Strain identifier

BacDive ID: 5326

Type strain: Yes

Species: Enterococcus raffinosus

Strain Designation: 1789/79, 1789-79

Strain history: CIP <- 1990, NCTC <- 1988, J.A.E. Farrow, AFRC, Reading, UK <- R.R. Facklam, CDC: strain 1789-79

NCBI tax ID(s): 1218093 (strain), 71452 (species)

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General

@ref: 2139

BacDive-ID: 5326

DSM-Number: 5633

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

description: Enterococcus raffinosus 1789/79 is a microaerophile, mesophilic, Gram-positive bacterium that was isolated from blood culture.

NCBI tax id

NCBI tax idMatching level
71452species
1218093strain

strain history

@refhistory
2139<- NCTC <- J.A.E. Farrow <- R.R. Facklam, 1789/79
67770ATCC 49427 <-- NCTC 12192 <-- J. A. E. Farrow 1789/79 <-- R. R. Facklam.
122132CIP <- 1990, NCTC <- 1988, J.A.E. Farrow, AFRC, Reading, UK <- R.R. Facklam, CDC: strain 1789-79

doi: 10.13145/bacdive5326.20230509.8.1

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 raffinosus
  • full scientific name: Enterococcus raffinosus Collins et al. 1989

@ref: 2139

domain: Bacteria

phylum: Firmicutes

class: Bacilli

order: Lactobacillales

family: Enterococcaceae

genus: Enterococcus

species: Enterococcus raffinosus

full scientific name: Enterococcus raffinosus Collins et al. 1989

strain designation: 1789/79, 1789-79

type strain: yes

Morphology

cell morphology

  • @ref: 122132
  • gram stain: positive
  • cell shape: coccus-shaped
  • motility: no

colony morphology

@reftype of hemolysisincubation periodhemolysis ability
2139gamma1-2 days
1221321

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
2139COLUMBIA 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
2139TRYPTICASE 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
40632MEDIUM 29- Brain heart agaryesDistilled water make up to (1000.000 ml);Brain heart infusion agar (52.000 g)
122132CIP Medium 29yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=29

culture temp

@refgrowthtypetemperaturerange
2139positivegrowth37mesophilic
40632positivegrowth37mesophilic
49573positivegrowth37mesophilic
67770positivegrowth37mesophilic
122132positivegrowth25-41
122132nogrowth10psychrophilic
122132nogrowth45thermophilic

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
2139microaerophile
49573aerobe
122132facultative anaerobe

halophily

  • @ref: 122132
  • salt: NaCl
  • growth: positive
  • tested relation: growth
  • concentration: 6.5 %

murein

  • @ref: 2139
  • murein short key: A11.31
  • type: A4alpha L-Lys-D-Asp

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
122132esculin+hydrolysis4853
122132hippurate+hydrolysis606565
122132nitrate-reduction17632
122132nitrite-reduction16301
68381arginine-hydrolysis29016
68381D-ribose+builds acid from16988
68381D-mannitol+builds acid from16899
68381lactose-builds acid from17716
68381trehalose+builds acid from27082
68381raffinose-builds acid from16634
68381sucrose+builds acid from17992
68381alpha-cyclodextrin-builds acid from40585
68381glycogen-builds acid from28087
68381pullulan-builds acid from27941
68381maltose+builds acid from17306
68381methyl beta-D-glucopyranoside+builds acid from320055
68381D-tagatose+builds acid from16443
68381urea-hydrolysis16199

metabolite production

  • @ref: 68381
  • Chebi-ID: 15688
  • metabolite: acetoin
  • production: yes

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-test
6838115688acetoin+
12213215688acetoin+

enzymes

@refvalueactivityec
2139catalase-1.11.1.6
2139cytochrome-c oxidase-1.9.3.1
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
68381urease-3.5.1.5
68381beta-mannosidase-3.2.1.25
68381glycyl tryptophan arylamidase+
68381N-acetyl-beta-glucosaminidase-3.2.1.52
68381pyrrolidonyl arylamidase+3.4.19.3
68381beta-galactosidase-3.2.1.23
68381Alanyl-Phenylalanyl-Proline arylamidase+
68381alkaline phosphatase-3.1.3.1
68381alpha-galactosidase+3.2.1.22
68381beta-glucuronidase-3.2.1.31
68381arginine dihydrolase-3.5.3.6
122132oxidase-
122132beta-galactosidase+3.2.1.23
122132alcohol dehydrogenase-1.1.1.1
122132catalase-1.11.1.6
122132gamma-glutamyltransferase-2.3.2.2
122132lysine decarboxylase-4.1.1.18
122132ornithine 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
122132--++-+----+----+----

