7579

domain: Bacteria

phylum: Proteobacteria

class: Gammaproteobacteria

order: Enterobacteriales, not validated

family: Yersiniaceae

genus: Yersinia

species: Yersinia bercovieri

full scientific name: Yersinia bercovieri Wauters et al. 1988

type strain: yes

Morphology

cell morphology

@refmotilityconfidencegram stain
69480yes98.874
6948099.972negative

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
7579TRYPTICASE 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
32936MEDIUM 3 - Columbia agaryesColumbia agar (39.000 g);distilled water (1000.000 ml)
116787CIP Medium 72yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72
116787CIP Medium 3yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=3

culture temp

@refgrowthtypetemperaturerange
7579positivegrowth30mesophilic
32936positivegrowth30mesophilic
48413positivegrowth30-37mesophilic

Physiology and metabolism

oxygen tolerance

  • @ref: 48413
  • oxygen tolerance: aerobe

spore formation

@refspore formationconfidence
69481no100
69480no98.302

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
6836829016arginine-hydrolysis

metabolite production

@refChebi-IDmetaboliteproduction
6836815688acetoinno
6836835581indoleno
6836816136hydrogen sulfideno

metabolite tests

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

enzymes

@refvalueactivityec
68368cytochrome oxidase-1.9.3.1
68368gelatinase-
68368tryptophan deaminase-4.1.99.1
68368urease+3.5.1.5
68368ornithine decarboxylase-4.1.1.17
68368lysine decarboxylase-4.1.1.18
68368arginine dihydrolase-3.5.3.6
68368beta-galactosidase+3.2.1.23

fatty acid profile

  • fatty acids

    @reffatty acidpercentageECL
    48413C12:0712
    48413C14:01.814
    48413C16:030.516
    48413C12:0 ALDE ?1.210.915
    48413C14:0 3OH/C16:1 ISO I6.915.485
    48413C16:1 ω7c2515.819
    48413C17:0 CYCLO17.716.888
    48413C18:1 ω7c /12t/9t8.517.824
    48413unknown 13.9610.813.961
    48413unknown 14.5030.614.503
  • type of FA analysis: whole cell analysis
  • method/protocol: CCUG

API 20E

@refONPGADH ArgLDC LysODCCITH2SURETDA TrpINDVPGELGLUMANINOSorRHASACMELAMYARAOX
7579+-----+----++-+-+-++-

Isolation, sampling and environmental information

isolation

@refsample typecountryorigin.countrycontinent
7579human stoolFranceFRAEurope
48413Human fecesFranceFRAEurope
116787Human, StoolFranceFRAEurope

isolation source categories

Cat1Cat2Cat3
#Host Body Product#Gastrointestinal tract#Feces (Stool)
#Host#Human

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
75791Risk group (German classification)
1167872Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Yersinia bercovieri strain ATCC 43970 16S ribosomal RNA gene, partial sequenceDQ011931433ena349968
20218Yersinia bercovieri strain CCUG 26329 16S ribosomal RNA gene, partial sequenceEF1791211461ena634
20218Yersinia bercovieri ATCC 43970 16S ribosomal RNA gene, partial sequenceFJ518720408ena349968
7579Yersinia bercovieri 16S ribosomal RNA gene, partial sequenceAF3663771461ena349968

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Yersinia bercovieri ATCC 43970GCA_013282745chromosomencbi349968
66792Yersinia bercovieri ATCC 43970GCA_000167975contigncbi349968
66792Yersinia bercovieri ATCC 43970349968.9completepatric349968
66792Yersinia bercovieri ATCC 43970349968.5wgspatric349968
66792Yersinia bercovieri ATCC 43970638341238draftimg349968

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
gram-positiveno98.787no
anaerobicno96.799yes
halophileno94.408no
spore-formingno94.064no
glucose-utilyes94.724no
motileyes90.344no
flagellatedyes64.577no
aerobicyes87.79no
thermophileno99.251yes
glucose-fermentyes93.708yes

External links

@ref: 7579

culture collection no.: DSM 18528, ATCC 43970, CCUG 26329, CIP 103323, CNY 7506

straininfo link

  • @ref: 74718
  • straininfo: 45179

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
7579Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 18528)https://www.dsmz.de/collection/catalogue/details/culture/DSM-18528
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
32936Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/15108
48413Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 26329)https://www.ccug.se/strain?id=26329
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)
68368Automatically annotated from API 20E
69480Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmannhttps://diaspora-project.de/progress.html#genomesPredictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)
69481Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch10.21203/rs.3.rs-2527258/v1Predictions based on the model GenomeNet Sporulation v. 1
74718Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID45179.1StrainInfo: A central database for resolving microbial strain identifiers
116787Curators of the CIPCollection of Institut Pasteur (CIP 103323)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20103323