Strain identifier

BacDive ID: 5219

Type strain: Yes

Species: Yersinia similis

Strain Designation: Y228

Strain history: CIP <- 2008, CCUG <- 2006, H. Scholz, Bundeswehr Inst. für Mikrobiol., Munich, Germany: strain Y228

NCBI tax ID(s): 367190 (species)

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General

@ref: 7370

BacDive-ID: 5219

DSM-Number: 18211

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

description: Yersinia similis Y228 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from rabbit.

NCBI tax id

  • NCBI tax id: 367190
  • Matching level: species

strain history

@refhistory
7370<- H. Meyer <- H. Neubauer, München; Y228 <- S. Aleksic, Hygiene Institut, Hamburg
122619CIP <- 2008, CCUG <- 2006, H. Scholz, Bundeswehr Inst. für Mikrobiol., Munich, Germany: strain Y228

doi: 10.13145/bacdive5219.20230509.8.1

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 similis
  • full scientific name: Yersinia similis Sprague et al. 2008

@ref: 7370

domain: Bacteria

phylum: Proteobacteria

class: Gammaproteobacteria

order: Enterobacteriales, not validated

family: Yersiniaceae

genus: Yersinia

species: Yersinia similis

full scientific name: Yersinia similis Sprague et al. 2008

strain designation: Y228

type strain: yes

Morphology

cell morphology

@refgram staincell shapemotility
32388negativerod-shapedyes
122619negativerod-shapedno

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
7370COLUMBIA BLOOD AGAR (DSMZ Medium 429)yeshttps://mediadive.dsmz.de/medium/429Name: COLUMBIA BLOOD AGAR (DSMZ Medium 429) Composition: Horse blood 40.0 g/l Columbia agar base
37859MEDIUM 72- for trypto casein soja agaryesDistilled water make up to (1000.000 ml);Trypto casein soy agar (40.000 g)
122619CIP Medium 72yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72

culture temp

@refgrowthtypetemperaturerange
7370positivegrowth30mesophilic
37859positivegrowth30mesophilic
59706positivegrowth30mesophilic

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
59706aerobe
122619facultative anaerobe

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3238815428glycine+carbon source
3238826546rhamnose+carbon source
3238827082trehalose+carbon source
3238817632nitrate+reduction
68371Potassium 5-ketogluconate-builds acid from
68371Potassium 2-ketogluconate-builds acid from
6837118333D-arabitol+builds acid from
6837118287L-fucose-builds acid from
6837128847D-fucose-builds acid from
6837116443D-tagatose-builds acid from
6837162318D-lyxose-builds acid from
6837132528turanose-builds acid from
6837128066gentiobiose-builds acid from
6837117151xylitol-builds acid from
6837128087glycogen-builds acid from
6837128017starch-builds acid from
6837116634raffinose-builds acid from
683716731melezitose-builds acid from
6837115443inulin-builds acid from
6837127082trehalose+builds acid from
6837117992sucrose-builds acid from
6837128053melibiose-builds acid from
6837117716lactose-builds acid from
6837117306maltose+builds acid from
6837117057cellobiose-builds acid from
6837117814salicin-builds acid from
683714853esculin+builds acid from
6837118305arbutin+builds acid from
6837127613amygdalin-builds acid from
6837159640N-acetylglucosamine+builds acid from
68371320061methyl alpha-D-glucopyranoside-builds acid from
6837143943methyl alpha-D-mannoside-builds acid from
6837117924D-sorbitol-builds acid from
6837116899D-mannitol+builds acid from
6837117268myo-inositol-builds acid from
6837116813galactitol-builds acid from
6837162345L-rhamnose+builds acid from
6837117266L-sorbose-builds acid from
6837116024D-mannose+builds acid from
6837115824D-fructose+builds acid from
6837117634D-glucose+builds acid from
6837112936D-galactose+builds acid from
6837174863methyl beta-D-xylopyranoside-builds acid from
6837115963ribitol-builds acid from
6837165328L-xylose-builds acid from
6837165327D-xylose+builds acid from
6837116988D-ribose-builds acid from
6837130849L-arabinose+builds acid from
6837117108D-arabinose-builds acid from
6837117113erythritol-builds acid from
6837117754glycerol+builds acid from
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
12261917632nitrate+reduction
12261916301nitrite-reduction

