Strain identifier

BacDive ID: 23989

Type strain: Yes

Species: Yersinia wautersii

Strain Designation: 12-219N1

Strain history: CIP <- 2013, C. Savin, Inst. Pasteur, Paris, France <- Shimane Prefectural Inst. of Public Healt & Environm. Science, Nishihamasada, Matsue, Japon: strain 12-219N1

NCBI tax ID(s): 1341643 (species)

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General

@ref: 20922

BacDive-ID: 23989

DSM-Number: 27350

keywords: genome sequence, 16S sequence, Bacteria, mesophilic, Gram-negative, motile, rod-shaped

description: Yersinia wautersii 12-219N1 is a mesophilic, Gram-negative, motile bacterium that was isolated from human.

NCBI tax id

  • NCBI tax id: 1341643
  • Matching level: species

strain history

@refhistory
20922<- C. Savin, CIP; 12-219N1 <- Shimane Pref. Inst. of Public Health and Environmental Sciences, Matsue, Japan
123915CIP <- 2013, C. Savin, Inst. Pasteur, Paris, France <- Shimane Prefectural Inst. of Public Healt & Environm. Science, Nishihamasada, Matsue, Japon: strain 12-219N1

doi: 10.13145/bacdive23989.20250331.9.3

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 wautersii
  • full scientific name: Yersinia wautersii Savin et al. 2014

@ref: 20922

domain: Bacteria

phylum: Proteobacteria

class: Gammaproteobacteria

order: Enterobacteriales, not validated

family: Yersiniaceae

genus: Yersinia

species: Yersinia wautersii

full scientific name: Yersinia wautersii Savin et al. 2014

strain designation: 12-219N1

type strain: yes

Morphology

cell morphology

@refgram stainconfidencecell shapemotility
125438negative97.833
123915negativerod-shapedyes

multimedia

  • @ref: 20922
  • multimedia content: https://www.dsmz.de/microorganisms/photos/DSM_27350.jpg
  • intellectual property rights: © Leibniz-Institut DSMZ

Culture and growth conditions

culture medium

@refnamegrowthcompositionlink
36210MEDIUM 72- for trypto casein soja agaryesDistilled water make up to (1000.000 ml);Trypto casein soy agar (40.000 g)
20922TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535)yesName: TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535) Composition: Trypticase soy broth 30.0 g/l Agar 15.0 g/l Distilled waterhttps://mediadive.dsmz.de/medium/535
123915CIP Medium 72yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72

culture temp

@refgrowthtypetemperature
20922positivegrowth28
36210positivegrowth30

Physiology and metabolism

oxygen tolerance

  • @ref: 125439
  • oxygen tolerance: obligate aerobe
  • confidence: 99.7

spore formation

  • @ref: 125439
  • spore formation: no
  • confidence: 93.7

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
68382alpha-fucosidase-3.2.1.51
68382beta-glucosidase-3.2.1.21
68382alpha-glucosidase-3.2.1.20
68382beta-glucuronidase-3.2.1.31
68382alpha-galactosidase-3.2.1.22
68382naphthol-AS-BI-phosphohydrolase-
68382acid phosphatase-3.1.3.2
68382alpha-chymotrypsin-3.4.21.1
68382cystine arylamidase-3.4.11.3
68382trypsin-3.4.21.4
68382valine arylamidase-
68382leucine arylamidase-3.4.11.1
68382lipase (C 14)-
68382esterase (C 4)-
68382esterase lipase (C 8)-
68382alkaline phosphatase-3.1.3.1
68368ornithine decarboxylase-4.1.1.17
68368lysine decarboxylase-4.1.1.18
68382alpha-mannosidase-3.2.1.24
68382N-acetyl-beta-glucosaminidase-3.2.1.52
68382beta-galactosidase-3.2.1.23
68368cytochrome oxidase-1.9.3.1
68368gelatinase-
68368tryptophan deaminase-4.1.99.1
68368urease+3.5.1.5
68368arginine dihydrolase+3.5.3.6
68368beta-galactosidase+3.2.1.23

