Strain identifier

BacDive ID: 5228

Type strain: Yes

Species: Yersinia massiliensis

Strain Designation: 50640

Strain history: CIP <- 2006, M. Drancourt, Timone Hosp., Marseille, France: strain 50640, "Yersinia phocaeense"

NCBI tax ID(s): 1205683 (strain), 419257 (species)

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General

@ref: 15996

BacDive-ID: 5228

DSM-Number: 21859

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

description: Yersinia massiliensis 50640 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from dialysis unit from the hospital water distribution system.

NCBI tax id

NCBI tax idMatching level
419257species
1205683strain

strain history

@refhistory
375232006, M. Drancourt, Timone Hosp., Marseille, France: strain 50640, "Yersinia phocaeense"
15996<- CIP <- M. Drancourt, Timone Hospital, Marseille, France; 50640 (Yersinia phocaeense)
120856CIP <- 2006, M. Drancourt, Timone Hosp., Marseille, France: strain 50640, "Yersinia phocaeense"

doi: 10.13145/bacdive5228.20230509.8.1

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: 15996

domain: Bacteria

phylum: Proteobacteria

class: Gammaproteobacteria

order: Enterobacteriales, not validated

family: Yersiniaceae

genus: Yersinia

species: Yersinia massiliensis

full scientific name: Yersinia massiliensis Merhej et al. 2008 emend. Souza et al. 2011

strain designation: 50640

type strain: yes

Morphology

cell morphology

@refgram staincell shapemotilityconfidence
32262negativeovoid-shapedyes
69480yes99.035
69480negative99.983
120856negativerod-shapedyes

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
15996TRYPTICASE 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
37523MEDIUM 72- for trypto casein soja agaryesDistilled water make up to (1000.000 ml);Trypto casein soy agar (40.000 g)
120856CIP Medium 72yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72

culture temp

@refgrowthtypetemperaturerange
15996positivegrowth28mesophilic
32262positivegrowth28-37mesophilic
37523positivegrowth30mesophilic
59901positivegrowth30mesophilic

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
59901aerobe
120856facultative anaerobe

spore formation

@refspore formationconfidence
69481no100
69480no99.35

compound production

  • @ref: 15996
  • compound: indol

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3226222599arabinose+carbon source
3226217234glucose+carbon source
3226229864mannitol+carbon source
3226230911sorbitol+carbon source
3226217992sucrose+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
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
6836817632nitrate-reduction
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
12085617632nitrate+reduction
12085616301nitrite-reduction

metabolite production

@refChebi-IDmetaboliteproduction
3226235581indoleyes
6836817997dinitrogenno
6836816301nitriteno
6836815688acetoinyes
6836835581indoleyes
6836816136hydrogen sulfideno
12085635581indoleyes

metabolite tests

@refChebi-IDmetaboliteindole testvoges-proskauer-test
3226235581indole+
6836815688acetoin+
6836835581indole+

enzymes

@refvalueactivityec
32262catalase+1.11.1.6
32262urease+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
120856oxidase-
120856catalase+1.11.1.6
120856urease+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
120856-++--++-+-++-+-+++--

API 20E

@refONPGADH ArgLDC LysODCCITH2SURETDA TrpINDVPGELGLUMANINOSorRHASACMELAMYARAOXNO2N2
15996+--++-+-++-++++-+-++---

API 50CHac

@refGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
120856+--+++---+++++--+++--+-++++++/--++------+----++-+-+

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentsampling dateisolation date
15996dialysis unit from the hospital water distribution systemMarseillesFranceFRAEurope
59901Water,dialysis unit from hospital water systemMarseille,Timone hospitalFranceFRAEurope2000-04-28
120856Environment, Water, dyalisisMarseilleFranceFRAEurope2000

isolation source categories

Cat1Cat2
#Environmental#Aquatic
#Infection#Medical device
#Infection#Medical environment

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
159961Risk group (German classification)
1208562Risk group (French classification)

Sequence information

16S sequences

  • @ref: 15996
  • description: Yersinia massiliensis strain CCUG 53443 16S ribosomal RNA gene, partial sequence
  • accession: EF179119
  • length: 1461
  • database: ena
  • NCBI tax ID: 1205683

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Yersinia massiliensis CCUG 53443GCA_000312485scaffoldncbi1205683
66792Yersinia massiliensis CIP109351GCA_902170765contigncbi419257
66792Yersinia massiliensis CCUG 534431205683.4wgspatric1205683
66792Yersinia massiliensis strain CIP109351419257.13wgspatric419257
66792Yersinia massiliensis CCUG 534432551306129draftimg1205683

GC content

  • @ref: 32262
  • GC-content: 49.3

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileyes90.13no
flagellatedyes64.803no
gram-positiveno98.653no
anaerobicno97.227yes
aerobicyes90.343yes
halophileno93.853no
spore-formingno94.953no
glucose-utilyes95.196no
glucose-fermentyes92.897yes
thermophileno99.541yes

External links

@ref: 15996

culture collection no.: DSM 21859, CCUG 53443, CIP 109351

straininfo link

  • @ref: 74720
  • straininfo: 343823

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

@idauthorscataloguedoi/urltitleID_cross_referencepubmed
15996Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 21859)https://www.dsmz.de/collection/catalogue/details/culture/DSM-21859
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
32262Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2850328776041
37523Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/7083
59901Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 53443)https://www.ccug.se/strain?id=53443
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
74720Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID343823.1StrainInfo: A central database for resolving microbial strain identifiers
120856Curators of the CIPCollection of Institut Pasteur (CIP 109351)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20109351