API 50CHac

@refGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
122132+--++--+-++++++--+++++++++++++++-++---+--+--++++-

API rID32STR

@refADH Argbeta GLUbeta GARbeta GURalpha GALPALRIBMANSORLACTRERAFSACLARADARLCDEXVPAPPAbeta GALPyrAbeta NAGGTAHIPGLYGPULMALMELMLZMbeta DGTAGbeta MANURE
2139----+-++--+-++/-+/--++-+-+---+--++--
2139-++/--+-+++-+-+++-++-+-++/---+++++--

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
122132+++++-++-+++---++-++--+--+----+--+--+----------------------+--------------------------+------------

Isolation, sampling and environmental information

isolation

@refsample typesampling datecountryorigin.countrycontinent
2139blood culture
49573Human blood1979USAUSANorth America
67770Blood culture
122132Human, Blood

isolation source categories

Cat1Cat2Cat3
#Infection#Patient#Blood culture
#Host Body Product#Fluids#Blood

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
21392Risk group (German classification)
1221322Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
2139Enterococcus raffinosus 16S rRNA geneY182961425ena71452
67770Enterococcus raffinosus gene for 16S ribosomal RNA, partial sequence, strain: JCM 8733LC0970711496ena71452

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Enterococcus raffinosus NBRC 1004921218093.3wgspatric1218093
66792Enterococcus raffinosus strain DSM 563371452.3wgspatric71452
66792Enterococcus raffinosus NBRC 1004922731957560draftimg1218093
67770Enterococcus raffinosus NBRC 100492GCA_001544115contigncbi1218093
67770Enterococcus raffinosus DSM 5633GCA_001886185contigncbi71452

GC content

@refGC-contentmethod
213940.0thermal denaturation, midpoint method (Tm)
6777040thermal denaturation, midpoint method (Tm)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
motileno92.194no
gram-positiveyes87.652no
anaerobicno93.649no
aerobicno95.823no
halophileyes66.596no
spore-formingno88.163no
thermophileno99.731yes
glucose-utilyes87.735no
flagellatedno94.753no
glucose-fermentyes83.554no

External links

@ref: 2139

culture collection no.: DSM 5633, ATCC 49427, NCTC 12192, CCUG 29292, CIP 103329, LMG 12888, JCM 8733, NBRC 100492, CCM 4216, CDC 1789-79, NCAIM B.02061, NCIMB 12901, VTT E-97812

straininfo link

  • @ref: 74815
  • straininfo: 10344

literature

  • topic: Phylogeny
  • Pubmed-ID: 7699030
  • title: DNA hybridization and contour-clamped homogeneous electric field electrophoresis for identification of enterococci to the species level.
  • authors: Donabedian S, Chow JW, Shlaes DM, Green M, Zervos MJ
  • journal: J Clin Microbiol
  • DOI: 10.1128/jcm.33.1.141-145.1995
  • year: 1995
  • mesh: Blotting, Southern, DNA, Bacterial/*genetics, Electrophoresis, Agar Gel/methods, Enterococcus/*classification/genetics, Gram-Negative Bacterial Infections/microbiology, Humans, Nucleic Acid Hybridization, Species Specificity
  • topic2: Enzymology

Reference

@idauthorscataloguedoi/urltitle
2139Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 5633)https://www.dsmz.de/collection/catalogue/details/culture/DSM-5633
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
40632Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/15115
49573Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 29292)https://www.ccug.se/strain?id=29292
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)
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
68371Automatically annotated from API 50CH acid
68381Automatically annotated from API rID32STR
68382Automatically annotated from API zym
74815Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID10344.1StrainInfo: A central database for resolving microbial strain identifiers
122132Curators of the CIPCollection of Institut Pasteur (CIP 103329)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20103329