Strain identifier

BacDive ID: 5339

Type strain: No

Species: Enterococcus villorum

Strain Designation: DS 1390-83, Johnson 2757, SS1503

Strain history: CIP <- 2001, CCUG <- 2000, CDC, Atlanta, USA <- D.D. Johnson, South Dakota Ste Univ., Brookings, SD, USA

NCBI tax ID(s): 1158604 (strain), 112904 (species)

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General

@ref: 6055

BacDive-ID: 5339

DSM-Number: 15688

keywords: genome sequence, 16S sequence, Bacteria, microaerophile, spore-forming, mesophilic, animal pathogen

description: Enterococcus villorum DS 1390-83 is a microaerophile, spore-forming, mesophilic animal pathogen that was isolated from piglet, 2-4 days old.

NCBI tax id

NCBI tax idMatching level
1158604strain
112904species

strain history

@refhistory
6055<- CCUG <- R. R. Facklam, CDC <- D. D. Johnson
123841CIP <- 2001, CCUG <- 2000, CDC, Atlanta, USA <- D.D. Johnson, South Dakota Ste Univ., Brookings, SD, USA

doi: 10.13145/bacdive5339.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/bacillota
  • domain: Bacteria
  • phylum: Bacillota
  • class: Bacilli
  • order: Lactobacillales
  • family: Enterococcaceae
  • genus: Enterococcus
  • species: Enterococcus villorum
  • full scientific name: Enterococcus villorum Vancanneyt et al. 2001

  • synonyms

    • @ref: 20215
    • synonym: Enterococcus porcinus

@ref: 6055

domain: Bacteria

phylum: Firmicutes

class: Bacilli

order: Lactobacillales

family: Enterococcaceae

genus: Enterococcus

species: Enterococcus villorum

full scientific name: Enterococcus villorum Vancanneyt et al. 2001

strain designation: DS 1390-83, Johnson 2757, SS1503

type strain: no

Morphology

cell morphology

@refmotilityconfidencegram staincell shape
69480no90.206
69480100positive
123841nopositivecoccus-shaped

colony morphology

  • @ref: 123841
  • hemolysis ability: 1

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
6055TRYPTICASE SOY YEAST EXTRACT MEDIUM (DSMZ Medium 92)yeshttps://mediadive.dsmz.de/medium/92Name: TRYPTICASE SOY YEAST EXTRACT MEDIUM (DSMZ Medium 92) Composition: Trypticase soy broth 30.0 g/l Agar 15.0 g/l Yeast extract 3.0 g/l Distilled water
6055COLUMBIA BLOOD MEDIUM (DSMZ Medium 693)yeshttps://mediadive.dsmz.de/medium/693Name: COLUMBIA BLOOD MEDIUM (DSMZ Medium 693) Composition: Defibrinated sheep blood 50.0 g/l Columbia agar base
34929MEDIUM 6 - Columbia agar with 10 % horse bloodyesDistilled water make up to (1000.000 ml);Columbia agar (39.000 g);Horseblood (100.000 ml)
123841CIP Medium 6yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=6

culture temp

@refgrowthtypetemperaturerange
6055positivegrowth37mesophilic
34929positivegrowth37mesophilic
55737positivegrowth37mesophilic
123841positivegrowth10-45

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
6055microaerophile
55737aerobe
123841facultative anaerobe

spore formation

@refspore formationconfidence
69481yes100
69480no99.893

halophily

  • @ref: 123841
  • salt: NaCl
  • growth: positive
  • tested relation: growth
  • concentration: 6.5 %

metabolite utilization

@refmetaboliteutilization activitykind of utilization testedChebi-ID
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
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
123841esculin+hydrolysis4853
123841hippurate+hydrolysis606565
123841nitrate-reduction17632
123841nitrite-reduction16301
123841nitrate+respiration17632

metabolite tests

  • @ref: 123841
  • Chebi-ID: 15688
  • metabolite: acetoin
  • voges-proskauer-test: -

