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

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/bacdive135017.20250331.9.3

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

@refgram stainconfidencecell shapemotility
125438positive93.653
33738positivecoccus-shapedno

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

@refgrowthtypetemperature
33738positivegrowth37
67770positivegrowth37
33738positivegrowth25-45
33738nogrowth10

Physiology and metabolism

oxygen tolerance

@refoxygen toleranceconfidence
33738facultative anaerobe
125439obligate aerobe93.9

halophily

  • @ref: 33738
  • salt: NaCl
  • growth: positive
  • tested relation: growth
  • concentration: 6.5 %

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
337384853esculin+hydrolysis
33738606565hippurate+hydrolysis
3373817632nitrate-reduction
3373816301nitrite-reduction
6837118305arbutin+builds acid from
68371320061methyl alpha-D-glucopyranoside-builds acid from
6837115824D-fructose+builds acid from
6837117634D-glucose+builds acid from
6837112936D-galactose+builds acid from
6837117113erythritol-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
6837117716lactose+builds acid from
6837117306maltose+builds acid from
6837117057cellobiose+builds acid from
6837117814salicin+builds acid from
683714853esculin+builds acid from
6837159640N-acetylglucosamine+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
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

metabolite tests

  • @ref: 33738
  • 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-galactosidase+3.2.1.23
68382alpha-galactosidase-3.2.1.22
68382naphthol-AS-BI-phosphohydrolase-
68382acid phosphatase-3.1.3.2
68382cystine arylamidase-3.4.11.3
68382leucine arylamidase+3.4.11.1
68382lipase (C 14)-
68382esterase (C 4)+
68382esterase lipase (C 8)+
68382alkaline phosphatase-3.1.3.1
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
68382beta-glucuronidase-3.2.1.31
68382alpha-chymotrypsin-3.4.21.1
68382trypsin-3.4.21.4
68382valine arylamidase-

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 12287AJ2713291512nuccore112904
67770Enterococcus villorum gene for 16S ribosomal RNA, partial sequence, strain: JCM 11557LC3117441496nuccore112904
124043Enterococcus villorum gene for 16S rRNA, partial sequence, strain: NBRC 100699.AB6812301484nuccore112904

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

@refmodeltraitdescriptionpredictionconfidencetraining_data
125439BacteriaNetoxygen_toleranceOxygenic conditions needed for growthobligate aerobe93.9
125439BacteriaNetgram_stainReaction to gram-stainingpositive71.4
125439BacteriaNetmotilityAbility to perform movementyes52.5
125439BacteriaNetspore_formationAbility to form endo- or exosporesno55.7
125438gram-positivegram-positivePositive reaction to Gram-stainingyes93.653no
125438anaerobicanaerobicAbility to grow under anoxygenic conditions (including facultative anaerobes)no91.118no
125438spore-formingspore-formingAbility to form endo- or exosporesno81.322no
125438aerobicaerobicAbility to grow under oxygenic conditions (including facultative aerobes)no97.716yes
125438thermophilethermophilicAbility to grow at temperatures above or equal to 45°Cno97no
125438motile2+flagellatedAbility to perform flagellated movementno89.5no

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
124043Isabel Schober, Julia KoblitzData extracted from sequence databases, automatically matched based on designation and taxonomy
125438Julia Koblitz, Lorenz Christian Reimer, Rüdiger Pukall, Jörg OvermannPredicting bacterial phenotypic traits through improved machine learning using high-quality, curated datasets10.1101/2024.08.12.607695
125439Philipp Münch, René Mreches, Martin Binder, Hüseyin Anil Gündüz, Xiao-Yin To, Alice McHardydeepG: Deep Learning for Genome Sequence Data. R package version 0.3.1https://github.com/GenomeNet/deepG