metabolite production

@refChebi-IDmetaboliteproduction
6836815688acetoinyes
6836835581indoleno
6836816136hydrogen sulfideno
12261935581indoleno

metabolite tests

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

enzymes

@refvalueactivityec
32388catalase+1.11.1.6
32388urease+3.5.1.5
68382alpha-fucosidase-3.2.1.51
68382alpha-mannosidase-3.2.1.24
68382N-acetyl-beta-glucosaminidase+3.2.1.52
68382beta-glucosidase+3.2.1.21
68382alpha-glucosidase+3.2.1.20
68382beta-glucuronidase-3.2.1.31
68382beta-galactosidase-3.2.1.23
68382alpha-galactosidase-3.2.1.22
68382naphthol-AS-BI-phosphohydrolase+
68382acid phosphatase+3.1.3.2
68382alpha-chymotrypsin-3.4.21.1
68382trypsin+3.4.21.4
68382cystine arylamidase-3.4.11.3
68382valine arylamidase-
68382leucine arylamidase+3.4.11.1
68382lipase (C 14)-
68382esterase lipase (C 8)-
68382esterase (C 4)-
68382alkaline phosphatase+3.1.3.1
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
122619oxidase-
122619catalase+1.11.1.6
122619urease+3.5.1.5

API zym

@refControlAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
122619-+---+--+-++---+++--

API 20E

@refONPGADH ArgLDC LysODCCITH2SURETDA TrpINDVPGELGLUMANINOSorRHASACMELAMYARAOX
7370+---+-+--+-++--+---+-

API 50CHac

@refGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
122619+--+-+---++++-+--+---+-++--+---+------------++/-+/---

Isolation, sampling and environmental information

isolation

@refsample typecountryorigin.countrycontinent
7370rabbitGermanyDEUEurope
59706Oryctolagus cuniculusGermanyDEUEurope
122619Oryctolagus cuniculusGermanyDEUEurope

isolation source categories

  • Cat1: #Host
  • Cat2: #Mammals
  • Cat3: #Leporidae (Rabbit/Hare)

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: AM182404
  • 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
73702Risk group (German classification)
1226192Risk group (French classification)

Sequence information

16S sequences

  • @ref: 32388
  • description: Yersinia similis partial 16S rRNA gene, type strain Y228T
  • accession: AM182404
  • length: 1488
  • database: nuccore
  • NCBI tax ID: 367190

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Yersinia similis Y228GCA_001053095contigncbi367190
66792Yersinia similis strain 228 strain Y_sim_228367190.12plasmidpatric367190
66792Yersinia similis Y2282706794595draftimg1328310

GC content

  • @ref: 32388
  • GC-content: 48.3

External links

@ref: 7370

culture collection no.: DSM 18211, CCUG 52882, LMG 23763, CIP 109846

straininfo link

  • @ref: 74711
  • straininfo: 303083

literature

  • topic: Phylogeny
  • Pubmed-ID: 18398201
  • title: Yersinia similis sp. nov.
  • authors: Sprague LD, Scholz HC, Amann S, Busse HJ, Neubauer H
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijs.0.65417-0
  • year: 2008
  • mesh: Base Sequence, DNA, Bacterial/genetics, Genes, Bacterial, Genetic Markers, Lipid Metabolism, Molecular Sequence Data, Phenotype, Phylogeny, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Species Specificity, Terminology as Topic, Yersinia/*classification/*genetics/metabolism
  • topic2: Metabolism

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmed
7370Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 18211)https://www.dsmz.de/collection/catalogue/details/culture/DSM-18211
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
32388Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2861328776041
37859Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/7637
59706Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 52882)https://www.ccug.se/strain?id=52882
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
68371Automatically annotated from API 50CH acid
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.https://microbeatlas.org/MicrobeAtlas 1.0 beta
74711Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID303083.1StrainInfo: A central database for resolving microbial strain identifiers
122619Curators of the CIPCollection of Institut Pasteur (CIP 109846)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20109846