API zym

@refControlAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
123915--------------------

API 20E

@refONPGADH ArgLDC LysODCCITH2SURETDA TrpINDVPGELGLUMANINOSorRHASACMELAMYARAOX
20922++----+----++--+-+-+-

Isolation, sampling and environmental information

isolation

@refsample typecountryorigin.countrycontinentisolation date
20922humanRepublic of KoreaKORAsia
123915Human, Human stoolsRepublic of KoreaKORAsia1993

isolation source categories

  • Cat1: #Host
  • Cat2: #Human

taxonmaps

  • @ref: 69479
  • File name: preview.99_140.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_6;96_106;97_113;98_124;99_140&stattab=map
  • Last taxonomy: Yersiniaceae
  • 16S sequence: HG326166
  • Sequence Identity:
  • Total samples: 33336
  • soil counts: 1734
  • aquatic counts: 5584
  • animal counts: 23907
  • plant counts: 2111

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
1239152Risk group (French classification)
209222Risk group (German classification)

Sequence information

16S sequences

  • @ref: 20922
  • description: Yersinia wautersii partial 16S rRNA gene, type strain 12-219N1T
  • accession: HG326166
  • length: 1476
  • database: nuccore
  • NCBI tax ID: 1341643

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Yersinia wautersii 12-219N1GCA_000493435scaffoldncbi1341643
66792Yersinia wautersii 12-219N12636416087draftimg1341643

Genome-based predictions

predictions

@refmodeltraitdescriptionpredictionconfidencetraining_data
125438gram-positivegram-positivePositive reaction to Gram-stainingno97.833no
125438anaerobicanaerobicAbility to grow under anoxygenic conditions (including facultative anaerobes)no85.856no
125438aerobicaerobicAbility to grow under oxygenic conditions (including facultative aerobes)no66.197no
125438spore-formingspore-formingAbility to form endo- or exosporesno89.122no
125438thermophilethermophilicAbility to grow at temperatures above or equal to 45°Cno95.929yes
125438motile2+flagellatedAbility to perform flagellated movementyes63.362no
125439BacteriaNetspore_formationAbility to form endo- or exosporesno93.7
125439BacteriaNetmotilityAbility to perform movementno59.4
125439BacteriaNetgram_stainReaction to gram-stainingnegative89.5
125439BacteriaNetoxygen_toleranceOxygenic conditions needed for growthobligate aerobe99.7

External links

@ref: 20922

culture collection no.: DSM 27350, CIP 110607

straininfo link

  • @ref: 87964
  • straininfo: 397397

Reference

@idauthorstitledoi/urlcatalogue
20215Parte, 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 DSMZ10.1099/ijsem.0.004332
20922Curators of the DSMZhttps://www.dsmz.de/collection/catalogue/details/culture/DSM-27350Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 27350)
36210Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/30409
66792Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg OvermannAutomatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)https://diaspora-project.de/progress.html#genomes
68368Automatically annotated from API 20E
68382Automatically annotated from API zym
69479João F Matias Rodrigues, Janko Tackmann,Gregor Rot, Thomas SB Schmidt, Lukas Malfertheiner, Mihai Danaila,Marija Dmitrijeva, Daniela Gaio, Nicolas Näpflin and Christian von Mering. University of Zurich.MicrobeAtlas 1.0 betahttps://microbeatlas.org/
87964Reimer, 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 identifiers10.60712/SI-ID397397.1
123915Curators of the CIPhttps://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20110607Collection of Institut Pasteur (CIP 110607)
125438Julia Koblitz, Lorenz Christian Reimer, Rüdiger Pukall, Jörg OvermannPredicting bacterial phenotypic traits through improved machine learning using high-quality, curated datasets10.1101/2024.08.12.607695
125439Philipp Münch, René Mreches, Martin Binder, Hüseyin Anil Gündüz, Xiao-Yin To, Alice McHardydeepG: Deep Learning for Genome Sequence Data. R package version 0.3.1https://github.com/GenomeNet/deepG