Strain identifier

BacDive ID: 5229

Type strain: Yes

Species: Yersinia entomophaga

Strain Designation: SpK, MH96

Strain history: CIP <- 2010, DSMZ <- M.R.H. Hurst, Lincoln Research Centre <- E. Lang, DSMZ, Braunschweig, Germany: strain MH96

NCBI tax ID(s): 935293 (species)

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General

@ref: 16300

BacDive-ID: 5229

DSM-Number: 22339

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

description: Yersinia entomophaga SpK is an aerobe, mesophilic, Gram-negative animal pathogen that was isolated from diseased grass grub larvae.

NCBI tax id

  • NCBI tax id: 935293
  • Matching level: species

strain history

@refhistory
16300<- M. R. H. Hurst, AgResearch Ltd, Christchurch, New Zealand; MH96
119085CIP <- 2010, DSMZ <- M.R.H. Hurst, Lincoln Research Centre <- E. Lang, DSMZ, Braunschweig, Germany: strain MH96

doi: 10.13145/bacdive5229.20230509.8.1

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 entomophaga
  • full scientific name: Yersinia entomophaga Hurst et al. 2011

@ref: 16300

domain: Bacteria

phylum: Proteobacteria

class: Gammaproteobacteria

order: Enterobacteriales, not validated

family: Yersiniaceae

genus: Yersinia

species: Yersinia entomophaga

full scientific name: Yersinia entomophaga Hurst et al. 2011

strain designation: SpK, MH96

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
29891negative1.7 µm0.7 µmrod-shapedyes
69480yes98.783
69480negative99.971
119085negativerod-shapedyes

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
16300TRYPTICASE 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
37580MEDIUM 72- for trypto casein soja agaryesDistilled water make up to (1000.000 ml);Trypto casein soy agar (40.000 g)
119085CIP Medium 72yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72

culture temp

@refgrowthtypetemperaturerange
16300positivegrowth28mesophilic
29891positivegrowth25-42
29891positiveoptimum33.5mesophilic
37580positivegrowth30mesophilic
62142positivegrowth30mesophilic

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
62142aerobe
119085facultative anaerobe

spore formation

@refspore formationconfidence
29891no
69481no100
69480no99.109

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
2989117057cellobiose+carbon source
2989116947citrate+carbon source
2989117754glycerol+carbon source
2989128053melibiose+carbon source
2989117992sucrose+carbon source
68371Potassium 5-ketogluconate+builds acid from
68371Potassium 2-ketogluconate-builds acid from
6837124265gluconate+builds acid from
6837118403L-arabitol-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
6837117306maltose+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
11908517632nitrate+reduction
11908516301nitrite-reduction

metabolite production

@refChebi-IDmetaboliteproduction
6836815688acetoinyes
6836835581indoleno
6836816136hydrogen sulfideno
11908535581indoleno

metabolite tests

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

enzymes

@refvalueactivityec
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
119085oxidase-
119085catalase+1.11.1.6
119085urease-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
119085-+++-++-+-++++-+-+--

API 20E

@refONPGADH ArgLDC LysODCCITH2SURETDA TrpINDVPGELGLUMANINOSorRHASACMELAMYARAOX
16300+--++----++++---+++--

API 50CHac

@refGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
119085+---+----++++----+---+----+/-++/-+++--+-----------+-+

Isolation, sampling and environmental information

isolation

@refsample typehost speciesgeographic locationcountryorigin.countrycontinentsampling date
16300diseased grass grub (Costelytra zealandica) larvaeCostelytra zealandicaSouth Island pasture landNew ZealandNZLAustralia and Oceania
62142Diseased Costelytra zealandica grass grub larvaeNew ZealandNZLAustralia and Oceania2000
119085Animal, Disased larvae of New-Zealand grass grup, Castelytra sp.New ZealandNZLAustralia and Oceania

isolation source categories

  • Cat1: #Host
  • Cat2: #Arthropoda
  • Cat3: #Insecta

Safety information

risk assessment

@refpathogenicity animalbiosafety levelbiosafety level comment
16300yes1Risk group (German classification)
1190852Risk group (French classification)

Sequence information

16S sequences

  • @ref: 16300
  • description: Yersinia sp. MH-1 clone ye16s 16S ribosomal RNA gene, partial sequence
  • accession: DQ400782
  • length: 1513
  • database: ena
  • NCBI tax ID: 935293

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Yersinia entomophaga MH96GCA_001656035chromosomencbi935293
66792Yersinia entomophaga MH962795385501completeimg935293

GC content

@refGC-contentmethod
1630049.3high performance liquid chromatography (HPLC)
2989149.3

Genome-based predictions

predictions

  • trait: spore-forming
  • prediction: no
  • confidence: 100
  • training_data: no

External links

@ref: 16300

culture collection no.: DSM 22339, ATCC BAA 1678, CIP 110202, CCUG 59867

straininfo link

  • @ref: 74721
  • straininfo: 377109

literature

  • topic: Phylogeny
  • Pubmed-ID: 20495033
  • title: Yersinia entomophaga sp. nov., isolated from the New Zealand grass grub Costelytra zealandica.
  • authors: Hurst MRH, Becher SA, Young SD, Nelson TL, Glare TR
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijs.0.024406-0
  • year: 2010
  • mesh: Animals, Bacterial Proteins/genetics, Bacterial Typing Techniques, Cluster Analysis, Coleoptera/*microbiology, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Larva/microbiology, Molecular Sequence Data, Multilocus Sequence Typing, New Zealand, Nucleic Acid Hybridization, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Yersinia/*classification/genetics/*isolation & purification/physiology
  • topic2: Genetics

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmed
16300Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 22339)https://www.dsmz.de/collection/catalogue/details/culture/DSM-22339
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
29891Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2626428776041
37580Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/8035
62142Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 59867)https://www.ccug.se/strain?id=59867
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
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
74721Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID377109.1StrainInfo: A central database for resolving microbial strain identifiers
119085Curators of the CIPCollection of Institut Pasteur (CIP 110202)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20110202