Strain identifier

BacDive ID: 136990

Type strain: No

Species: Yersinia massiliensis

Strain history: CIP <- 2006, M. Drancourt, Timone Hosp., Marseille, France: strain 823, "Yersinia phocaeense"

NCBI tax ID(s): 419257 (species)

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General

@ref: 36800

BacDive-ID: 136990

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

description: Yersinia massiliensis CIP 109352 is an aerobe, mesophilic, motile bacterium of the family Yersiniaceae.

NCBI tax id

  • NCBI tax id: 419257
  • Matching level: species

strain history

@refhistory
368002006, M. Drancourt, Timone Hosp., Marseille, France: strain 823, "Yersinia phocaeense"
36800CIP <- 2006, M. Drancourt, Timone Hosp., Marseille, France: strain 823, "Yersinia phocaeense"

doi: 10.13145/bacdive136990.20230509.8.1

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 massiliensis
  • full scientific name: Yersinia massiliensis Merhej et al. 2008

@ref: 36800

domain: Bacteria

phylum: Proteobacteria

class: Gammaproteobacteria

order: Enterobacterales

family: Yersiniaceae

genus: Yersinia

species: Yersinia massiliensis

type strain: no

Morphology

cell morphology

@refmotilityconfidencegram staincell shape
69480yes98.91
6948099.934negative
36800yesnegativerod-shaped

Culture and growth conditions

culture medium

@refnamegrowthcompositionlink
36800MEDIUM 72- for trypto casein soja agaryesDistilled water make up to (1000.000 ml);Trypto casein soy agar (40.000 g)
36800CIP Medium 72yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72

culture temp

@refgrowthtypetemperaturerange
36800positivegrowth37mesophilic
59902positivegrowth30mesophilic

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
59902aerobe
36800facultative anaerobe

spore formation

@refspore formationconfidence
69481no100
69480no97.997

metabolite utilization

@refmetaboliteutilization activitykind of utilization testedChebi-ID
68371Potassium 5-ketogluconate+builds acid from
68371Potassium 2-ketogluconate-builds acid from
68371gluconate+builds acid from24265
68371L-arabitol-builds acid from18403
68371D-arabitol+builds acid from18333
68371L-fucose+builds acid from18287
68371D-fucose-builds acid from28847
68371D-tagatose-builds acid from16443
68371D-lyxose-builds acid from62318
68371turanose-builds acid from32528
68371gentiobiose+builds acid from28066
68371xylitol-builds acid from17151
68371glycogen-builds acid from28087
68371starch-builds acid from28017
68371raffinose-builds acid from16634
68371melezitose-builds acid from6731
68371inulin-builds acid from15443
68371trehalose+builds acid from27082
68371sucrose+builds acid from17992
68371melibiose-builds acid from28053
68371lactose-builds acid from17716
68371maltose+builds acid from17306
68371cellobiose+builds acid from17057
68371salicin+builds acid from17814
68371esculin+builds acid from4853
68371arbutin+builds acid from18305
68371amygdalin-builds acid from27613
68371N-acetylglucosamine+builds acid from59640
68371methyl alpha-D-glucopyranoside-builds acid from320061
68371methyl alpha-D-mannoside-builds acid from43943
68371D-sorbitol+builds acid from17924
68371D-mannitol+builds acid from16899
68371myo-inositol+builds acid from17268
68371galactitol-builds acid from16813
68371L-rhamnose-builds acid from62345
68371L-sorbose+builds acid from17266
68371D-mannose+builds acid from16024
68371D-fructose+builds acid from15824
68371D-glucose+builds acid from17634
68371D-galactose+builds acid from12936
68371methyl beta-D-xylopyranoside-builds acid from74863
68371ribitol-builds acid from15963
68371L-xylose-builds acid from65328
68371D-xylose+builds acid from65327
68371D-ribose+builds acid from16988
68371L-arabinose+builds acid from30849
68371D-arabinose-builds acid from17108
68371erythritol-builds acid from17113
68371glycerol+builds acid from17754
36800nitrate+reduction17632
36800nitrite-reduction16301
68374ornithine-degradation18257
68374arginine-hydrolysis29016
68374lysine-degradation25094
68374urea+hydrolysis16199
68374L-arabitol-builds acid from18403
68374D-galacturonic acid+builds acid from18024
68374Potassium 5-ketogluconate-builds acid from
68374D-mannitol+builds acid from16899
68374maltose-builds acid from17306
68374ribitol-builds acid from15963
68374palatinose-builds acid from18394
68374malonate-assimilation15792
68374tryptophan+energy source27897
68374D-glucose+builds acid from17634
68374sucrose-builds acid from17992
68374L-arabinose+builds acid from30849
68374D-arabitol+builds acid from18333
68374trehalose+builds acid from27082
68374L-rhamnose-builds acid from62345
68374myo-inositol-builds acid from17268
68374cellobiose-builds acid from17057
68374sorbitol+builds acid from30911