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
123841oxidase-
123841beta-galactosidase+3.2.1.23
123841alcohol dehydrogenase+1.1.1.1
123841gelatinase-
123841amylase-
123841catalase-1.11.1.6
123841gamma-glutamyltransferase+2.3.2.2
123841lysine decarboxylase-4.1.1.18
123841ornithine decarboxylase-4.1.1.17

API zym

@refControlAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
123841--++---------+------

API 50CHac

@refGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
123841----++---++++--------++/-+++++++-+------+---------+/-

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
123841---------------+--+-------------------------------------------+--+--------------------+------------

Isolation, sampling and environmental information

isolation

@refsample typesampling dategeographic locationcountryorigin.countrycontinentisolation date
6055piglet, 2-4 days old
55737Piglet,2-4 days old1981DakotaUSAUSANorth America
123841Animal, PigletDakotaUnited States of AmericaUSANorth America1981

isolation source categories

  • Cat1: #Host
  • Cat2: #Mammals
  • Cat3: #Suidae (Pig,Swine)

Safety information

risk assessment

@refpathogenicity animalbiosafety levelbiosafety level comment
6055yes2Risk group (German classification)
1238412Risk group (French classification)

Sequence information

16S sequences

  • @ref: 20218
  • description: Enterococcus villorum 16S ribosomal RNA gene, partial sequence
  • accession: AF335596
  • length: 1536
  • database: ena
  • NCBI tax ID: 112904

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Enterococcus villorum ATCC 700913GCA_000407205scaffoldncbi1158604
66792Enterococcus villorum ATCC 700913GCA_000393935scaffoldncbi1158604
66792Enterococcus villorum ATCC 700913 [PRJNA202675]1158604.3wgspatric1158604
66792Enterococcus villorum ATCC 700913 [PRJNA206358]1158604.4wgspatric1158604
66792Enterococcus villorum ATCC 7009132558860910draftimg1158604
66792Enterococcus villorum ATCC 7009132545824674draftimg1158604

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingyes100no
motileno96.242no
flagellatedno98.166no
gram-positiveyes95.44no
anaerobicno97.21yes
aerobicno94.815no
halophileyes92.873no
spore-formingno89.073no
thermophileno99.576no
glucose-utilyes90.897no
glucose-fermentyes90.031no

External links

@ref: 6055

culture collection no.: DSM 15688, ATCC 700913, CCUG 43229, CIP 107172, NCIMB 13634

straininfo link

  • @ref: 74828
  • straininfo: 13247

literature

  • topic: Phylogeny
  • Pubmed-ID: 11594604
  • title: Enterococcus porcinus sp. nov. and Enterococcus ratti sp. nov., associated with enteric disorders in animals.
  • authors: Teixeira LM, Carvalho MG, Espinola MM, Steigerwalt AG, Douglas MP, Brenner DJ, Facklam RR
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/00207713-51-5-1737
  • year: 2001
  • mesh: Animals, Bacterial Proteins/analysis, DNA, Bacterial/analysis/genetics, DNA, Ribosomal/analysis/genetics, Diarrhea/microbiology/*veterinary, Electrophoresis, Gel, Pulsed-Field, Enterococcus/*classification/genetics/isolation & purification/physiology, Gram-Positive Bacterial Infections/microbiology/*veterinary, Molecular Sequence Data, Nucleic Acid Hybridization, RNA, Ribosomal, 16S/genetics, Rats, Sequence Analysis, DNA, Swine, Swine Diseases/*microbiology, Terminology as Topic
  • topic2: Enzymology

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
6055Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 15688)https://www.dsmz.de/collection/catalogue/details/culture/DSM-15688
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
20218Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P.10.1016/j.syapm.2013.11.002StrainInfo introduces electronic passports for microorganisms.Syst Appl Microbiol. 37: 42-50 201424321274
34929Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/4578
55737Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 43229)https://www.ccug.se/strain?id=43229
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)
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
74828Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID13247.1StrainInfo: A central database for resolving microbial strain identifiers
123841Curators of the CIPCollection of Institut Pasteur (CIP 107172)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20107172