Strain identifier

BacDive ID: 135017

Type strain: Yes

Species: Enterococcus villorum

Strain Designation: 88-5474

Strain history: CIP <- 2001, LMG <- 1992, L. Devriese, Ghent Univ., Ghent, Belgium <- R. Higgins, strain: 88-5474

NCBI tax ID(s): 112904 (species)

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General

@ref: 33738

BacDive-ID: 135017

keywords: genome sequence, 16S sequence, Bacteria, facultative anaerobe, mesophilic, Gram-positive, coccus-shaped

description: Enterococcus villorum 88-5474 is a facultative anaerobe, mesophilic, Gram-positive bacterium of the family Enterococcaceae.

NCBI tax id

  • NCBI tax id: 112904
  • Matching level: species

strain history

@refhistory
67770LMG 12287 <-- L. A. Devriese 88-5474 <-- R. Higgins.
33738CIP <- 2001, LMG <- 1992, L. Devriese, Ghent Univ., Ghent, Belgium <- R. Higgins, strain: 88-5474

doi: 10.13145/bacdive135017.20230509.8.1

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: 33738

domain: Bacteria

phylum: Firmicutes

class: Bacilli

order: Lactobacillales

family: Enterococcaceae

genus: Enterococcus

species: Enterococcus villorum

strain designation: 88-5474

type strain: yes

Morphology

cell morphology

  • @ref: 33738
  • gram stain: positive
  • cell shape: coccus-shaped
  • motility: no

colony morphology

  • @ref: 33738
  • hemolysis ability: 1

Culture and growth conditions

culture medium

@refnamegrowthcompositionlink
33738MEDIUM 72- for trypto casein soja agaryesDistilled water make up to (1000.000 ml);Trypto casein soy agar (40.000 g)
33738CIP Medium 72yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72

culture temp

@refgrowthtypetemperaturerange
33738positivegrowth37mesophilic
67770positivegrowth37mesophilic
33738positivegrowth25-45
33738nogrowth10psychrophilic

Physiology and metabolism

oxygen tolerance

  • @ref: 33738
  • oxygen tolerance: facultative anaerobe

halophily

  • @ref: 33738
  • 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
33738esculin+hydrolysis4853
33738hippurate+hydrolysis606565
33738nitrate-reduction17632
33738nitrite-reduction16301

metabolite tests

  • @ref: 33738
  • Chebi-ID: 15688
  • metabolite: acetoin
  • voges-proskauer-test: -

enzymes

@refvalueactivityec
33738oxidase-
33738beta-galactosidase+3.2.1.23
33738alcohol dehydrogenase+1.1.1.1
33738gelatinase-
33738amylase-
33738catalase-1.11.1.6
33738gamma-glutamyltransferase-2.3.2.2
33738lysine decarboxylase-4.1.1.18
33738ornithine decarboxylase-4.1.1.17
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
33738--++-+-------+------

API 50CHac

@refGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
33738+/----++---++++--------++/-+++++++--+-----+---------+/-

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
33738------------------+-------------------------------------------+--+--------------------+------------

Isolation, sampling and environmental information

isolation

@refcountryorigin.countrycontinentsample type
33738CanadaCANNorth America
56599CanadaCANNorth AmericaPig intestine,gut of a piglet
67770CanadaCANNorth AmericaPig intestine
33738CanadaCANNorth AmericaAnimal, Pig

isolation source categories

Cat1Cat2Cat3
#Host Body-Site#Gastrointestinal tract#Large intestine
#Host Body-Site#Gastrointestinal tract#Small intestine
#Host#Mammals#Suidae (Pig,Swine)
#Host#Juvenile

Safety information

risk assessment

  • @ref: 33738
  • biosafety level: 2
  • biosafety level comment: Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
67770Enterococcus villorum 16S rRNA gene, strain LMG 12287AJ2713291512ena112904
67770Enterococcus villorum gene for 16S ribosomal RNA, partial sequence, strain: JCM 11557LC3117441496ena112904

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Enterococcus villorum NBRC 100699GCA_007990225contigncbi112904
66792Enterococcus villorum strain NBRC 100699112904.202wgspatric112904

GC content

  • @ref: 67770
  • GC-content: 35
  • method: high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
motileno96.228no
flagellatedno98.226no
gram-positiveyes95.161no
anaerobicno97.052no
halophileyes92.61no
spore-formingno90.066no
glucose-utilyes91.17no
aerobicno94.995no
thermophileno99.571yes
glucose-fermentyes89.862no

External links

@ref: 33738

culture collection no.: CIP 107282, LMG 12287, CCM 4887, CCUG 45025, NBRC 100699, JCM 11557, KCTC 13904

straininfo link

  • @ref: 92444
  • straininfo: 6920

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny11321084Enterococcus villorum sp. nov., an enteroadherent bacterium associated with diarrhoea in piglets.Vancanneyt M, Snauwaert C, Cleenwerck I, Baele M, Descheemaeker P, Goossens H, Pot B, Vandamme P, Swings J, Haesebrouck F, Devriese LAInt J Syst Evol Microbiol10.1099/00207713-51-2-3932001Animals, *Bacterial Adhesion, Bacterial Proteins/isolation & purification, Base Composition, Diarrhea/*veterinary, Enterococcus/*classification, Intestines/*microbiology, Molecular Sequence Data, Nucleic Acid Hybridization, Phenotype, Polymerase Chain Reaction, Sequence Analysis, DNA, Swine, Swine Diseases/*microbiology, Terminology as TopicGenetics
Phylogeny27260143Enterococcus Xinjiangensis sp. nov., Isolated from Yogurt of Xinjiang, China.Ren X, Li M, Guo DCurr Microbiol10.1007/s00284-016-1065-12016Bacterial Proteins/genetics/metabolism, Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Enterococcus/classification/genetics/*isolation & purification/metabolism, Fermentation, Phylogeny, RNA, Ribosomal, 16S/genetics, Yogurt/*microbiologyMetabolism

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
33738Curators of the CIPhttps://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20107282Collection of Institut Pasteur (CIP 107282)
56599Curators of the CCUGhttps://www.ccug.se/strain?id=45025Culture Collection University of Gothenburg (CCUG) (CCUG 45025)
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
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
68371Automatically annotated from API 50CH acid
68382Automatically annotated from API zym
92444Reimer, 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-ID6920.1