metabolite production

@refChebi-IDmetaboliteproduction
6837435581indoleyes
3680035581indoleyes

metabolite tests

  • @ref: 68374
  • Chebi-ID: 35581
  • metabolite: indole
  • indole test: +

enzymes

@refvalueactivityec
68374L-aspartate arylamidase-3.4.11.21
68374alpha-maltosidase-
68374alpha-galactosidase-3.2.1.22
68374alpha-glucosidase-3.2.1.20
68374beta-galactosidase+3.2.1.23
68374N-acetyl-beta-glucosaminidase+3.2.1.52
68374beta-glucuronidase-3.2.1.31
68374beta-glucosidase+3.2.1.21
68374lipase+
68374urease+3.5.1.5
68374lysine decarboxylase-4.1.1.18
68374arginine dihydrolase-3.5.3.6
68374ornithine decarboxylase-4.1.1.17
36800oxidase-
36800catalase+1.11.1.6
36800urease+3.5.1.5
68382alkaline phosphatase+3.1.3.1
68382esterase (C 4)+
68382esterase lipase (C 8)+
68382lipase (C 14)-
68382leucine arylamidase+3.4.11.1
68382valine arylamidase+
68382cystine arylamidase-3.4.11.3
68382trypsin+3.4.21.4
68382alpha-chymotrypsin-3.4.21.1
68382acid phosphatase+3.1.3.2
68382naphthol-AS-BI-phosphohydrolase+
68382alpha-galactosidase-3.2.1.22
68382beta-galactosidase+3.2.1.23
68382beta-glucuronidase-3.2.1.31
68382alpha-glucosidase-3.2.1.20
68382beta-glucosidase+3.2.1.21
68382N-acetyl-beta-glucosaminidase+3.2.1.52
68382alpha-mannosidase-3.2.1.24
68382alpha-fucosidase-3.2.1.51

API zym

@refControlAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
36800-+++-++-+-++-+--++--

API 50CHac

@refGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
36800+--+++---+++++--+++--+-+++++--++------+----++-+-+

API ID32E

@refODCADH ArgLDC LysURELARLGAT5KGLIPRPbeta GLUMANMALADOPLEbeta GURMNTINDbeta NAGbeta GALGLUSACLARADARLalpha GLUalpha GALTRERHAINOCELSORalphaMALAspA
59902---+-+-++++-----++++-++--+---+--

Isolation, sampling and environmental information

isolation

@refgeographic locationcountryorigin.countrycontinentsample typesampling dateisolation date
36800MarseilleFranceFRAEurope
59902Marseille,Timone hospitalFranceFRAEuropeWater,well2006-08-01
36800MarseilleFranceFRAEuropeEnvironment, Water2006

isolation source categories

Cat1Cat2Cat3
#Environmental#Aquatic
#Engineered#Built environment#Water reservoir (Aquarium/pool)

Safety information

risk assessment

  • @ref: 36800
  • biosafety level: 2
  • biosafety level comment: Risk group (French classification)

Sequence information

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Yersinia massiliensis strain CIP109352419257.11wgspatric419257
66792Yersinia massiliensis CIP109352GCA_902170715contigncbi419257

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
gram-positiveno98.617no
anaerobicno97.298yes
halophileno93.191no
spore-formingno94.566no
glucose-utilyes95.548no
aerobicyes89.66yes
flagellatedyes58.158no
thermophileno99.006yes
motileyes90.252no
glucose-fermentyes92.678no

External links

@ref: 36800

culture collection no.: CIP 109352, CCUG 53444

straininfo link

  • @ref: 93983
  • straininfo: 362259

literature

  • topic: Phylogeny
  • Pubmed-ID: 18398169
  • title: Yersinia massiliensis sp. nov., isolated from fresh water.
  • authors: Merhej V, Adekambi T, Pagnier I, Raoult D, Drancourt M
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijs.0.65219-0
  • year: 2008
  • mesh: Base Sequence, DNA Primers/genetics, DNA, Bacterial/genetics, Fermentation, Fresh Water/microbiology, Genes, Bacterial, Microscopy, Electron, Transmission, Molecular Sequence Data, Phenotype, Phylogeny, Point Mutation, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Rhamnose/metabolism, Sequence Homology, Nucleic Acid, Species Specificity, Terminology as Topic, Yersinia/*classification/genetics/*isolation & purification/metabolism
  • topic2: Genetics

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
36800Curators of the CIPhttps://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20109352Collection of Institut Pasteur (CIP 109352)
59902Curators of the CCUGhttps://www.ccug.se/strain?id=53444Culture Collection University of Gothenburg (CCUG) (CCUG 53444)
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
68371Automatically annotated from API 50CH acid
68374Automatically annotated from API ID32E
68382Automatically annotated from API zym
69480Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg OvermannPredictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)https://diaspora-project.de/progress.html#genomes
69481Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. MünchPredictions based on the model GenomeNet Sporulation v. 110.21203/rs.3.rs-2527258/v1
93983Reimer, 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-ID362259.1